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<div class="contentContainer"><a href="#_A_">A</a> <a href="#_B_">B</a> <a href="#_C_">C</a> <a href="#_D_">D</a> <a href="#_E_">E</a> <a href="#_F_">F</a> <a href="#_G_">G</a> <a href="#_H_">H</a> <a href="#_I_">I</a> <a href="#_J_">J</a> <a href="#_K_">K</a> <a href="#_L_">L</a> <a href="#_M_">M</a> <a href="#_N_">N</a> <a href="#_O_">O</a> <a href="#_P_">P</a> <a href="#_Q_">Q</a> <a href="#_R_">R</a> <a href="#_S_">S</a> <a href="#_T_">T</a> <a href="#_U_">U</a> <a href="#_V_">V</a> <a href="#_W_">W</a> <a href="#_X_">X</a> <a href="#_Y_">Y</a> <a href="#_Z_">Z</a> <a name="_A_">
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<h2 class="title">A</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#A_STATE">A_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#A_STATE">A_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel"><span class="strong">AbstractRateMatrix</span></a> - Class in <a href="./jebl/evolution/substmodel/package-summary.html">jebl.evolution.substmodel</a></dt>
<dd>
<div class="block">abstract base class for all rate matrices</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImmediateSequenceImporter.Callback.html#add(jebl.evolution.sequences.Sequence)">add(Sequence)</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/ImmediateSequenceImporter.Callback.html" title="interface in jebl.evolution.io">ImmediateSequenceImporter.Callback</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CladeSystem.html#add(jebl.evolution.trees.RootedTree)">add(RootedTree)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CladeSystem.html" title="class in jebl.evolution.trees">CladeSystem</a></dt>
<dd>
<div class="block">adds all the clades in the tree</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#addCharacter(char, int)">addCharacter(char, int)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#addCoalescentEvent(double)">addCoalescentEvent(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#addEdge(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node, double)">addEdge(Node, Node, double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">Add a new edge between two existing (non adjacent yet) nodes.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#addFeedbackAction(java.lang.String, jebl.util.SimpleListener)">addFeedbackAction(String, SimpleListener)</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#addFeedbackAction(java.lang.String, java.lang.String, jebl.util.SimpleListener)">addFeedbackAction(String, String, SimpleListener)</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#addFeedbackAction(java.lang.String, jebl.util.SimpleListener)">addFeedbackAction(String, SimpleListener)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">Equivalent to <a href="./jebl/util/ProgressListener.html#addFeedbackAction(java.lang.String, java.lang.String, jebl.util.SimpleListener)"><code>addFeedbackAction(label,"",listener)</code></a></div>
</dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#addFeedbackAction(java.lang.String, java.lang.String, jebl.util.SimpleListener)">addFeedbackAction(String, String, SimpleListener)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">Adds an action that can choose to provide feedback.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.Wrapper.html#addFeedbackAction(java.lang.String, jebl.util.SimpleListener)">addFeedbackAction(String, SimpleListener)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.Wrapper.html" title="class in jebl.util">ProgressListener.Wrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.Wrapper.html#addFeedbackAction(java.lang.String, java.lang.String, jebl.util.SimpleListener)">addFeedbackAction(String, String, SimpleListener)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.Wrapper.html" title="class in jebl.util">ProgressListener.Wrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#addGaps(int)">addGaps(int)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#addMigrationEvent(double, int)">addMigrationEvent(double, int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#addNode(jebl.evolution.graphs.Node)">addNode(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Adds a new node at the midpoint of the edge connecting the given node to its parent.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#addNode(jebl.evolution.graphs.Edge)">addNode(Edge)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Adds a new node at the midpoint of the given edge</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#addNothingEvent(double)">addNothingEvent(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#addProfileCharacter(jebl.evolution.align.ProfileCharacter)">addProfileCharacter(ProfileCharacter)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#addProgress(double)">addProgress(double)</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd>
<div class="block">Increments the progress of the current sub task by this much.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/aligners/Aligner.html#addProgressListener(jebl.util.ProgressListener)">addProgressListener(ProgressListener)</a></span> - Method in interface jebl.evolution.aligners.<a href="./jebl/evolution/aligners/Aligner.html" title="interface in jebl.evolution.aligners">Aligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ClusteringTreeBuilder.html#addProgressListener(jebl.util.ProgressListener)">addProgressListener(ProgressListener)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ClusteringTreeBuilder.html" title="class in jebl.evolution.trees">ClusteringTreeBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ConsensusTreeBuilder.html#addProgressListener(jebl.util.ProgressListener)">addProgressListener(ProgressListener)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ConsensusTreeBuilder.html" title="class in jebl.evolution.trees">ConsensusTreeBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilder.html#addProgressListener(jebl.util.ProgressListener)">addProgressListener(ProgressListener)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilder.html" title="interface in jebl.evolution.trees">TreeBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#addSampleEvent(double)">addSampleEvent(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#addSequence(jebl.evolution.sequences.Sequence)">addSequence(Sequence)</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd>
<div class="block">Adds a sequence to this alignment</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#addTaxa(java.util.Set)">addTaxa(Set<Taxon>)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd>
<div class="block">set the taxa for this character with a previously constructed Set<Taxon></div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/Character.html#addTaxon(jebl.evolution.taxa.Taxon)">addTaxon(Taxon)</a></span> - Method in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/Character.html" title="interface in jebl.evolution.characters">Character</a></dt>
<dd>
<div class="block">add a taxon with this character</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#addTaxon(jebl.evolution.taxa.Taxon)">addTaxon(Taxon)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#addTaxon(jebl.evolution.taxa.Taxon)">addTaxon(Taxon)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#addTreeToDensityMap(jebl.evolution.trees.CalculateSplitRates.DensityMap, jebl.evolution.trees.RootedTree)">addTreeToDensityMap(CalculateSplitRates.DensityMap, RootedTree)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align"><span class="strong">Align</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#Align(jebl.evolution.align.scores.Scores, float)">Align(Scores, float)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/BartonSternberg.html#align(java.util.List, jebl.util.ProgressListener, boolean, boolean)">align(List<Sequence>, ProgressListener, boolean, boolean)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/BartonSternberg.html" title="class in jebl.evolution.align">BartonSternberg</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/AlignCommand.html" title="class in jebl.evolution.align"><span class="strong">AlignCommand</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd>
<div class="block">A command line interface for the algorithms in jebl.evolution.align.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignCommand.html#AlignCommand()">AlignCommand()</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/AlignCommand.html" title="class in jebl.evolution.align">AlignCommand</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignCommand.html#AlignCommand(java.lang.String, java.lang.String)">AlignCommand(String, String)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/AlignCommand.html" title="class in jebl.evolution.align">AlignCommand</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/aligners/Aligner.html" title="interface in jebl.evolution.aligners"><span class="strong">Aligner</span></a> - Interface in <a href="./jebl/evolution/aligners/package-summary.html">jebl.evolution.aligners</a></dt>
<dd>
<div class="block">As of 2006-12-06, this interface is not used anywhere in JEBL, and it doesn't have
any implementing classes.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/PairwiseAligner.Result.html#alignment">alignment</a></span> - Variable in class jebl.evolution.align.<a href="./jebl/evolution/align/PairwiseAligner.Result.html" title="class in jebl.evolution.align">PairwiseAligner.Result</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/alignments/Alignment.html" title="interface in jebl.evolution.alignments"><span class="strong">Alignment</span></a> - Interface in <a href="./jebl/evolution/alignments/package-summary.html">jebl.evolution.alignments</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/AlignmentExporter.html" title="interface in jebl.evolution.io"><span class="strong">AlignmentExporter</span></a> - Interface in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/AlignmentImporter.html" title="interface in jebl.evolution.io"><span class="strong">AlignmentImporter</span></a> - Interface in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html" title="class in jebl.evolution.align"><span class="strong">AlignmentTreeBuilderFactory</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html#AlignmentTreeBuilderFactory()">AlignmentTreeBuilderFactory()</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html" title="class in jebl.evolution.align">AlignmentTreeBuilderFactory</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.Result.html" title="class in jebl.evolution.align"><span class="strong">AlignmentTreeBuilderFactory.Result</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/aligners/Aligner.html#alignSequences(java.util.Collection)">alignSequences(Collection<Sequence>)</a></span> - Method in interface jebl.evolution.aligners.<a href="./jebl/evolution/aligners/Aligner.html" title="interface in jebl.evolution.aligners">Aligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#allocateMatrices(int, int)">allocateMatrices(int, int)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#allocateMatrices(int, int)">allocateMatrices(int, int)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#ALT_YEAST">ALT_YEAST</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#AMINO_ACID">AMINO_ACID</a></span> - Static variable in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#AMINO_ACID_IDENTITY">AMINO_ACID_IDENTITY</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/substmodel/AminoAcidModel.html" title="class in jebl.evolution.substmodel"><span class="strong">AminoAcidModel</span></a> - Class in <a href="./jebl/evolution/substmodel/package-summary.html">jebl.evolution.substmodel</a></dt>
<dd>
<div class="block">base class of rate matrices for amino acids</div>
</dd>
<dt><a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences"><span class="strong">AminoAcids</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd>
<div class="block">Uninstantiable utility class with only static methods.</div>
</dd>
<dt><a href="./jebl/evolution/align/scores/AminoAcidScores.html" title="class in jebl.evolution.align.scores"><span class="strong">AminoAcidScores</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/AminoAcidScores.html#AminoAcidScores()">AminoAcidScores()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/AminoAcidScores.html" title="class in jebl.evolution.align.scores">AminoAcidScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/AminoAcidScores.html#AminoAcidScores(float, float)">AminoAcidScores(float, float)</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/AminoAcidScores.html" title="class in jebl.evolution.align.scores">AminoAcidScores</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/AminoAcidState.html" title="class in jebl.evolution.sequences"><span class="strong">AminoAcidState</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ByteBuilder.html#append(char)">append(char)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ByteBuilder.html" title="class in jebl.evolution.io">ByteBuilder</a></dt>
<dd>
<div class="block">Appends an ASCII character (see <a href="./jebl/evolution/io/ByteBuilder.html#isCharacterAscii(char)"><code>ByteBuilder.isCharacterAscii(char)</code></a>) to this ByteBuilder.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ByteBuilder.html#append(java.lang.CharSequence)">append(CharSequence)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ByteBuilder.html" title="class in jebl.evolution.io">ByteBuilder</a></dt>
<dd>
<div class="block">Appends an ASCII CharSequence to this ByteBuilder.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ByteBuilder.html#append(java.lang.CharSequence, int, int)">append(CharSequence, int, int)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ByteBuilder.html" title="class in jebl.evolution.io">ByteBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#appendMatch(jebl.evolution.align.AlignmentResult, jebl.evolution.align.AlignmentResult)">appendMatch(AlignmentResult, AlignmentResult)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#ASCIDIAN_MT">ASCIDIAN_MT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#assertAllTreesHaveTheSameTaxa(java.util.List)">assertAllTreesHaveTheSameTaxa(List<? extends Tree>)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd>
<div class="block">Checks whether all of the trees passed in have the same taxa sets (ignoring
order of taxa), and throws an IllegalArgumentException if this is not the case.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#asText(jebl.evolution.trees.Tree)">asText(Tree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#asText(jebl.evolution.trees.Tree, int)">asText(Tree, int)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><a href="./jebl/util/Attributable.html" title="interface in jebl.util"><span class="strong">Attributable</span></a> - Interface in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd>
<div class="block">Interface for associating attributeNames with an object.</div>
</dd>
<dt><a href="./jebl/util/Attributable.Utils.html" title="class in jebl.util"><span class="strong">Attributable.Utils</span></a> - Class in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd> </dd>
<dt><a href="./jebl/util/AttributableHelper.html" title="class in jebl.util"><span class="strong">AttributableHelper</span></a> - Class in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/AttributableHelper.html#AttributableHelper()">AttributableHelper()</a></span> - Constructor for class jebl.util.<a href="./jebl/util/AttributableHelper.html" title="class in jebl.util">AttributableHelper</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/AttributedCladeSystem.html" title="class in jebl.evolution.trees"><span class="strong">AttributedCladeSystem</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Stores a set of unique clades for a tree</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/AttributedCladeSystem.html#AttributedCladeSystem(java.lang.String)">AttributedCladeSystem(String)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/AttributedCladeSystem.html" title="class in jebl.evolution.trees">AttributedCladeSystem</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/AttributedCladeSystem.html#AttributedCladeSystem(java.lang.String, jebl.evolution.trees.RootedTree)">AttributedCladeSystem(String, RootedTree)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/AttributedCladeSystem.html" title="class in jebl.evolution.trees">AttributedCladeSystem</a></dt>
<dd> </dd>
</dl>
<a name="_B_">
<!-- -->
</a>
<h2 class="title">B</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#B_STATE">B_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#B_STATE">B_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#BACTERIAL">BACTERIAL</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/BartonSternberg.html" title="class in jebl.evolution.align"><span class="strong">BartonSternberg</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/BartonSternberg.html#BartonSternberg(jebl.evolution.align.scores.Scores, float, float, int, boolean, boolean)">BartonSternberg(Scores, float, float, int, boolean, boolean)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/BartonSternberg.html" title="class in jebl.evolution.align">BartonSternberg</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/BaseEdge.html" title="class in jebl.evolution.trees"><span class="strong">BaseEdge</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Common implementation of Attributable interface used by Nodes.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseEdge.html#BaseEdge()">BaseEdge()</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseEdge.html" title="class in jebl.evolution.trees">BaseEdge</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/BaseNode.html" title="class in jebl.evolution.trees"><span class="strong">BaseNode</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Common implementation of Attributable interface used by Nodes.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseNode.html#BaseNode()">BaseNode()</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseNode.html" title="class in jebl.evolution.trees">BaseNode</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments"><span class="strong">BasicAlignment</span></a> - Class in <a href="./jebl/evolution/alignments/package-summary.html">jebl.evolution.alignments</a></dt>
<dd>
<div class="block">A basic implementation of the Alignment interface.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#BasicAlignment()">BasicAlignment()</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd>
<div class="block">Constructs a basic alignment with no sequences.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#BasicAlignment(java.util.Collection)">BasicAlignment(Collection<? extends Sequence>)</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd>
<div class="block">Constructs a basic alignment from a collection of sequences.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#BasicAlignment(jebl.evolution.sequences.Sequence[])">BasicAlignment(Sequence[])</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd>
<div class="block">Constructs a basic alignment from an array of sequences.</div>
</dd>
<dt><a href="./jebl/evolution/distances/BasicDistanceMatrix.html" title="class in jebl.evolution.distances"><span class="strong">BasicDistanceMatrix</span></a> - Class in <a href="./jebl/evolution/distances/package-summary.html">jebl.evolution.distances</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/BasicDistanceMatrix.html#BasicDistanceMatrix(java.util.Collection, double[][])">BasicDistanceMatrix(Collection<Taxon>, double[][])</a></span> - Constructor for class jebl.evolution.distances.<a href="./jebl/evolution/distances/BasicDistanceMatrix.html" title="class in jebl.evolution.distances">BasicDistanceMatrix</a></dt>
<dd> </dd>
<dt><a href="./jebl/util/BasicProgressListener.html" title="class in jebl.util"><span class="strong">BasicProgressListener</span></a> - Class in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd>
<div class="block">A basic <a href="./jebl/util/ProgressListener.html" title="class in jebl.util"><code>ProgressListener</code></a> implementation that allows the caller to set the canceled
status.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/BasicProgressListener.html#BasicProgressListener()">BasicProgressListener()</a></span> - Constructor for class jebl.util.<a href="./jebl/util/BasicProgressListener.html" title="class in jebl.util">BasicProgressListener</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences"><span class="strong">BasicSequence</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd>
<div class="block">A default implementation of the Sequence interface.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#BasicSequence(jebl.evolution.sequences.SequenceType, jebl.evolution.taxa.Taxon, java.lang.CharSequence)">BasicSequence(SequenceType, Taxon, CharSequence)</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd>
<div class="block">Creates a sequence with a name corresponding to the taxon name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#BasicSequence(jebl.evolution.sequences.SequenceType, jebl.evolution.taxa.Taxon, jebl.evolution.sequences.State[])">BasicSequence(SequenceType, Taxon, State[])</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd>
<div class="block">Creates a sequence with a name corresponding to the taxon name</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#beginNextSubtask(java.lang.String)">beginNextSubtask(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd>
<div class="block">Convenience method to start the next operation AND set a new message.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#beginNextSubtask()">beginNextSubtask()</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd>
<div class="block">begins the next subtask.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#beginSubtask()">beginSubtask()</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd>
<div class="block">Used as an alternative to <a href="./jebl/util/CompositeProgressListener.html#beginNextSubtask()"><code>CompositeProgressListener.beginNextSubtask()</code></a>.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#beginSubtask(java.lang.String)">beginSubtask(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd>
<div class="block">Used as an alternative to <a href="./jebl/util/CompositeProgressListener.html#beginNextSubtask()"><code>CompositeProgressListener.beginNextSubtask()</code></a>.</div>
</dd>
<dt><a href="./jebl/evolution/treemetrics/BilleraMetric.html" title="class in jebl.evolution.treemetrics"><span class="strong">BilleraMetric</span></a> - Class in <a href="./jebl/evolution/treemetrics/package-summary.html">jebl.evolution.treemetrics</a></dt>
<dd>
<div class="block">Billera tree distance - sum of change in branch lengths required to transform one tree to the second
Note that this interface is not optimal for a large set where all pairs are required.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/treemetrics/BilleraMetric.html#BilleraMetric()">BilleraMetric()</a></span> - Constructor for class jebl.evolution.treemetrics.<a href="./jebl/evolution/treemetrics/BilleraMetric.html" title="class in jebl.evolution.treemetrics">BilleraMetric</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/Binomial.html" title="class in jebl.math"><span class="strong">Binomial</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">Binomial coefficients</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Binomial.html#Binomial()">Binomial()</a></span> - Constructor for class jebl.math.<a href="./jebl/math/Binomial.html" title="class in jebl.math">Binomial</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#BLEPHARISMA_NUC">BLEPHARISMA_NUC</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum45.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum45</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum45.html#Blosum45()">Blosum45()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum45.html" title="class in jebl.evolution.align.scores">Blosum45</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum50.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum50</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum50.html#Blosum50()">Blosum50()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum50.html" title="class in jebl.evolution.align.scores">Blosum50</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum55.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum55</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum55.html#Blosum55()">Blosum55()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum55.html" title="class in jebl.evolution.align.scores">Blosum55</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum60.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum60</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum60.html#Blosum60()">Blosum60()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum60.html" title="class in jebl.evolution.align.scores">Blosum60</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum62.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum62</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum62.html#Blosum62()">Blosum62()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum62.html" title="class in jebl.evolution.align.scores">Blosum62</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum65.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum65</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum65.html#Blosum65()">Blosum65()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum65.html" title="class in jebl.evolution.align.scores">Blosum65</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum70.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum70</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum70.html#Blosum70()">Blosum70()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum70.html" title="class in jebl.evolution.align.scores">Blosum70</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum75.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum75</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum75.html#Blosum75()">Blosum75()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum75.html" title="class in jebl.evolution.align.scores">Blosum75</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum80.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum80</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum80.html#Blosum80()">Blosum80()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum80.html" title="class in jebl.evolution.align.scores">Blosum80</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum85.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum85</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum85.html#Blosum85()">Blosum85()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum85.html" title="class in jebl.evolution.align.scores">Blosum85</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Blosum90.html" title="class in jebl.evolution.align.scores"><span class="strong">Blosum90</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum90.html#Blosum90()">Blosum90()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum90.html" title="class in jebl.evolution.align.scores">Blosum90</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_45">BLOSUM_45</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_50">BLOSUM_50</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_55">BLOSUM_55</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_60">BLOSUM_60</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_62">BLOSUM_62</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_65">BLOSUM_65</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_70">BLOSUM_70</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_75">BLOSUM_75</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_80">BLOSUM_80</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_85">BLOSUM_85</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#BLOSUM_90">BLOSUM_90</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/MaybeBoolean.html#booleanValue(jebl.util.MaybeBoolean)">booleanValue(MaybeBoolean)</a></span> - Static method in enum jebl.util.<a href="./jebl/util/MaybeBoolean.html" title="enum in jebl.util">MaybeBoolean</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/alignments/BootstrappedAlignment.html" title="class in jebl.evolution.alignments"><span class="strong">BootstrappedAlignment</span></a> - Class in <a href="./jebl/evolution/alignments/package-summary.html">jebl.evolution.alignments</a></dt>
<dd>
<div class="block">Date: 15/01/2006
Time: 10:13:50</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BootstrappedAlignment.html#BootstrappedAlignment(jebl.evolution.alignments.Alignment, long)">BootstrappedAlignment(Alignment, long)</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BootstrappedAlignment.html" title="class in jebl.evolution.alignments">BootstrappedAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BootstrappedAlignment.html#BootstrappedAlignment(jebl.evolution.alignments.Alignment, java.util.Random)">BootstrappedAlignment(Alignment, Random)</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BootstrappedAlignment.html" title="class in jebl.evolution.alignments">BootstrappedAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BootstrappedAlignment.html#BootstrappedAlignment(jebl.evolution.alignments.Alignment)">BootstrappedAlignment(Alignment)</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BootstrappedAlignment.html" title="class in jebl.evolution.alignments">BootstrappedAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html#build(jebl.evolution.alignments.Alignment, jebl.evolution.trees.TreeBuilderFactory.Method, jebl.evolution.trees.TreeBuilderFactory.DistanceModel, jebl.util.ProgressListener, boolean)">build(Alignment, TreeBuilderFactory.Method, TreeBuilderFactory.DistanceModel, ProgressListener, boolean)</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html" title="class in jebl.evolution.align">AlignmentTreeBuilderFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html#build(jebl.evolution.alignments.Alignment, jebl.evolution.trees.TreeBuilderFactory.Method, jebl.evolution.trees.TreeBuilderFactory.DistanceModel, jebl.util.ProgressListener)">build(Alignment, TreeBuilderFactory.Method, TreeBuilderFactory.DistanceModel, ProgressListener)</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html" title="class in jebl.evolution.align">AlignmentTreeBuilderFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html#build(java.util.List, jebl.evolution.trees.TreeBuilderFactory.Method, jebl.evolution.align.PairwiseAligner, jebl.util.ProgressListener)">build(List<Sequence>, TreeBuilderFactory.Method, PairwiseAligner, ProgressListener)</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html" title="class in jebl.evolution.align">AlignmentTreeBuilderFactory</a></dt>
<dd>
<div class="block">Will use model F84 for nucleotides and Jukes-Cantor for amino acid</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html#build(java.util.List, jebl.evolution.trees.TreeBuilderFactory.Method, jebl.evolution.align.PairwiseAligner, jebl.util.ProgressListener, jebl.evolution.trees.TreeBuilderFactory.DistanceModel)">build(List<Sequence>, TreeBuilderFactory.Method, PairwiseAligner, ProgressListener, TreeBuilderFactory.DistanceModel)</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html" title="class in jebl.evolution.align">AlignmentTreeBuilderFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html#build(java.util.List, jebl.evolution.trees.TreeBuilderFactory.Method, jebl.evolution.align.MultipleAligner, jebl.util.ProgressListener, boolean)">build(List<Sequence>, TreeBuilderFactory.Method, MultipleAligner, ProgressListener, boolean)</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.html" title="class in jebl.evolution.align">AlignmentTreeBuilderFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ClusteringTreeBuilder.html#build()">build()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ClusteringTreeBuilder.html" title="class in jebl.evolution.trees">ClusteringTreeBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilder.html#build()">build()</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilder.html" title="interface in jebl.evolution.trees">TreeBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.html#buildRooted(jebl.evolution.trees.RootedTree[], double, jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod)">buildRooted(RootedTree[], double, TreeBuilderFactory.ConsensusMethod)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.html" title="class in jebl.evolution.trees">TreeBuilderFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.html#buildRooted(jebl.evolution.trees.Tree[], double, jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod)">buildRooted(Tree[], double, TreeBuilderFactory.ConsensusMethod)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.html" title="class in jebl.evolution.trees">TreeBuilderFactory</a></dt>
<dd>
<div class="block">convenience method.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.html#buildUnRooted(jebl.evolution.trees.Tree[], jebl.evolution.taxa.Taxon, double, jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod)">buildUnRooted(Tree[], Taxon, double, TreeBuilderFactory.ConsensusMethod)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.html" title="class in jebl.evolution.trees">TreeBuilderFactory</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/ByteBuilder.html" title="class in jebl.evolution.io"><span class="strong">ByteBuilder</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Similar to a StringBuilder, but its internal buffer is a byte[] with
one entry for each character, so it can only correctly append single-byte
characters.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ByteBuilder.html#ByteBuilder(int)">ByteBuilder(int)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/ByteBuilder.html" title="class in jebl.evolution.io">ByteBuilder</a></dt>
<dd>
<div class="block">Constructs a ByteBuilder that will never grow beyond <code>maxCapacity</code>
bytes in length.</div>
</dd>
</dl>
<a name="_C_">
<!-- -->
</a>
<h2 class="title">C</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#C_STATE">C_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#C_STATE">C_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Coalescent.html#calculateAnalyticalLogLikelihood(jebl.evolution.coalescent.IntervalList)">calculateAnalyticalLogLikelihood(IntervalList)</a></span> - Static method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent">Coalescent</a></dt>
<dd>
<div class="block">Calculates the log likelihood of this set of coalescent intervals,
using an analytical integration over theta.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Coalescent.html#calculateLogLikelihood()">calculateLogLikelihood()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent">Coalescent</a></dt>
<dd>
<div class="block">Calculates the log likelihood of this set of coalescent intervals,
given a demographic model.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Coalescent.html#calculateLogLikelihood(jebl.evolution.coalescent.IntervalList, jebl.evolution.coalescent.DemographicFunction)">calculateLogLikelihood(IntervalList, DemographicFunction)</a></span> - Static method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent">Coalescent</a></dt>
<dd>
<div class="block">Calculates the log likelihood of this set of coalescent intervals,
given a demographic model.</div>
</dd>
<dt><a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees"><span class="strong">CalculateSplitRates</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Created by IntelliJ IDEA.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#CalculateSplitRates(jebl.evolution.io.NexusImporter)">CalculateSplitRates(NexusImporter)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/BasicProgressListener.html#cancel()">cancel()</a></span> - Method in class jebl.util.<a href="./jebl/util/BasicProgressListener.html" title="class in jebl.util">BasicProgressListener</a></dt>
<dd>
<div class="block">Sets this progress listener as cancel, so that <a href="./jebl/util/BasicProgressListener.html#isCanceled()"><code>BasicProgressListener.isCanceled()</code></a> will return true.</div>
</dd>
<dt><a href="./jebl/util/Cancelable.html" title="interface in jebl.util"><span class="strong">Cancelable</span></a> - Interface in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd>
<div class="block">Checks whether some operation has been cancelled; This will typically
be used as a callback because it can only query whether a task has
been cancelled, rather than cancel it (there is no cancel() method).</div>
</dd>
<dt><a href="./jebl/evolution/distances/CannotBuildDistanceMatrixException.html" title="class in jebl.evolution.distances"><span class="strong">CannotBuildDistanceMatrixException</span></a> - Exception in <a href="./jebl/evolution/distances/package-summary.html">jebl.evolution.distances</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/CannotBuildDistanceMatrixException.html#CannotBuildDistanceMatrixException(java.lang.String, java.lang.String, java.lang.String)">CannotBuildDistanceMatrixException(String, String, String)</a></span> - Constructor for exception jebl.evolution.distances.<a href="./jebl/evolution/distances/CannotBuildDistanceMatrixException.html" title="class in jebl.evolution.distances">CannotBuildDistanceMatrixException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/CannotBuildDistanceMatrixException.html#CannotBuildDistanceMatrixException(java.lang.String)">CannotBuildDistanceMatrixException(String)</a></span> - Constructor for exception jebl.evolution.distances.<a href="./jebl/evolution/distances/CannotBuildDistanceMatrixException.html" title="class in jebl.evolution.distances">CannotBuildDistanceMatrixException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#CANONICAL_STATE_COUNT">CANONICAL_STATE_COUNT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#CANONICAL_STATE_COUNT">CANONICAL_STATE_COUNT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#CANONICAL_STATE_COUNT">CANONICAL_STATE_COUNT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#CANONICAL_STATES">CANONICAL_STATES</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#CANONICAL_STATES">CANONICAL_STATES</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#CANONICAL_STATES">CANONICAL_STATES</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences"><span class="strong">CanonicalSequence</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd>
<div class="block">A default implementation of the Sequence interface
that converts sequence characters to
States such that calling getString() will always return
uppercase residues with nucleotide U residues converted to T</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#CanonicalSequence(jebl.evolution.sequences.SequenceType, jebl.evolution.taxa.Taxon, java.lang.CharSequence)">CanonicalSequence(SequenceType, Taxon, CharSequence)</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd>
<div class="block">Creates a sequence with a name corresponding to the taxon name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#CanonicalSequence(jebl.evolution.sequences.SequenceType, jebl.evolution.taxa.Taxon, jebl.evolution.sequences.State[])">CanonicalSequence(SequenceType, Taxon, State[])</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd>
<div class="block">Creates a sequence with a name corresponding to the taxon name</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#cardinality()">cardinality()</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent"><span class="strong">CataclysmicDemographic</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#CataclysmicDemographic()">CataclysmicDemographic()</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd>
<div class="block">Construct demographic model with default settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#CataclysmicDemographic(double, double, double, double)">CataclysmicDemographic(double, double, double, double)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd>
<div class="block">Construct demographic model with given settings</div>
</dd>
<dt><a href="./jebl/evolution/characters/Character.html" title="interface in jebl.evolution.characters"><span class="strong">Character</span></a> - Interface in <a href="./jebl/evolution/characters/package-summary.html">jebl.evolution.characters</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/characters/CharacterType.html" title="interface in jebl.evolution.characters"><span class="strong">CharacterType</span></a> - Interface in <a href="./jebl/evolution/characters/package-summary.html">jebl.evolution.characters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ByteBuilder.html#charAt(int)">charAt(int)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ByteBuilder.html" title="class in jebl.evolution.io">ByteBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#CHEMICAL_CLASSIFICATION">CHEMICAL_CLASSIFICATION</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#choleskyFactor(double[][])">choleskyFactor(double[][])</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">Cholesky factorization (aka Cholesky Decomposition)
This factorization can be used when square matrix is symmetric and positive definite.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#choleskySolve(double[][], double[])">choleskySolve(double[][], double[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">Cholesky solve
Once the matrix is decomposed with the above routine, one can solve the triangular factor with backsubstitution.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Binomial.html#choose(double, double)">choose(double, double)</a></span> - Static method in class jebl.math.<a href="./jebl/math/Binomial.html" title="class in jebl.math">Binomial</a></dt>
<dd>
<div class="block">Binomial coefficient n choose k</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Binomial.html#choose2(int)">choose2(int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/Binomial.html" title="class in jebl.math">Binomial</a></dt>
<dd>
<div class="block">get n choose 2</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#CILIATE">CILIATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/treemetrics/CladeHeightMetric.html" title="class in jebl.evolution.treemetrics"><span class="strong">CladeHeightMetric</span></a> - Class in <a href="./jebl/evolution/treemetrics/package-summary.html">jebl.evolution.treemetrics</a></dt>
<dd>
<div class="block">For each clade_j in treeB, find the MRCA_j of the taxa in clade_j in treeA.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/treemetrics/CladeHeightMetric.html#CladeHeightMetric()">CladeHeightMetric()</a></span> - Constructor for class jebl.evolution.treemetrics.<a href="./jebl/evolution/treemetrics/CladeHeightMetric.html" title="class in jebl.evolution.treemetrics">CladeHeightMetric</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treemetrics/CladeHeightMetric.html#CladeHeightMetric(java.util.List)">CladeHeightMetric(List<Taxon>)</a></span> - Constructor for class jebl.evolution.treemetrics.<a href="./jebl/evolution/treemetrics/CladeHeightMetric.html" title="class in jebl.evolution.treemetrics">CladeHeightMetric</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/CladeSystem.html" title="class in jebl.evolution.trees"><span class="strong">CladeSystem</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Stores a set of unique clades for a tree</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CladeSystem.html#CladeSystem()">CladeSystem()</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/CladeSystem.html" title="class in jebl.evolution.trees">CladeSystem</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CladeSystem.html#CladeSystem(jebl.evolution.trees.RootedTree)">CladeSystem(RootedTree)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/CladeSystem.html" title="class in jebl.evolution.trees">CladeSystem</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#cleanSequence(java.lang.CharSequence, jebl.evolution.sequences.SequenceType)">cleanSequence(CharSequence, SequenceType)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">Produce a clean sequence filtered of spaces and digits.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#clear()">clear()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#clear(int)">clear(int)</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#clearAllProgress()">clearAllProgress()</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd>
<div class="block">Clear all progress, including that of previous subtasks.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#clearLastMetaComment()">clearLastMetaComment()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#closeReader()">closeReader()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#CLUSTALW">CLUSTALW</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/ClusteringTreeBuilder.html" title="class in jebl.evolution.trees"><span class="strong">ClusteringTreeBuilder</span></a><<a href="./jebl/evolution/trees/ClusteringTreeBuilder.html" title="type parameter in ClusteringTreeBuilder">T</a> extends <a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a>> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">An abstract base class for clustering algorithms from pairwise distances</div>
</dd>
<dt><a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent"><span class="strong">Coalescent</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">A likelihood function for the coalescent.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Coalescent.html#Coalescent(jebl.evolution.trees.RootedTree, jebl.evolution.coalescent.DemographicFunction)">Coalescent(RootedTree, DemographicFunction)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent">Coalescent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Coalescent.html#Coalescent(jebl.evolution.coalescent.IntervalList, jebl.evolution.coalescent.DemographicFunction)">Coalescent(IntervalList, DemographicFunction)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent">Coalescent</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/treesimulation/CoalescentIntervalGenerator.html" title="class in jebl.evolution.treesimulation"><span class="strong">CoalescentIntervalGenerator</span></a> - Class in <a href="./jebl/evolution/treesimulation/package-summary.html">jebl.evolution.treesimulation</a></dt>
<dd>
<div class="block">This is a class that draws coalescent intervals under the given demographic function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/treesimulation/CoalescentIntervalGenerator.html#CoalescentIntervalGenerator(jebl.evolution.coalescent.DemographicFunction)">CoalescentIntervalGenerator(DemographicFunction)</a></span> - Constructor for class jebl.evolution.treesimulation.<a href="./jebl/evolution/treesimulation/CoalescentIntervalGenerator.html" title="class in jebl.evolution.treesimulation">CoalescentIntervalGenerator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#CODON">CODON</a></span> - Static variable in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences"><span class="strong">Codons</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#Codons()">Codons()</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences"><span class="strong">CodonSequence</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd>
<div class="block">A codon implementation of the Sequence interface.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#CodonSequence(jebl.evolution.taxa.Taxon, jebl.evolution.sequences.State[])">CodonSequence(Taxon, State[])</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd>
<div class="block">Creates a sequence with a name corresponding to the taxon name</div>
</dd>
<dt><a href="./jebl/evolution/sequences/CodonState.html" title="class in jebl.evolution.sequences"><span class="strong">CodonState</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd>
<div class="block">As of 2007-07-30, instances of this class are only constructed for non-ambigous
nucleotide triplets - see <a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences"><code>Codons</code></a>.</div>
</dd>
<dt><a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees"><span class="strong">CompactRootedTree</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A memory efficient rooted tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#CompactRootedTree(jebl.evolution.trees.RootedTree)">CompactRootedTree(RootedTree)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd>
<div class="block">Do all the hard work.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd>
<div class="block">Sequences are compared by their taxa</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcidState.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcidState.html" title="class in jebl.evolution.sequences">AminoAcidState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd>
<div class="block">Sequences are compared by their taxa</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd>
<div class="block">Sequences are compared by their taxa</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd>
<div class="block">Sequences are compared by their taxa</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/NucleotideState.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/NucleotideState.html" title="class in jebl.evolution.sequences">NucleotideState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#complement(jebl.evolution.sequences.NucleotideState[])">complement(NucleotideState[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#complement(jebl.util.FixedBitSet)">complement(FixedBitSet)</a></span> - Static method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#complement()">complement()</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#COMPLEMENTARY_STATES">COMPLEMENTARY_STATES</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util"><span class="strong">CompositeProgressListener</span></a> - Class in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd>
<div class="block">A <a href="./jebl/util/ProgressListener.html" title="class in jebl.util"><code>ProgressListener</code></a> that is suitable for a task that consists of several subtasks.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#CompositeProgressListener(jebl.util.ProgressListener, double...)">CompositeProgressListener(ProgressListener, double...)</a></span> - Constructor for class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd>
<div class="block">construct a new composite ProgressListener.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#CompositeProgressListener(jebl.util.ProgressListener, int)">CompositeProgressListener(ProgressListener, int)</a></span> - Constructor for class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd>
<div class="block">Construct a CompositeProgressListener with a number of evenly weighted subtasks.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#conceptuallyUnrooted()">conceptuallyUnrooted()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#conceptuallyUnrooted()">conceptuallyUnrooted()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#conceptuallyUnrooted()">conceptuallyUnrooted()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#conceptuallyUnrooted()">conceptuallyUnrooted()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#conceptuallyUnrooted()">conceptuallyUnrooted()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTree.html#conceptuallyUnrooted()">conceptuallyUnrooted()</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTree.html" title="interface in jebl.evolution.trees">RootedTree</a></dt>
<dd>
<div class="block">Due to current implementation limitations, trees store "branch" information in nodes.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#conceptuallyUnrooted()">conceptuallyUnrooted()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/MaybeBoolean.html#consensus(boolean, boolean)">consensus(boolean, boolean)</a></span> - Static method in enum jebl.util.<a href="./jebl/util/MaybeBoolean.html" title="enum in jebl.util">MaybeBoolean</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments"><span class="strong">ConsensusSequence</span></a> - Class in <a href="./jebl/evolution/alignments/package-summary.html">jebl.evolution.alignments</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#ConsensusSequence(jebl.evolution.taxa.Taxon, jebl.evolution.alignments.Alignment)">ConsensusSequence(Taxon, Alignment)</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd>
<div class="block">Creates a FilteredSequence wrapper to the given source sequence.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#ConsensusSequence(jebl.evolution.taxa.Taxon, jebl.evolution.alignments.Alignment, boolean)">ConsensusSequence(Taxon, Alignment, boolean)</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd>
<div class="block">Creates a FilteredSequence wrapper to the given source sequence.</div>
</dd>
<dt><a href="./jebl/evolution/trees/ConsensusTreeBuilder.html" title="class in jebl.evolution.trees"><span class="strong">ConsensusTreeBuilder</span></a><<a href="./jebl/evolution/trees/ConsensusTreeBuilder.html" title="type parameter in ConsensusTreeBuilder">T</a> extends <a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a>> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A <a href="./jebl/evolution/trees/TreeBuilder.html" title="interface in jebl.evolution.trees"><code>TreeBuilder</code></a> that builds a consensus tree for a set of trees on identical leaf sets.</div>
</dd>
<dt><a href="./jebl/evolution/trees/ConsensusTreeBuilder.Method.html" title="enum in jebl.evolution.trees"><span class="strong">ConsensusTreeBuilder.Method</span></a> - Enum in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Supported consensus methods.</div>
</dd>
<dt><a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent"><span class="strong">ConstantPopulation</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">This class models coalescent intervals for a constant population
(parameter: N0=present-day population size).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#ConstantPopulation()">ConstantPopulation()</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd>
<div class="block">Construct demographic model with default settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#ConstantPopulation(double)">ConstantPopulation(double)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd>
<div class="block">Construct demographic model with given settings</div>
</dd>
<dt><a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent"><span class="strong">ConstExponential</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">This class models exponential growth from an initial population size.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#ConstExponential()">ConstExponential()</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd>
<div class="block">Construct demographic model with default settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#ConstExponential(double, double, double)">ConstExponential(double, double, double)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd>
<div class="block">Construct demographic model with given settings</div>
</dd>
<dt><a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent"><span class="strong">ConstLogistic</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">This class models logistic growth from an initial population size.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#ConstLogistic()">ConstLogistic()</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd>
<div class="block">Construct demographic model with default settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#ConstLogistic(double, double, double, double)">ConstLogistic(double, double, double, double)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd>
<div class="block">Construct demographic model with given settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#constructConsensus(jebl.evolution.alignments.Alignment, boolean)">constructConsensus(Alignment, boolean)</a></span> - Static method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#contains(int)">contains(int)</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/CharacterType.html#CONTINUOUS">CONTINUOUS</a></span> - Static variable in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/CharacterType.html" title="interface in jebl.evolution.characters">CharacterType</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters"><span class="strong">ContinuousCharacter</span></a> - Class in <a href="./jebl/evolution/characters/package-summary.html">jebl.evolution.characters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#ContinuousCharacter(java.lang.String, java.lang.String)">ContinuousCharacter(String, String)</a></span> - Constructor for class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd>
<div class="block">Constructs a basic ContinuousCharacter object with no taxa added yet</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#ContinuousCharacter(java.lang.String, java.lang.String, java.util.Set)">ContinuousCharacter(String, String, Set<Taxon>)</a></span> - Constructor for class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd>
<div class="block">Constructs a basic ContinuousCharacter object with taxa added</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#copy(double[], double[])">copy(double[], double[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd>
<div class="block">Copy source vector into target vector</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#copy(double[][], double[][])">copy(double[][], double[][])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Copies all of source into dest - assumes dest to be large enough</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#copyIntervals(jebl.evolution.coalescent.Intervals)">copyIntervals(Intervals)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#copyMatrix(double[][])">copyMatrix(double[][])</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">copy one matrix into another</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#copyTree(jebl.evolution.trees.RootedTree)">copyTree(RootedTree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd>
<div class="block">This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#createExternalNode(jebl.evolution.taxa.Taxon)">createExternalNode(Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">Creates a new external node with the given taxon.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#createExternalNode(jebl.evolution.taxa.Taxon)">createExternalNode(Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Creates a new external node with the given taxon.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#createExternalNode(jebl.evolution.taxa.Taxon)">createExternalNode(Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">Creates a new external node with the given taxon.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#createInternalNode(java.util.List)">createInternalNode(List<? extends Node>)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">Once a SimpleRootedTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#createInternalNode(java.util.List)">createInternalNode(List<? extends Node>)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Once a SimpleRootedTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#createInternalNode(java.util.List)">createInternalNode(List<Node>)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">Once a SimpleTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#createNodeDensityComparator(jebl.evolution.trees.RootedTree)">createNodeDensityComparator(RootedTree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#createNodeDensityMinNodeHeightComparator(jebl.evolution.trees.RootedTree)">createNodeDensityMinNodeHeightComparator(RootedTree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#createNodes(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">createNodes(RootedTree, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Clones the entire tree structure from the given RootedTree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#createNodes(jebl.evolution.trees.Tree, jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">createNodes(Tree, Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Clones the entire tree structure from the given (unrooted) Tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MinimiserMonitor.Utils.html#createNullMonitor()">createNullMonitor()</a></span> - Static method in class jebl.math.<a href="./jebl/math/MinimiserMonitor.Utils.html" title="class in jebl.math">MinimiserMonitor.Utils</a></dt>
<dd>
<div class="block">Creates a MinimiserMonitor that looses all output</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.OEFactory.html#createOrderEnumerator(int)">createOrderEnumerator(int)</a></span> - Method in interface jebl.math.<a href="./jebl/math/OrderEnumerator.OEFactory.html" title="interface in jebl.math">OrderEnumerator.OEFactory</a></dt>
<dd>
<div class="block">For generating an ordering from 0..size-1.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MinimiserMonitor.Utils.html#createSimpleMonitor(java.io.PrintWriter)">createSimpleMonitor(PrintWriter)</a></span> - Static method in class jebl.math.<a href="./jebl/math/MinimiserMonitor.Utils.html" title="class in jebl.math">MinimiserMonitor.Utils</a></dt>
<dd>
<div class="block">Creates a MinimiserMonitor that outputs current minimum to a print stream</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MinimiserMonitor.Utils.html#createSplitMonitor(jebl.math.MinimiserMonitor, jebl.math.MinimiserMonitor)">createSplitMonitor(MinimiserMonitor, MinimiserMonitor)</a></span> - Static method in class jebl.math.<a href="./jebl/math/MinimiserMonitor.Utils.html" title="class in jebl.math">MinimiserMonitor.Utils</a></dt>
<dd>
<div class="block">creates a monitor such that all information sent to monitor is based on two sub monitors</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MinimiserMonitor.Utils.html#createStringMonitor()">createStringMonitor()</a></span> - Static method in class jebl.math.<a href="./jebl/math/MinimiserMonitor.Utils.html" title="class in jebl.math">MinimiserMonitor.Utils</a></dt>
<dd>
<div class="block">Creates a MinimiserMonitor that Stores output (use toString() to access current results)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MinimiserMonitor.Utils.html#createSystemErrorMonitor()">createSystemErrorMonitor()</a></span> - Static method in class jebl.math.<a href="./jebl/math/MinimiserMonitor.Utils.html" title="class in jebl.math">MinimiserMonitor.Utils</a></dt>
<dd>
<div class="block">Creates a MinimiserMonitor that outputs current minimum to a System.err</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MinimiserMonitor.Utils.html#createSystemOuptutMonitor()">createSystemOuptutMonitor()</a></span> - Static method in class jebl.math.<a href="./jebl/math/MinimiserMonitor.Utils.html" title="class in jebl.math">MinimiserMonitor.Utils</a></dt>
<dd>
<div class="block">Creates a MinimiserMonitor that outputs current minimum to a System.out</div>
</dd>
</dl>
<a name="_D_">
<!-- -->
</a>
<h2 class="title">D</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#D_STATE">D_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#D_STATE">D_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#DEBUGsubTreeRep(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">DEBUGsubTreeRep(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ConsensusTreeBuilder.html#DEFAULT_SUPPORT_ATTRIBUTE_NAME">DEFAULT_SUPPORT_ATTRIBUTE_NAME</a></span> - Static variable in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ConsensusTreeBuilder.html" title="class in jebl.evolution.trees">ConsensusTreeBuilder</a></dt>
<dd>
<div class="block">Name of attribute specifing amount of support for branch</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#deleteInternalNode(jebl.evolution.graphs.Node)">deleteInternalNode(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Removes an internal node in this tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#deleteMatrixColumn(double[][], int)">deleteMatrixColumn(double[][], int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">takes a matrix and deletes a column</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#deleteMatrixRow(double[][], int)">deleteMatrixRow(double[][], int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">takes a matrix and deletes a row</div>
</dd>
<dt><a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent"><span class="strong">DemographicFunction</span></a> - Interface in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">This interface provides methods that describe a demographic function.</div>
</dd>
<dt><a href="./jebl/evolution/coalescent/DemographicFunction.Utils.html" title="class in jebl.evolution.coalescent"><span class="strong">DemographicFunction.Utils</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/IllegalCharacterPolicy.html#description">description</a></span> - Variable in enum jebl.evolution.io.<a href="./jebl/evolution/io/IllegalCharacterPolicy.html" title="enum in jebl.evolution.io">IllegalCharacterPolicy</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/FastaImporter.html#descriptionPropertyName">descriptionPropertyName</a></span> - Static variable in class jebl.evolution.io.<a href="./jebl/evolution/io/FastaImporter.html" title="class in jebl.evolution.io">FastaImporter</a></dt>
<dd>
<div class="block">Name of Jebl sequence property which stores sequence description (i.e.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#detachChildren(jebl.evolution.graphs.Node, java.util.List)">detachChildren(Node, List<Integer>)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/NumericalDerivative.html#diagonalHessian(jebl.math.MultivariateFunction, double[])">diagonalHessian(MultivariateFunction, double[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/NumericalDerivative.html" title="class in jebl.math">NumericalDerivative</a></dt>
<dd>
<div class="block">determine diagonal of Hessian</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/CharacterType.html#DISCRETE">DISCRETE</a></span> - Static variable in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/CharacterType.html" title="interface in jebl.evolution.characters">CharacterType</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters"><span class="strong">DiscreteCharacter</span></a> - Class in <a href="./jebl/evolution/characters/package-summary.html">jebl.evolution.characters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#DiscreteCharacter(java.lang.String, java.lang.String, int)">DiscreteCharacter(String, String, int)</a></span> - Constructor for class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd>
<div class="block">Constructs a basic DiscreteCharacter object with no taxa added yet</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#DiscreteCharacter(java.lang.String, java.lang.String, int, java.util.Set)">DiscreteCharacter(String, String, int, Set<Taxon>)</a></span> - Constructor for class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd>
<div class="block">Constructs a basic DiscreteCharacter object with taxa</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#displayIntervals()">displayIntervals()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#displayStatistics()">displayStatistics()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.Result.html#distance">distance</a></span> - Variable in class jebl.evolution.align.<a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.Result.html" title="class in jebl.evolution.align">AlignmentTreeBuilderFactory.Result</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBiPartitionInfo.html#distance(jebl.evolution.trees.TreeBiPartitionInfo, jebl.evolution.trees.TreeBiPartitionInfo, jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm)">distance(TreeBiPartitionInfo, TreeBiPartitionInfo, TreeBiPartitionInfo.DistanceNorm)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBiPartitionInfo.html" title="class in jebl.evolution.trees">TreeBiPartitionInfo</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/distances/DistanceMatrix.html" title="interface in jebl.evolution.distances"><span class="strong">DistanceMatrix</span></a> - Interface in <a href="./jebl/evolution/distances/package-summary.html">jebl.evolution.distances</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/DistanceMatrixImporter.html" title="interface in jebl.evolution.io"><span class="strong">DistanceMatrixImporter</span></a> - Interface in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/DistanceMatrixImporter.Triangle.html" title="enum in jebl.evolution.io"><span class="strong">DistanceMatrixImporter.Triangle</span></a> - Enum in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/BartonSternberg.html#doAlign(java.util.List, jebl.evolution.trees.RootedTree, jebl.util.ProgressListener)">doAlign(List<Sequence>, RootedTree, ProgressListener)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/BartonSternberg.html" title="class in jebl.evolution.align">BartonSternberg</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/BartonSternberg.html#doAlign(jebl.evolution.alignments.Alignment, jebl.evolution.alignments.Alignment, jebl.util.ProgressListener)">doAlign(Alignment, Alignment, ProgressListener)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/BartonSternberg.html" title="class in jebl.evolution.align">BartonSternberg</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/BartonSternberg.html#doAlign(jebl.evolution.alignments.Alignment, jebl.evolution.sequences.Sequence, jebl.util.ProgressListener)">doAlign(Alignment, Sequence, ProgressListener)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/BartonSternberg.html" title="class in jebl.evolution.align">BartonSternberg</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/MultipleAligner.html#doAlign(java.util.List, jebl.evolution.trees.RootedTree, jebl.util.ProgressListener)">doAlign(List<Sequence>, RootedTree, ProgressListener)</a></span> - Method in interface jebl.evolution.align.<a href="./jebl/evolution/align/MultipleAligner.html" title="interface in jebl.evolution.align">MultipleAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/MultipleAligner.html#doAlign(jebl.evolution.alignments.Alignment, jebl.evolution.alignments.Alignment, jebl.util.ProgressListener)">doAlign(Alignment, Alignment, ProgressListener)</a></span> - Method in interface jebl.evolution.align.<a href="./jebl/evolution/align/MultipleAligner.html" title="interface in jebl.evolution.align">MultipleAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/MultipleAligner.html#doAlign(jebl.evolution.alignments.Alignment, jebl.evolution.sequences.Sequence, jebl.util.ProgressListener)">doAlign(Alignment, Sequence, ProgressListener)</a></span> - Method in interface jebl.evolution.align.<a href="./jebl/evolution/align/MultipleAligner.html" title="interface in jebl.evolution.align">MultipleAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd>
<div class="block">Performs the alignment, abstract.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/MaximalSegmentPair.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/MaximalSegmentPair.html" title="class in jebl.evolution.align">MaximalSegmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunsch.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunsch.html" title="class in jebl.evolution.align">NeedlemanWunsch</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#doAlignment(java.lang.String, java.lang.String, int, int)">doAlignment(String, String, int, int)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#doAlignment(jebl.evolution.align.Profile, jebl.evolution.align.Profile, int, int, int, int, int, int)">doAlignment(Profile, Profile, int, int, int, int, int, int)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#doAlignment(jebl.evolution.align.Profile, jebl.evolution.align.Profile, int, int, int, int, int, int, boolean, boolean)">doAlignment(Profile, Profile, int, int, int, int, int, int, boolean, boolean)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#doAlignment(java.lang.String, java.lang.String, jebl.util.ProgressListener, boolean)">doAlignment(String, String, ProgressListener, boolean)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#doAlignment(java.lang.String, java.lang.String, jebl.util.ProgressListener)">doAlignment(String, String, ProgressListener)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#doAlignment(jebl.evolution.align.Profile, jebl.evolution.align.Profile, jebl.util.ProgressListener, boolean)">doAlignment(Profile, Profile, ProgressListener, boolean)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#doAlignment(jebl.evolution.sequences.Sequence, jebl.evolution.sequences.Sequence, jebl.util.ProgressListener)">doAlignment(Sequence, Sequence, ProgressListener)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html" title="class in jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/OldNeedlemanWunschAffine.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/OldNeedlemanWunschAffine.html" title="class in jebl.evolution.align">OldNeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/OverlapAlign.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/OverlapAlign.html" title="class in jebl.evolution.align">OverlapAlign</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/PairwiseAligner.html#doAlignment(jebl.evolution.sequences.Sequence, jebl.evolution.sequences.Sequence, jebl.util.ProgressListener)">doAlignment(Sequence, Sequence, ProgressListener)</a></span> - Method in interface jebl.evolution.align.<a href="./jebl/evolution/align/PairwiseAligner.html" title="interface in jebl.evolution.align">PairwiseAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWaterman.html#doAlignment(java.lang.String, java.lang.String, jebl.util.ProgressListener)">doAlignment(String, String, ProgressListener)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWaterman.html" title="class in jebl.evolution.align">SmithWaterman</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWaterman.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWaterman.html" title="class in jebl.evolution.align">SmithWaterman</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpace.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpace.html" title="class in jebl.evolution.align">SmithWatermanLinearSpace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#doAlignment(java.lang.String, java.lang.String, jebl.util.ProgressListener)">doAlignment(String, String, ProgressListener)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align">SmithWatermanLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#doAlignment(java.lang.String, java.lang.String)">doAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align">SmithWatermanLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#doMatch(jebl.evolution.align.Output, java.lang.String, boolean)">doMatch(Output, String, boolean)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd>
<div class="block">Print the score, the F matrix, and the alignment</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#doMatch(jebl.evolution.align.Output, java.lang.String)">doMatch(Output, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd>
<div class="block">Print the score and the alignment</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Scores.html#duplicate(jebl.evolution.align.scores.Scores)">duplicate(Scores)</a></span> - Static method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Scores.html" title="class in jebl.evolution.align.scores">Scores</a></dt>
<dd> </dd>
</dl>
<a name="_E_">
<!-- -->
</a>
<h2 class="title">E</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#E_STATE">E_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#ECHINODERM_MT">ECHINODERM_MT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/graphs/Edge.html" title="interface in jebl.evolution.graphs"><span class="strong">Edge</span></a> - Interface in <a href="./jebl/evolution/graphs/package-summary.html">jebl.evolution.graphs</a></dt>
<dd>
<div class="block">Represents a node in a graph or tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#edgeFraction">edgeFraction</a></span> - Variable in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent"><span class="strong">EmpiricalDemographicFunction</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#EmpiricalDemographicFunction(double[], double[], boolean)">EmpiricalDemographicFunction(double[], double[], boolean)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#EMPTY">EMPTY</a></span> - Static variable in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">A ProgressListener that ignores all events and always returns false from
<a href="./jebl/util/ProgressListener.html#isCanceled()"><code>ProgressListener.isCanceled()</code></a>.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MachineAccuracy.html#EPSILON">EPSILON</a></span> - Static variable in class jebl.math.<a href="./jebl/math/MachineAccuracy.html" title="class in jebl.math">MachineAccuracy</a></dt>
<dd>
<div class="block">machine accuracy constant</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#equal(jebl.evolution.trees.RootedTree, jebl.evolution.trees.RootedTree)">equal(RootedTree, RootedTree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd>
<div class="block">Compares 2 trees and returns true if they have the same topology.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#equals(jebl.evolution.taxa.Taxon)">equals(Taxon)</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/HashPair.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class jebl.util.<a href="./jebl/util/HashPair.html" title="class in jebl.util">HashPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#EUPLOTID_NUC">EUPLOTID_NUC</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Coalescent.html#evaluate(double[])">evaluate(double[])</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent">Coalescent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateFunction.html#evaluate(double[])">evaluate(double[])</a></span> - Method in interface jebl.math.<a href="./jebl/math/MultivariateFunction.html" title="interface in jebl.math">MultivariateFunction</a></dt>
<dd>
<div class="block">compute function value</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalLineFunction.html#evaluate(double)">evaluate(double)</a></span> - Method in class jebl.math.<a href="./jebl/math/OrthogonalLineFunction.html" title="class in jebl.math">OrthogonalLineFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateFunction.html#evaluate(double)">evaluate(double)</a></span> - Method in interface jebl.math.<a href="./jebl/math/UnivariateFunction.html" title="interface in jebl.math">UnivariateFunction</a></dt>
<dd>
<div class="block">compute function value</div>
</dd>
<dt><a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent"><span class="strong">Expansion</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">This class models exponential growth from an initial ancestral population size.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#Expansion()">Expansion()</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd>
<div class="block">Construct demographic model with default settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#Expansion(double, double, double)">Expansion(double, double, double)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd>
<div class="block">Construct demographic model with given settings</div>
</dd>
<dt><a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent"><span class="strong">ExponentialGrowth</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#ExponentialGrowth()">ExponentialGrowth()</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd>
<div class="block">Construct demographic model with default settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#ExponentialGrowth(double, double)">ExponentialGrowth(double, double)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd>
<div class="block">Construct demographic model with given settings</div>
</dd>
<dt><a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent"><span class="strong">ExponentialLogistic</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">This class models logistic growth from an initial exponential phase.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#ExponentialLogistic()">ExponentialLogistic()</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd>
<div class="block">Construct demographic model with default settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#ExponentialLogistic(double, double, double, double, double)">ExponentialLogistic(double, double, double, double, double)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd>
<div class="block">Construct demographic model with given settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/AlignmentExporter.html#exportAlignment(jebl.evolution.alignments.Alignment)">exportAlignment(Alignment)</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/AlignmentExporter.html" title="interface in jebl.evolution.io">AlignmentExporter</a></dt>
<dd>
<div class="block">export one alignment.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/MEGAExporter.html#exportAlignment(jebl.evolution.alignments.Alignment, java.lang.String)">exportAlignment(Alignment, String)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/MEGAExporter.html" title="class in jebl.evolution.io">MEGAExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/MEGAExporter.html#exportAlignment(jebl.evolution.alignments.Alignment)">exportAlignment(Alignment)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/MEGAExporter.html" title="class in jebl.evolution.io">MEGAExporter</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Files created by this export method won't be importable by MEGA (because they don't have titles). Use <a href="./jebl/evolution/io/MEGAExporter.html#exportAlignment(jebl.evolution.alignments.Alignment, java.lang.String)"><code>MEGAExporter.exportAlignment(jebl.evolution.alignments.Alignment, String)</code></a> instead.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#exportAlignment(jebl.evolution.alignments.Alignment)">exportAlignment(Alignment)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd>
<div class="block">exportAlignment.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/PHYLIPExporter.html#exportAlignment(jebl.evolution.alignments.Alignment)">exportAlignment(Alignment)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/PHYLIPExporter.html" title="class in jebl.evolution.io">PHYLIPExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#exportExcludeKeys">exportExcludeKeys</a></span> - Static variable in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#exportMatrix(jebl.evolution.distances.DistanceMatrix)">exportMatrix(DistanceMatrix)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/FastaExporter.html#exportSequences(java.util.Collection)">exportSequences(Collection<? extends Sequence>)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/FastaExporter.html" title="class in jebl.evolution.io">FastaExporter</a></dt>
<dd>
<div class="block">export alignment or set of sequences.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#exportSequences(java.util.Collection)">exportSequences(Collection<? extends Sequence>)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd>
<div class="block">export alignment.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/SequenceExporter.html#exportSequences(java.util.Collection)">exportSequences(Collection<? extends Sequence>)</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/SequenceExporter.html" title="interface in jebl.evolution.io">SequenceExporter</a></dt>
<dd>
<div class="block">exportSequences.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NewickExporter.html#exportTree(jebl.evolution.trees.Tree)">exportTree(Tree)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NewickExporter.html" title="class in jebl.evolution.io">NewickExporter</a></dt>
<dd>
<div class="block">Export a single tree</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#exportTree(jebl.evolution.trees.Tree)">exportTree(Tree)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd>
<div class="block">Export a single tree</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/PHYLIPExporter.html#exportTree(jebl.evolution.trees.Tree)">exportTree(Tree)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/PHYLIPExporter.html" title="class in jebl.evolution.io">PHYLIPExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/TreeExporter.html#exportTree(jebl.evolution.trees.Tree)">exportTree(Tree)</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/TreeExporter.html" title="interface in jebl.evolution.io">TreeExporter</a></dt>
<dd>
<div class="block">Export a single tree</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NewickExporter.html#exportTrees(java.util.Collection)">exportTrees(Collection<? extends Tree>)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NewickExporter.html" title="class in jebl.evolution.io">NewickExporter</a></dt>
<dd>
<div class="block">Export a collection of trees</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#exportTrees(java.util.Collection)">exportTrees(Collection<? extends Tree>)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/PHYLIPExporter.html#exportTrees(java.util.Collection)">exportTrees(Collection<? extends Tree>)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/PHYLIPExporter.html" title="class in jebl.evolution.io">PHYLIPExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/TreeExporter.html#exportTrees(java.util.Collection)">exportTrees(Collection<? extends Tree>)</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/TreeExporter.html" title="interface in jebl.evolution.io">TreeExporter</a></dt>
<dd>
<div class="block">Export a collection of trees</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#exportTreesWithTranslation(java.util.Collection, java.util.Map)">exportTreesWithTranslation(Collection<? extends Tree>, Map<String, String>)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
</dl>
<a name="_F_">
<!-- -->
</a>
<h2 class="title">F</h2>
<dl>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#f2minx">f2minx</a></span> - Variable in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">curvature at minimum</div>
</dd>
<dt><a href="./jebl/evolution/distances/F84DistanceMatrix.html" title="class in jebl.evolution.distances"><span class="strong">F84DistanceMatrix</span></a> - Class in <a href="./jebl/evolution/distances/package-summary.html">jebl.evolution.distances</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/F84DistanceMatrix.html#F84DistanceMatrix(jebl.evolution.alignments.Alignment, jebl.util.ProgressListener)">F84DistanceMatrix(Alignment, ProgressListener)</a></span> - Constructor for class jebl.evolution.distances.<a href="./jebl/evolution/distances/F84DistanceMatrix.html" title="class in jebl.evolution.distances">F84DistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/F84DistanceMatrix.html#F84DistanceMatrix(jebl.evolution.alignments.Alignment)">F84DistanceMatrix(Alignment)</a></span> - Constructor for class jebl.evolution.distances.<a href="./jebl/evolution/distances/F84DistanceMatrix.html" title="class in jebl.evolution.distances">F84DistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#F_STATE">F_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/FastaExporter.html" title="class in jebl.evolution.io"><span class="strong">FastaExporter</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Class for exporting a fasta file format.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/FastaExporter.html#FastaExporter(java.io.Writer)">FastaExporter(Writer)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/FastaExporter.html" title="class in jebl.evolution.io">FastaExporter</a></dt>
<dd>
<div class="block">Constructor</div>
</dd>
<dt><a href="./jebl/evolution/io/FastaImporter.html" title="class in jebl.evolution.io"><span class="strong">FastaImporter</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Class for importing Fasta sequential file format.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/FastaImporter.html#FastaImporter(java.io.File, jebl.evolution.sequences.SequenceType)">FastaImporter(File, SequenceType)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/FastaImporter.html" title="class in jebl.evolution.io">FastaImporter</a></dt>
<dd>
<div class="block">Use this constructor if you are reading from a file.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/FastaImporter.html#FastaImporter(java.io.Reader, jebl.evolution.sequences.SequenceType)">FastaImporter(Reader, SequenceType)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/FastaImporter.html" title="class in jebl.evolution.io">FastaImporter</a></dt>
<dd>
<div class="block">This constuctor takes a reader.</div>
</dd>
<dt><a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees"><span class="strong">FilteredRootedTree</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#FilteredRootedTree(jebl.evolution.trees.RootedTree)">FilteredRootedTree(RootedTree)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences"><span class="strong">FilteredSequence</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#FilteredSequence(jebl.evolution.sequences.Sequence)">FilteredSequence(Sequence)</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd>
<div class="block">Creates a FilteredSequence wrapper to the given source sequence.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#findEndBlock()">findEndBlock()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Read ahead to the end of the current block.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#findMinimum(jebl.math.MultivariateFunction, double[])">findMinimum(MultivariateFunction, double[])</a></span> - Method in class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd>
<div class="block">Find minimum close to vector x</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#findMinimum(jebl.math.MultivariateFunction, double[], int, int)">findMinimum(MultivariateFunction, double[], int, int)</a></span> - Method in class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd>
<div class="block">Find minimum close to vector x
(desired fractional digits for each parameter is specified)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#findMinimum(jebl.math.MultivariateFunction, double[], int, int, jebl.math.MinimiserMonitor)">findMinimum(MultivariateFunction, double[], int, int, MinimiserMonitor)</a></span> - Method in class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd>
<div class="block">Find minimum close to vector x
(desired fractional digits for each parameter is specified)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#findMinimum(double, jebl.math.UnivariateFunction)">findMinimum(double, UnivariateFunction)</a></span> - Method in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">Find minimum
(first estimate given)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#findMinimum(double, jebl.math.UnivariateFunction, int)">findMinimum(double, UnivariateFunction, int)</a></span> - Method in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">Find minimum
(first estimate given, desired number of fractional digits specified)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#findMinimum(jebl.math.UnivariateFunction)">findMinimum(UnivariateFunction)</a></span> - Method in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">Find minimum
(no first estimate given)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#findMinimum(jebl.math.UnivariateFunction, int)">findMinimum(UnivariateFunction, int)</a></span> - Method in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">Find minimum
(no first estimate given, desired number of fractional digits specified)</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#findNextBlock()">findNextBlock()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Read ahead to the next block in the input.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#findTimeIntervals()">findTimeIntervals()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/TracebackPlotter.html#finishedTraceBack()">finishedTraceBack()</a></span> - Method in interface jebl.evolution.align.<a href="./jebl/evolution/align/TracebackPlotter.html" title="interface in jebl.evolution.align">TracebackPlotter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ClusteringTreeBuilder.html#fireSetProgress(double)">fireSetProgress(double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ClusteringTreeBuilder.html" title="class in jebl.evolution.trees">ClusteringTreeBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/HashPair.html#first">first</a></span> - Variable in class jebl.util.<a href="./jebl/util/HashPair.html" title="class in jebl.util">HashPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/NumericalDerivative.html#firstDerivative(jebl.math.UnivariateFunction, double)">firstDerivative(UnivariateFunction, double)</a></span> - Static method in class jebl.math.<a href="./jebl/math/NumericalDerivative.html" title="class in jebl.math">NumericalDerivative</a></dt>
<dd>
<div class="block">determine first derivative</div>
</dd>
<dt><a href="./jebl/evolution/parsimony/FitchParsimony.html" title="class in jebl.evolution.parsimony"><span class="strong">FitchParsimony</span></a> - Class in <a href="./jebl/evolution/parsimony/package-summary.html">jebl.evolution.parsimony</a></dt>
<dd>
<div class="block">Class for reconstructing characters using Fitch parsimony.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/parsimony/FitchParsimony.html#FitchParsimony(java.util.List, boolean)">FitchParsimony(List<Pattern>, boolean)</a></span> - Constructor for class jebl.evolution.parsimony.<a href="./jebl/evolution/parsimony/FitchParsimony.html" title="class in jebl.evolution.parsimony">FitchParsimony</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/parsimony/FitchParsimony.html#FitchParsimony(jebl.evolution.alignments.Patterns, boolean)">FitchParsimony(Patterns, boolean)</a></span> - Constructor for class jebl.evolution.parsimony.<a href="./jebl/evolution/parsimony/FitchParsimony.html" title="class in jebl.evolution.parsimony">FitchParsimony</a></dt>
<dd> </dd>
<dt><a href="./jebl/util/FixedBitSet.html" title="class in jebl.util"><span class="strong">FixedBitSet</span></a> - Class in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd>
<div class="block">A bit-set of fixed size.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#FixedBitSet(int)">FixedBitSet(int)</a></span> - Constructor for class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#FixedBitSet(jebl.util.FixedBitSet)">FixedBitSet(FixedBitSet)</a></span> - Constructor for class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#FLATWORM_MT">FLATWORM_MT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#fminx">fminx</a></span> - Variable in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">function value at minimum</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#forFiles(jebl.util.ProgressListener, java.util.List)">forFiles(ProgressListener, List<File>)</a></span> - Static method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Scores.html#forMatrix(jebl.evolution.align.scores.ScoreMatrix)">forMatrix(ScoreMatrix)</a></span> - Static method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Scores.html" title="class in jebl.evolution.align.scores">Scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#formatScore(float)">formatScore(float)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#fractionEqual(jebl.evolution.sequences.State)">fractionEqual(State)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd>
<div class="block">Determine how much in common these potentially ambigous states have as a fraction between 0 and 1
2 non-ambiguous states will return 0.</div>
</dd>
</dl>
<a name="_G_">
<!-- -->
</a>
<h2 class="title">G</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#G_STATE">G_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#G_STATE">G_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/GammaFunction.html" title="class in jebl.math"><span class="strong">GammaFunction</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">gamma function</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/GammaFunction.html#GammaFunction()">GammaFunction()</a></span> - Constructor for class jebl.math.<a href="./jebl/math/GammaFunction.html" title="class in jebl.math">GammaFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#GAP_STATE">GAP_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#GAP_STATE">GAP_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#GAP_STATE">GAP_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#gapFraction()">gapFraction()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/GaplessSequence.html" title="class in jebl.evolution.sequences"><span class="strong">GaplessSequence</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GaplessSequence.html#GaplessSequence(jebl.evolution.sequences.Sequence)">GaplessSequence(Sequence)</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GaplessSequence.html" title="class in jebl.evolution.sequences">GaplessSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalSearch.html#generateFactory(boolean)">generateFactory(boolean)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrthogonalSearch.html" title="class in jebl.math">OrthogonalSearch</a></dt>
<dd>
<div class="block">Generate a MultivariateMinimum.Factory for an OrthogonalSearch</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.Factory.html#generateNewMinimiser()">generateNewMinimiser()</a></span> - Method in interface jebl.math.<a href="./jebl/math/MultivariateMinimum.Factory.html" title="interface in jebl.math">MultivariateMinimum.Factory</a></dt>
<dd>
<div class="block">Generate a new Multivariate Minimum</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#generateScores(java.lang.String)">generateScores(String)</a></span> - Static method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd>
<div class="block">For any matrix.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#generateScores(java.lang.String, int)">generateScores(String, int)</a></span> - Static method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd>
<div class="block">For Blosum and Pam matrices</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#generateScores(java.lang.String, float)">generateScores(String, float)</a></span> - Static method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd>
<div class="block">For calculated nucleotide matrices.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#GENETIC_CODES">GENETIC_CODES</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use <a href="./jebl/evolution/sequences/GeneticCode.html#getGeneticCodes()"><code>GeneticCode.getGeneticCodes()</code></a> instead</i></div>
</div>
</dd>
<dt><a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences"><span class="strong">GeneticCode</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd>
<div class="block">A set of standard genetic codes.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MostProbableTopology.html#get(int, double)">get(int, double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MostProbableTopology.html" title="class in jebl.evolution.trees">MostProbableTopology</a></dt>
<dd>
<div class="block">Get the most probable tree(s)</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Graph.html#getAdjacencies(jebl.evolution.graphs.Node)">getAdjacencies(Node)</a></span> - Method in interface jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Graph.html" title="interface in jebl.evolution.graphs">Graph</a></dt>
<dd>
<div class="block">Returns a list of nodes connected to this node by an edge</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getAdjacencies(jebl.evolution.graphs.Node)">getAdjacencies(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getAdjacencies(jebl.evolution.graphs.Node)">getAdjacencies(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getAdjacencies(jebl.evolution.graphs.Node)">getAdjacencies(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getAdjacencies(jebl.evolution.graphs.Node)">getAdjacencies(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getAdjacencies(jebl.evolution.graphs.Node)">getAdjacencies(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getAdjacencies(jebl.evolution.graphs.Node)">getAdjacencies(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getAdjacencies(jebl.evolution.graphs.Node)">getAdjacencies(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getAdjusted(jebl.math.OrderEnumerator, int)">getAdjusted(OrderEnumerator, int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalHints.Utils.html#getAdjusted(jebl.math.OrthogonalHints, int)">getAdjusted(OrthogonalHints, int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrthogonalHints.Utils.html" title="class in jebl.math">OrthogonalHints.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getAdjustedFactory(jebl.math.OrderEnumerator.OEFactory, int)">getAdjustedFactory(OrderEnumerator.OEFactory, int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html#getAlignments()">getAlignments()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html" title="class in jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt>
<dd>
<div class="block">The indices for these correspond to those for the getScoreMatrix() matrix.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#getAllTaxa()">getAllTaxa()</a></span> - Static method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/AminoAcidScores.html#getAlphabet()">getAlphabet()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/AminoAcidScores.html" title="class in jebl.evolution.align.scores">AminoAcidScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#getAlphabet()">getAlphabet()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoreMatrix.html#getAlphabet()">getAlphabet()</a></span> - Method in interface jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoreMatrix.html" title="interface in jebl.evolution.align.scores">ScoreMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/SubstScoreMatrix.html#getAlphabet()">getAlphabet()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/SubstScoreMatrix.html" title="class in jebl.evolution.align.scores">SubstScoreMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.Utils.html#getAlphabet(jebl.evolution.sequences.SequenceType)">getAlphabet(SequenceType)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.Utils.html" title="class in jebl.evolution.sequences">SequenceType.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getAlternating(jebl.math.OrderEnumerator, jebl.math.OrderEnumerator)">getAlternating(OrderEnumerator, OrderEnumerator)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getAlternatingFactory(jebl.math.OrderEnumerator.OEFactory, jebl.math.OrderEnumerator.OEFactory)">getAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getArgmax(int[])">getArgmax(int[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Find the maximum "argument".</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getArgmax(double[])">getArgmax(double[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Find the maximum "argument" (of a double array).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#getArgument(int)">getArgument(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#getArgument(int)">getArgument(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#getArgument(int)">getArgument(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#getArgument(int)">getArgument(int)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">Returns the value of the nth argument of this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#getArgument(int)">getArgument(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd>
<div class="block">Returns the value of the nth argument of this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#getArgument(int)">getArgument(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#getArgument(int)">getArgument(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getArgument(int)">getArgument(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#getArgumentCount()">getArgumentCount()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#getArgumentCount()">getArgumentCount()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#getArgumentCount()">getArgumentCount()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#getArgumentCount()">getArgumentCount()</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">Returns the number of arguments for this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#getArgumentCount()">getArgumentCount()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd>
<div class="block">Returns the number of arguments for this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#getArgumentCount()">getArgumentCount()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#getArgumentCount()">getArgumentCount()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getArgumentCount()">getArgumentCount()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#getArgumentName(int)">getArgumentName(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#getArgumentName(int)">getArgumentName(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#getArgumentName(int)">getArgumentName(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#getArgumentName(int)">getArgumentName(int)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">Returns the name of the nth argument of this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#getArgumentName(int)">getArgumentName(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd>
<div class="block">Returns the name of the nth argument of this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#getArgumentName(int)">getArgumentName(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#getArgumentName(int)">getArgumentName(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getArgumentName(int)">getArgumentName(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseEdge.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseEdge.html" title="class in jebl.evolution.trees">BaseEdge</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseNode.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseNode.html" title="class in jebl.evolution.trees">BaseNode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Attributable.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in interface jebl.util.<a href="./jebl/util/Attributable.html" title="interface in jebl.util">Attributable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/AttributableHelper.html#getAttribute(java.lang.String)">getAttribute(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/AttributableHelper.html" title="class in jebl.util">AttributableHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseEdge.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseEdge.html" title="class in jebl.evolution.trees">BaseEdge</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseNode.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseNode.html" title="class in jebl.evolution.trees">BaseNode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Attributable.html#getAttributeMap()">getAttributeMap()</a></span> - Method in interface jebl.util.<a href="./jebl/util/Attributable.html" title="interface in jebl.util">Attributable</a></dt>
<dd>
<div class="block">Gets the entire attribute map.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/AttributableHelper.html#getAttributeMap()">getAttributeMap()</a></span> - Method in class jebl.util.<a href="./jebl/util/AttributableHelper.html" title="class in jebl.util">AttributableHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseEdge.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseEdge.html" title="class in jebl.evolution.trees">BaseEdge</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseNode.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseNode.html" title="class in jebl.evolution.trees">BaseNode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Attributable.html#getAttributeNames()">getAttributeNames()</a></span> - Method in interface jebl.util.<a href="./jebl/util/Attributable.html" title="interface in jebl.util">Attributable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/AttributableHelper.html#getAttributeNames()">getAttributeNames()</a></span> - Method in class jebl.util.<a href="./jebl/util/AttributableHelper.html" title="class in jebl.util">AttributableHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#getAvailableAminoAcidScores()">getAvailableAminoAcidScores()</a></span> - Static method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#getAvailableNucleotideScores()">getAvailableNucleotideScores()</a></span> - Static method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getBiasAlternating(jebl.math.OrderEnumerator, jebl.math.OrderEnumerator)">getBiasAlternating(OrderEnumerator, OrderEnumerator)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getBiasAlternatingFactory(jebl.math.OrderEnumerator.OEFactory, jebl.math.OrderEnumerator.OEFactory)">getBiasAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ClusteringTreeBuilder.html#getBuilder(jebl.evolution.trees.TreeBuilderFactory.Method, jebl.evolution.distances.DistanceMatrix)">getBuilder(TreeBuilderFactory.Method, DistanceMatrix)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ClusteringTreeBuilder.html" title="class in jebl.evolution.trees">ClusteringTreeBuilder</a></dt>
<dd>
<div class="block">A factory method to create a ClusteringTreeBuilder</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.html#getBuilder(jebl.evolution.trees.TreeBuilderFactory.Method, jebl.evolution.distances.DistanceMatrix)">getBuilder(TreeBuilderFactory.Method, DistanceMatrix)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.html" title="class in jebl.evolution.trees">TreeBuilderFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#getCanonicalStateCount()">getCanonicalStateCount()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#getCanonicalStateCount()">getCanonicalStateCount()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getCanonicalStateCount()">getCanonicalStateCount()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getCanonicalStateCount()">getCanonicalStateCount()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Get number of canonical states</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#getCanonicalStates()">getCanonicalStates()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#getCanonicalStates()">getCanonicalStates()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getCanonicalStates()">getCanonicalStates()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getCanonicalStates()">getCanonicalStates()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Get a list of canonical states ordered by their indices.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#getCanonicalStates()">getCanonicalStates()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#getCataclysmTime()">getCataclysmTime()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getChildren(jebl.evolution.graphs.Node)">getChildren(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getChildren(jebl.evolution.graphs.Node)">getChildren(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getChildren(jebl.evolution.graphs.Node)">getChildren(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getChildren(jebl.evolution.graphs.Node)">getChildren(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getChildren(jebl.evolution.graphs.Node)">getChildren(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTree.html#getChildren(jebl.evolution.graphs.Node)">getChildren(Node)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTree.html" title="interface in jebl.evolution.trees">RootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getChildren(jebl.evolution.graphs.Node)">getChildren(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SortedRootedTree.html#getChildren(jebl.evolution.graphs.Node)">getChildren(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SortedRootedTree.html" title="class in jebl.evolution.trees">SortedRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CladeSystem.html#getClade(int)">getClade(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CladeSystem.html" title="class in jebl.evolution.trees">CladeSystem</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CladeSystem.html#getCladeCount()">getCladeCount()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CladeSystem.html" title="class in jebl.evolution.trees">CladeSystem</a></dt>
<dd>
<div class="block">get number of unique clades</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CladeSystem.html#getCladeFrequency(int)">getCladeFrequency(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CladeSystem.html" title="class in jebl.evolution.trees">CladeSystem</a></dt>
<dd>
<div class="block">get clade frequency</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CladeSystem.html#getCladeString(int)">getCladeString(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CladeSystem.html" title="class in jebl.evolution.trees">CladeSystem</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getCleanString()">getCleanString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getCleanString()">getCleanString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getCleanString()">getCleanString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.html#getCoalescentEvents(int)">getCoalescentEvents(int)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.html" title="interface in jebl.evolution.coalescent">IntervalList</a></dt>
<dd>
<div class="block">Returns the number coalescent events in an interval</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#getCoalescentEvents(int)">getCoalescentEvents(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#getCode()">getCode()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd>
<div class="block">Returns the 1 letter code for this state.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getCodeLength()">getCodeLength()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getCodeTable()">getCodeTable()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Returns a length-64 string that for each nucleotide triplet contains the single-character
amino acid code (see <a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences"><code>AminoAcids</code></a> to which that triplet is translated in this genetic code.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getCodonsForAminoAcid(jebl.evolution.sequences.AminoAcidState)">getCodonsForAminoAcid(AminoAcidState)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#getColumn(double[][], int)">getColumn(double[][], int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">takes a matrix and gets a column, then returns it as a vector</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalHints.Utils.html#getCombined(jebl.math.OrthogonalHints, int, jebl.math.OrthogonalHints, int)">getCombined(OrthogonalHints, int, OrthogonalHints, int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrthogonalHints.Utils.html" title="class in jebl.math">OrthogonalHints.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#getCommonAncestorNode(jebl.evolution.trees.RootedTree, java.util.Set)">getCommonAncestorNode(RootedTree, Set<Node>)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd>
<div class="block">Gets the most recent common ancestor (MRCA) node of a set of tip nodes.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getComplementaryState(jebl.evolution.sequences.NucleotideState)">getComplementaryState(NucleotideState)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getConstant(int)">getConstant(int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getConstantFactory(int)">getConstantFactory(int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(double[])">getCopy(double[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of doubles</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(double[], int, int)">getCopy(double[], int, int)</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of doubles from index start (inclusive) to index end (exclusive)</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(double[], int)">getCopy(double[], int)</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of doubles from index start (inclusive) to end</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(byte[])">getCopy(byte[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of bytes</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(java.lang.String[])">getCopy(String[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of Strings</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(double[][])">getCopy(double[][])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of doubles</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(int[][])">getCopy(int[][])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones a matrix of ints</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(double[][][])">getCopy(double[][][])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of doubles</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(byte[][])">getCopy(byte[][])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of bytes</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(boolean[][])">getCopy(boolean[][])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of booleans</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(int[])">getCopy(int[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of ints</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getCopy(int[], int)">getCopy(int[], int)</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Clones an array of ints</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/NumberFormatter.html#getDecimalPlaces()">getDecimalPlaces()</a></span> - Method in class jebl.util.<a href="./jebl/util/NumberFormatter.html" title="class in jebl.util">NumberFormatter</a></dt>
<dd>
<div class="block">Get the number of decimal places to display when formatted.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#getDeclineRate()">getDeclineRate()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd>
<div class="block">returns the positive-valued decline rate</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SequenceAlignmentsDistanceMatrix.html#getDefaultDistanceModel(java.util.List)">getDefaultDistanceModel(List<Sequence>)</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/SequenceAlignmentsDistanceMatrix.html" title="class in jebl.evolution.align">SequenceAlignmentsDistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Graph.Utils.html#getDegree(jebl.evolution.graphs.Graph, jebl.evolution.graphs.Node)">getDegree(Graph, Node)</a></span> - Static method in class jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Graph.Utils.html" title="class in jebl.evolution.graphs">Graph.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Node.html#getDegree()">getDegree()</a></span> - Method in interface jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Node.html" title="interface in jebl.evolution.graphs">Node</a></dt>
<dd>
<div class="block">Get the number of edges connected to this node.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#getDemographic(double)">getDemographic(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#getDemographic(double)">getDemographic(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#getDemographic(double)">getDemographic(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#getDemographic(double)">getDemographic(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#getDemographic(double)">getDemographic(double)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">Gets the value of the demographic function N(t) at time t.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#getDemographic(double)">getDemographic(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd>
<div class="block">Gets the value of the demographic function N(t) at time t.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#getDemographic(double)">getDemographic(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#getDemographic(double)">getDemographic(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getDemographic(double)">getDemographic(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/LogisticGrowth.html#getDemographic(double)">getDemographic(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent">LogisticGrowth</a></dt>
<dd>
<div class="block">Gets the value of the demographic function N(t) at time t.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/Character.html#getDesc()">getDesc()</a></span> - Method in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/Character.html" title="interface in jebl.evolution.characters">Character</a></dt>
<dd>
<div class="block">return the description of the character</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#getDesc()">getDesc()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#getDesc()">getDesc()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#getDescendantTips(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">getDescendantTips(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd>
<div class="block">Gets a set of tip nodes descended from the given node.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getDescription()">getDescription()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Returns the description of the genetic code</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#getDimension()">getDimension()</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/MatrixExponential.html#getDimension()">getDimension()</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/MatrixExponential.html" title="class in jebl.evolution.substmodel">MatrixExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/RateMatrix.html#getDimension()">getDimension()</a></span> - Method in interface jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/RateMatrix.html" title="interface in jebl.evolution.substmodel">RateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/BasicDistanceMatrix.html#getDistance(int, int)">getDistance(int, int)</a></span> - Method in class jebl.evolution.distances.<a href="./jebl/evolution/distances/BasicDistanceMatrix.html" title="class in jebl.evolution.distances">BasicDistanceMatrix</a></dt>
<dd>
<div class="block">Gets the distance at a particular row and column</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/BasicDistanceMatrix.html#getDistance(jebl.evolution.taxa.Taxon, jebl.evolution.taxa.Taxon)">getDistance(Taxon, Taxon)</a></span> - Method in class jebl.evolution.distances.<a href="./jebl/evolution/distances/BasicDistanceMatrix.html" title="class in jebl.evolution.distances">BasicDistanceMatrix</a></dt>
<dd>
<div class="block">Gets the distance between 2 taxa</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/DistanceMatrix.html#getDistance(int, int)">getDistance(int, int)</a></span> - Method in interface jebl.evolution.distances.<a href="./jebl/evolution/distances/DistanceMatrix.html" title="interface in jebl.evolution.distances">DistanceMatrix</a></dt>
<dd>
<div class="block">Gets the distance at a particular row and column</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/DistanceMatrix.html#getDistance(jebl.evolution.taxa.Taxon, jebl.evolution.taxa.Taxon)">getDistance(Taxon, Taxon)</a></span> - Method in interface jebl.evolution.distances.<a href="./jebl/evolution/distances/DistanceMatrix.html" title="interface in jebl.evolution.distances">DistanceMatrix</a></dt>
<dd>
<div class="block">Gets the distance between 2 taxa</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/BasicDistanceMatrix.html#getDistances()">getDistances()</a></span> - Method in class jebl.evolution.distances.<a href="./jebl/evolution/distances/BasicDistanceMatrix.html" title="class in jebl.evolution.distances">BasicDistanceMatrix</a></dt>
<dd>
<div class="block">Gets a 2-dimensional array containing the distances</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/DistanceMatrix.html#getDistances()">getDistances()</a></span> - Method in interface jebl.evolution.distances.<a href="./jebl/evolution/distances/DistanceMatrix.html" title="interface in jebl.evolution.distances">DistanceMatrix</a></dt>
<dd>
<div class="block">Gets a 2-dimensional array containing the distances</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Graph.html#getEdge(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdge(Node, Node)</a></span> - Method in interface jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Graph.html" title="interface in jebl.evolution.graphs">Graph</a></dt>
<dd>
<div class="block">Returns the Edge that connects these two nodes</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getEdge(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdge(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getEdge(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdge(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getEdge(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdge(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">Returns the Edge that connects these two nodes</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getEdge(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdge(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getEdge(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdge(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd>
<div class="block">Returns the Edge that connects these two nodes</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getEdge(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdge(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Returns the Edge that connects these two nodes</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getEdge(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdge(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">Returns the Edge that connects these two nodes</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Graph.html#getEdgeLength(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdgeLength(Node, Node)</a></span> - Method in interface jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Graph.html" title="interface in jebl.evolution.graphs">Graph</a></dt>
<dd>
<div class="block">Returns the length of the edge that connects these two nodes</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getEdgeLength(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdgeLength(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getEdgeLength(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdgeLength(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getEdgeLength(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdgeLength(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getEdgeLength(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdgeLength(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getEdgeLength(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdgeLength(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getEdgeLength(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdgeLength(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getEdgeLength(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getEdgeLength(Node, Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Graph.html#getEdges(jebl.evolution.graphs.Node)">getEdges(Node)</a></span> - Method in interface jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Graph.html" title="interface in jebl.evolution.graphs">Graph</a></dt>
<dd>
<div class="block">Returns a list of edges connected to this node</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Graph.html#getEdges()">getEdges()</a></span> - Method in interface jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Graph.html" title="interface in jebl.evolution.graphs">Graph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getEdges(jebl.evolution.graphs.Node)">getEdges(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getEdges()">getEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getEdges(jebl.evolution.graphs.Node)">getEdges(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getEdges()">getEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getEdges(jebl.evolution.graphs.Node)">getEdges(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">Returns a list of edges connected to this node</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getEdges()">getEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getEdges(jebl.evolution.graphs.Node)">getEdges(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd>
<div class="block">Returns a list of edges connected to this node</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getEdges()">getEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getEdges(jebl.evolution.graphs.Node)">getEdges(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd>
<div class="block">Returns a list of edges connected to this node</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getEdges()">getEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getEdges(jebl.evolution.graphs.Node)">getEdges(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Returns a list of edges connected to this node</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getEdges()">getEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getEdges(jebl.evolution.graphs.Node)">getEdges(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">Returns a list of edges connected to this node</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getEdges()">getEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#getEquilibriumFrequencies()">getEquilibriumFrequencies()</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/RateMatrix.html#getEquilibriumFrequencies()">getEquilibriumFrequencies()</a></span> - Method in interface jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/RateMatrix.html" title="interface in jebl.evolution.substmodel">RateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#getEquilibriumFrequency(int)">getEquilibriumFrequency(int)</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/RateMatrix.html#getEquilibriumFrequency(int)">getEquilibriumFrequency(int)</a></span> - Method in interface jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/RateMatrix.html" title="interface in jebl.evolution.substmodel">RateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/BartonSternberg.html#getEstimatedScores()">getEstimatedScores()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/BartonSternberg.html" title="class in jebl.evolution.align">BartonSternberg</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getExternalEdges()">getExternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getExternalEdges()">getExternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getExternalEdges()">getExternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">The set of external edges.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getExternalEdges()">getExternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd>
<div class="block">The set of external edges.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getExternalEdges()">getExternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd>
<div class="block">The set of external edges.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getExternalEdges()">getExternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">The set of external edges.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getExternalEdges()">getExternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">The set of external edges.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Tree.html#getExternalEdges()">getExternalEdges()</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#getExternalNodeCount(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">getExternalNodeCount(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd>
<div class="block">Return the number of external nodes under this node.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getExternalNodes()">getExternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getExternalNodes()">getExternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getExternalNodes()">getExternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getExternalNodes()">getExternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getExternalNodes()">getExternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getExternalNodes()">getExternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getExternalNodes()">getExternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Tree.html#getExternalNodes()">getExternalNodes()</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/NumberFormatter.html#getFormattedValue(double)">getFormattedValue(double)</a></span> - Method in class jebl.util.<a href="./jebl/util/NumberFormatter.html" title="class in jebl.util">NumberFormatter</a></dt>
<dd>
<div class="block">Returns a string containing the current value for this column with
appropriate formatting.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/BasicProgressListener.html#getFractionCompleted()">getFractionCompleted()</a></span> - Method in class jebl.util.<a href="./jebl/util/BasicProgressListener.html" title="class in jebl.util">BasicProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#getFullName()">getFullName()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd>
<div class="block">A descriptive name for this state.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#getGaplessLocation(jebl.evolution.sequences.Sequence, int)">getGaplessLocation(Sequence, int)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">Gets the site location index for this sequence excluding
any gaps.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#getGappedLocation(jebl.evolution.sequences.Sequence, int)">getGappedLocation(Sequence, int)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">Gets the site location index for this sequence that corresponds
to a location given excluding all gaps.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#getGapState()">getGapState()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#getGapState()">getGapState()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getGapState()">getGapState()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getGapState()">getGapState()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Get state corresponding to a gap</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getGeneticCodes()">getGeneticCodes()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Returns an iterable that allows you to iterate over all the standard genetic codes</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getGeneticCodesArray()">getGeneticCodesArray()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#getGrowthRate()">getGrowthRate()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd>
<div class="block">returns growth rate.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getHeight(jebl.evolution.graphs.Node)">getHeight(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getHeight(jebl.evolution.graphs.Node)">getHeight(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getHeight(jebl.evolution.graphs.Node)">getHeight(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getHeight(jebl.evolution.graphs.Node)">getHeight(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getHeight(jebl.evolution.graphs.Node)">getHeight(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTree.html#getHeight(jebl.evolution.graphs.Node)">getHeight(Node)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTree.html" title="interface in jebl.evolution.trees">RootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getHeight(jebl.evolution.graphs.Node)">getHeight(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TransformedRootedTree.html#getHeight(jebl.evolution.graphs.Node)">getHeight(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TransformedRootedTree.html" title="class in jebl.evolution.trees">TransformedRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#getImmutableProfileCharacter(char)">getImmutableProfileCharacter(char)</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd>
<div class="block">An immutable ProfileCharacter that uses less memory than a mutable profile character.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#getIndex()">getIndex()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#getIntegral(double, double)">getIntegral(double, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd>
<div class="block">Calculates the integral 1/N(x) dx between start and finish.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#getIntegral(double, double)">getIntegral(double, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#getIntegral(double, double)">getIntegral(double, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#getIntegral(double, double)">getIntegral(double, double)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">Calculates the integral 1/N(x) dx between start and finish</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#getIntegral(double, double)">getIntegral(double, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#getIntegral(double, double)">getIntegral(double, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getIntegral(double, double)">getIntegral(double, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/LogisticGrowth.html#getIntegral(double, double)">getIntegral(double, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent">LogisticGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#getIntensity(double)">getIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#getIntensity(double)">getIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#getIntensity(double)">getIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#getIntensity(double)">getIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#getIntensity(double)">getIntensity(double)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">Returns value of demographic intensity function at time t
(= integral 1/N(x) dx from 0 to t).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#getIntensity(double)">getIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd>
<div class="block">Returns value of demographic intensity function at time t
(= integral 1/N(x) dx from 0 to t).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#getIntensity(double)">getIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#getIntensity(double)">getIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getIntensity(double)">getIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/LogisticGrowth.html#getIntensity(double)">getIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent">LogisticGrowth</a></dt>
<dd>
<div class="block">Returns value of demographic intensity function at time t
(= integral 1/N(x) dx from 0 to t).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getInternalEdges()">getInternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getInternalEdges()">getInternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getInternalEdges()">getInternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">The set of internal edges.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getInternalEdges()">getInternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd>
<div class="block">The set of internal edges.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getInternalEdges()">getInternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd>
<div class="block">The set of internal edges.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getInternalEdges()">getInternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">The set of internal edges.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getInternalEdges()">getInternalEdges()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">The set of internal edges.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Tree.html#getInternalEdges()">getInternalEdges()</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getInternalNodes()">getInternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getInternalNodes()">getInternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getInternalNodes()">getInternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getInternalNodes()">getInternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getInternalNodes()">getInternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getInternalNodes()">getInternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getInternalNodes()">getInternalNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Tree.html#getInternalNodes()">getInternalNodes()</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalHints.html#getInternalParameterBoundaries(int, double[])">getInternalParameterBoundaries(int, double[])</a></span> - Method in interface jebl.math.<a href="./jebl/math/OrthogonalHints.html" title="interface in jebl.math">OrthogonalHints</a></dt>
<dd>
<div class="block">A boundary is a value of a parameter for which values lower than the boundary and values
higher than the boundary are better treated as two separate functions (IE, they
are only piecewise connected), and minimisation should be performed over both ranges
individually (and then the true minimum taken as the minimuma of the ranges)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalHints.Utils.html#getInternalParameterBoundaries(jebl.math.OrthogonalHints, int)">getInternalParameterBoundaries(OrthogonalHints, int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrthogonalHints.Utils.html" title="class in jebl.math">OrthogonalHints.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.html#getInterval(int)">getInterval(int)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.html" title="interface in jebl.evolution.coalescent">IntervalList</a></dt>
<dd>
<div class="block">Gets an interval.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#getInterval(int)">getInterval(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treesimulation/CoalescentIntervalGenerator.html#getInterval(double, int, double)">getInterval(double, int, double)</a></span> - Method in class jebl.evolution.treesimulation.<a href="./jebl/evolution/treesimulation/CoalescentIntervalGenerator.html" title="class in jebl.evolution.treesimulation">CoalescentIntervalGenerator</a></dt>
<dd>
<div class="block">Calculates the waiting time to the next coalescent for a given critical value
(an intensity).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/treesimulation/IntervalGenerator.html#getInterval(double, int, double)">getInterval(double, int, double)</a></span> - Method in interface jebl.evolution.treesimulation.<a href="./jebl/evolution/treesimulation/IntervalGenerator.html" title="interface in jebl.evolution.treesimulation">IntervalGenerator</a></dt>
<dd>
<div class="block">Calculates the waiting time to the next coalescent for a given critical value
(an intensity).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.html#getIntervalCount()">getIntervalCount()</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.html" title="interface in jebl.evolution.coalescent">IntervalList</a></dt>
<dd>
<div class="block">get number of intervals</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#getIntervalCount()">getIntervalCount()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.html#getIntervalType(int)">getIntervalType(int)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.html" title="interface in jebl.evolution.coalescent">IntervalList</a></dt>
<dd>
<div class="block">Returns the type of interval observed.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#getIntervalType(int)">getIntervalType(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#getInverseIntensity(double)">getInverseIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#getInverseIntensity(double)">getInverseIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#getInverseIntensity(double)">getInverseIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#getInverseIntensity(double)">getInverseIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#getInverseIntensity(double)">getInverseIntensity(double)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">Returns value of inverse demographic intensity function
(returns time, needed for simulation of coalescent intervals).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#getInverseIntensity(double)">getInverseIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd>
<div class="block">Returns value of inverse demographic intensity function
(returns time, needed for simulation of coalescent intervals).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#getInverseIntensity(double)">getInverseIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#getInverseIntensity(double)">getInverseIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getInverseIntensity(double)">getInverseIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/LogisticGrowth.html#getInverseIntensity(double)">getInverseIntensity(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent">LogisticGrowth</a></dt>
<dd>
<div class="block">Returns value of demographic intensity function at time t
(= integral 1/N(x) dx from 0 to t).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitSystem.html#getLabelCount()">getLabelCount()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitSystem.html" title="class in jebl.evolution.trees">SplitSystem</a></dt>
<dd>
<div class="block">get number of labels</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#getLastDelimiter()">getLastDelimiter()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#getLastMetaComment()">getLastMetaComment()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use <a href="./jebl/evolution/io/ImportHelper.html#getMetaComments()"><code>ImportHelper.getMetaComments()</code></a> instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getLength()">getLength()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd>
<div class="block">Returns the length of the sequence</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getLength()">getLength()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Edge.html#getLength()">getLength()</a></span> - Method in interface jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Edge.html" title="interface in jebl.evolution.graphs">Edge</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getLength()">getLength()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd>
<div class="block">Returns the length of the sequence</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getLength()">getLength()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd>
<div class="block">Returns the length of the sequence</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getLength()">getLength()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd>
<div class="block">Returns the length of the sequence</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#getLength()">getLength()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd>
<div class="block">Returns the length of the sequence</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Sequence.html#getLength()">getLength()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences">Sequence</a></dt>
<dd>
<div class="block">Get the length of the sequence</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getLength(jebl.evolution.graphs.Node)">getLength(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getLength(jebl.evolution.graphs.Node)">getLength(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getLength(jebl.evolution.graphs.Node)">getLength(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getLength(jebl.evolution.graphs.Node)">getLength(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getLength(jebl.evolution.graphs.Node)">getLength(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTree.html#getLength(jebl.evolution.graphs.Node)">getLength(Node)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTree.html" title="interface in jebl.evolution.trees">RootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getLength(jebl.evolution.graphs.Node)">getLength(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TransformedRootedTree.html#getLength(jebl.evolution.graphs.Node)">getLength(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TransformedRootedTree.html" title="class in jebl.evolution.trees">TransformedRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.html#getLineageCount(int)">getLineageCount(int)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.html" title="interface in jebl.evolution.coalescent">IntervalList</a></dt>
<dd>
<div class="block">Returns the number of uncoalesced lineages within this interval.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.Utils.html#getLineageCount(jebl.evolution.coalescent.IntervalList, double)">getLineageCount(IntervalList, double)</a></span> - Static method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.Utils.html" title="class in jebl.evolution.coalescent">IntervalList.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#getLineageCount(int)">getLineageCount(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#getLineNumber()">getLineNumber()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Coalescent.html#getLowerBound(int)">getLowerBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent">Coalescent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#getLowerBound(int)">getLowerBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#getLowerBound(int)">getLowerBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#getLowerBound(int)">getLowerBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#getLowerBound(int)">getLowerBound(int)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">Returns the lower bound of the nth argument of this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#getLowerBound(int)">getLowerBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd>
<div class="block">Returns the lower bound of the nth argument of this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#getLowerBound(int)">getLowerBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#getLowerBound(int)">getLowerBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getLowerBound(int)">getLowerBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateFunction.html#getLowerBound(int)">getLowerBound(int)</a></span> - Method in interface jebl.math.<a href="./jebl/math/MultivariateFunction.html" title="interface in jebl.math">MultivariateFunction</a></dt>
<dd>
<div class="block">get lower bound of argument n</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalLineFunction.html#getLowerBound()">getLowerBound()</a></span> - Method in class jebl.math.<a href="./jebl/math/OrthogonalLineFunction.html" title="class in jebl.math">OrthogonalLineFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateFunction.html#getLowerBound()">getLowerBound()</a></span> - Method in interface jebl.math.<a href="./jebl/math/UnivariateFunction.html" title="interface in jebl.math">UnivariateFunction</a></dt>
<dd>
<div class="block">get lower bound of argument</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#getMatch()">getMatch()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#getMatch()">getMatch()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#getMatch(char[], char[])">getMatch(char[], char[])</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html#getMatch()">getMatch()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#getMatch()">getMatch()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html#getMatch()">getMatch()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html" title="class in jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpace.html#getMatch()">getMatch()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpace.html" title="class in jebl.evolution.align">SmithWatermanLinearSpace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#getMatch()">getMatch()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align">SmithWatermanLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html#getMatchScores(int)">getMatchScores(int)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html" title="class in jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Scores.html#getMatrixString()">getMatrixString()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Scores.html" title="class in jebl.evolution.align.scores">Scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SequenceShuffler.html#getMax()">getMax()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SequenceShuffler.html" title="class in jebl.evolution.align">SequenceShuffler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getMax(double[])">getMax(double[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Calculate the max of an array</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getMax(double[], int, int)">getMax(double[], int, int)</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Calculate the max of an array</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#getMaxTipHeight(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">getMaxTipHeight(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SequenceShuffler.html#getMean()">getMean()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SequenceShuffler.html" title="class in jebl.evolution.align">SequenceShuffler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getMean(double[])">getMean(double[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Calculate the mean value of an array</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#getMemoryRequiredForAlignment(int)">getMemoryRequiredForAlignment(int)</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/BasicProgressListener.html#getMessage()">getMessage()</a></span> - Method in class jebl.util.<a href="./jebl/util/BasicProgressListener.html" title="class in jebl.util">BasicProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#getMetaComments()">getMetaComments()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">This method has been introduced because this class previously skipped over consecutive comments and discarded all
but the last.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ConsensusTreeBuilder.html#getMethodDescription()">getMethodDescription()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ConsensusTreeBuilder.html" title="class in jebl.evolution.trees">ConsensusTreeBuilder</a></dt>
<dd>
<div class="block">Returns a human readable name of this consensus tree building method</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/treemetrics/BilleraMetric.html#getMetric(jebl.evolution.trees.RootedTree, jebl.evolution.trees.RootedTree)">getMetric(RootedTree, RootedTree)</a></span> - Method in class jebl.evolution.treemetrics.<a href="./jebl/evolution/treemetrics/BilleraMetric.html" title="class in jebl.evolution.treemetrics">BilleraMetric</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treemetrics/CladeHeightMetric.html#getMetric(jebl.evolution.trees.RootedTree, jebl.evolution.trees.RootedTree)">getMetric(RootedTree, RootedTree)</a></span> - Method in class jebl.evolution.treemetrics.<a href="./jebl/evolution/treemetrics/CladeHeightMetric.html" title="class in jebl.evolution.treemetrics">CladeHeightMetric</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treemetrics/RobinsonsFouldMetric.html#getMetric(jebl.evolution.trees.RootedTree, jebl.evolution.trees.RootedTree)">getMetric(RootedTree, RootedTree)</a></span> - Method in class jebl.evolution.treemetrics.<a href="./jebl/evolution/treemetrics/RobinsonsFouldMetric.html" title="class in jebl.evolution.treemetrics">RobinsonsFouldMetric</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treemetrics/RootedTreeMetric.html#getMetric(jebl.evolution.trees.RootedTree, jebl.evolution.trees.RootedTree)">getMetric(RootedTree, RootedTree)</a></span> - Method in interface jebl.evolution.treemetrics.<a href="./jebl/evolution/treemetrics/RootedTreeMetric.html" title="interface in jebl.evolution.treemetrics">RootedTreeMetric</a></dt>
<dd>
<div class="block">calculates the metric between two rooted trees</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SequenceShuffler.html#getMin()">getMin()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SequenceShuffler.html" title="class in jebl.evolution.align">SequenceShuffler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getMin(double[])">getMin(double[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Calculate the min of an array</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#getMinNodeHeight(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">getMinNodeHeight(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#getMinTipHeight(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">getMinTipHeight(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getMostFrequentState()">getMostFrequentState()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd>
<div class="block">Returns the most frequent state in this pattern</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getMostFrequentState(boolean)">getMostFrequentState(boolean)</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd>
<div class="block">Returns the most frequent state in this pattern, optionally including ambiguous states</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#getN0()">getN0()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd>
<div class="block">returns initial population size.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#getN1()">getN1()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#getN1()">getN1()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#getN1()">getN1()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/AminoAcidScores.html#getName()">getName()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/AminoAcidScores.html" title="class in jebl.evolution.align.scores">AminoAcidScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum45.html#getName()">getName()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum45.html" title="class in jebl.evolution.align.scores">Blosum45</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Blosum50.html#getName()">getName()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Blosum50.html" title="class in jebl.evolution.align.scores">Blosum50</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#getName()">getName()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoreMatrix.html#getName()">getName()</a></span> - Method in interface jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoreMatrix.html" title="interface in jebl.evolution.align.scores">ScoreMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/SubstScoreMatrix.html#getName()">getName()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/SubstScoreMatrix.html" title="class in jebl.evolution.align.scores">SubstScoreMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/Character.html#getName()">getName()</a></span> - Method in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/Character.html" title="interface in jebl.evolution.characters">Character</a></dt>
<dd>
<div class="block">return the name of the character</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/CharacterType.html#getName()">getName()</a></span> - Method in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/CharacterType.html" title="interface in jebl.evolution.characters">CharacterType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#getName()">getName()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#getName()">getName()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getName()">getName()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Returns the name of the genetic code</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getName()">getName()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getName()">getName()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">name of data type</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#getName()">getName()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>you probably want to use <a href="./jebl/evolution/sequences/State.html#getFullName()"><code>State.getFullName()</code></a> or <a href="./jebl/evolution/sequences/State.html#getCode()"><code>State.getCode()</code></a>.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/StateClassification.Default.html#getName()">getName()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/StateClassification.Default.html" title="class in jebl.evolution.sequences">StateClassification.Default</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/StateClassification.html#getName()">getName()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/StateClassification.html" title="interface in jebl.evolution.sequences">StateClassification</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#getName()">getName()</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd>
<div class="block">get the name of the taxon</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/TaxonomicLevel.html#getName()">getName()</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/TaxonomicLevel.html" title="class in jebl.evolution.taxa">TaxonomicLevel</a></dt>
<dd>
<div class="block">get the name of the taxonomic level</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ConsensusTreeBuilder.Method.html#getName()">getName()</a></span> - Method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/ConsensusTreeBuilder.Method.html" title="enum in jebl.evolution.trees">ConsensusTreeBuilder.Method</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.Method.html#getName()">getName()</a></span> - Method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.Method.html" title="enum in jebl.evolution.trees">TreeBuilderFactory.Method</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getNcbiTranslationTableNumber()">getNcbiTranslationTableNumber()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.html#getNext()">getNext()</a></span> - Method in interface jebl.math.<a href="./jebl/math/OrderEnumerator.html" title="interface in jebl.math">OrderEnumerator</a></dt>
<dd>
<div class="block">The next value in the enumeration</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#getNextBlockName()">getNextBlockName()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getNexusDataType()">getNexusDataType()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getNode(jebl.evolution.taxa.Taxon)">getNode(Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getNode(jebl.evolution.taxa.Taxon)">getNode(Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getNode(jebl.evolution.taxa.Taxon)">getNode(Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getNode(jebl.evolution.taxa.Taxon)">getNode(Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getNode(jebl.evolution.taxa.Taxon)">getNode(Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getNode(jebl.evolution.taxa.Taxon)">getNode(Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getNode(jebl.evolution.taxa.Taxon)">getNode(Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Tree.html#getNode(jebl.evolution.taxa.Taxon)">getNode(Taxon)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Graph.html#getNodes(jebl.evolution.graphs.Edge)">getNodes(Edge)</a></span> - Method in interface jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Graph.html" title="interface in jebl.evolution.graphs">Graph</a></dt>
<dd>
<div class="block">Returns an array of 2 nodes which are the nodes at either end of the edge.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Graph.html#getNodes()">getNodes()</a></span> - Method in interface jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Graph.html" title="interface in jebl.evolution.graphs">Graph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Graph.html#getNodes(int)">getNodes(int)</a></span> - Method in interface jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Graph.html" title="interface in jebl.evolution.graphs">Graph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getNodes(jebl.evolution.graphs.Edge)">getNodes(Edge)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getNodes()">getNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getNodes(int)">getNodes(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getNodes(jebl.evolution.graphs.Edge)">getNodes(Edge)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getNodes()">getNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getNodes(int)">getNodes(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getNodes(jebl.evolution.graphs.Edge)">getNodes(Edge)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">Returns an array of 2 nodes which are the nodes at either end of the edge.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getNodes()">getNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getNodes(int)">getNodes(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getNodes(jebl.evolution.graphs.Edge)">getNodes(Edge)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getNodes()">getNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getNodes(int)">getNodes(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getNodes(jebl.evolution.graphs.Edge)">getNodes(Edge)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd>
<div class="block">Returns an array of 2 nodes which are the nodes at either end of the edge.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getNodes()">getNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getNodes(int)">getNodes(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getNodes(jebl.evolution.graphs.Edge)">getNodes(Edge)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Returns an array of 2 nodes which are the nodes at either end of the edge.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getNodes()">getNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getNodes(int)">getNodes(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getNodes(jebl.evolution.graphs.Edge)">getNodes(Edge)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">Returns an array of 2 nodes which are the nodes at either end of the edge.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getNodes()">getNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getNodes(int)">getNodes(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#getNodes(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">getNodes(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd>
<div class="block">All nodes in subtree - parents before children (pre - order).</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#getNormalized(double[])">getNormalized(double[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalHints.Utils.html#getNull()">getNull()</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrthogonalHints.Utils.html" title="class in jebl.math">OrthogonalHints.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Coalescent.html#getNumArguments()">getNumArguments()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent">Coalescent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateFunction.html#getNumArguments()">getNumArguments()</a></span> - Method in interface jebl.math.<a href="./jebl/math/MultivariateFunction.html" title="interface in jebl.math">MultivariateFunction</a></dt>
<dd>
<div class="block">get number of arguments</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#getNumOfStates()">getNumOfStates()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getOrdered(int)">getOrdered(int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getOrderedFactory()">getOrderedFactory()</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/WAG.html#getOriginalFrequencies(double[])">getOriginalFrequencies(double[])</a></span> - Static method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/WAG.html" title="class in jebl.evolution.substmodel">WAG</a></dt>
<dd>
<div class="block">get the frequencies of the original data set that
formed the basis for the estimation of the rate matrix</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/WAG.html#getOriginalFrequencies()">getOriginalFrequencies()</a></span> - Static method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/WAG.html" title="class in jebl.evolution.substmodel">WAG</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Coalescent.html#getOrthogonalHints()">getOrthogonalHints()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent">Coalescent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateFunction.html#getOrthogonalHints()">getOrthogonalHints()</a></span> - Method in interface jebl.math.<a href="./jebl/math/MultivariateFunction.html" title="interface in jebl.math">MultivariateFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getParent(jebl.evolution.graphs.Node)">getParent(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getParent(jebl.evolution.graphs.Node)">getParent(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getParent(jebl.evolution.graphs.Node)">getParent(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getParent(jebl.evolution.graphs.Node)">getParent(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getParent(jebl.evolution.graphs.Node)">getParent(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTree.html#getParent(jebl.evolution.graphs.Node)">getParent(Node)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTree.html" title="interface in jebl.evolution.trees">RootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getParent(jebl.evolution.graphs.Node)">getParent(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getParentEdge(jebl.evolution.graphs.Node)">getParentEdge(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getParentEdge(jebl.evolution.graphs.Node)">getParentEdge(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getParentEdge(jebl.evolution.graphs.Node)">getParentEdge(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getParentEdge(jebl.evolution.graphs.Node)">getParentEdge(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#getPathLength(jebl.evolution.trees.Tree, jebl.evolution.graphs.Node, jebl.evolution.graphs.Node)">getPathLength(Tree, Node, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#getPatternCount()">getPatternCount()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Patterns.html#getPatternCount()">getPatternCount()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Patterns.html" title="interface in jebl.evolution.alignments">Patterns</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#getPatternCount()">getPatternCount()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#getPatternLength()">getPatternLength()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Patterns.html#getPatternLength()">getPatternLength()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Patterns.html" title="interface in jebl.evolution.alignments">Patterns</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#getPatternLength()">getPatternLength()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#getPatterns()">getPatterns()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Patterns.html#getPatterns()">getPatterns()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Patterns.html" title="interface in jebl.evolution.alignments">Patterns</a></dt>
<dd>
<div class="block">Get a list of all the patterns</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#getPatterns()">getPatterns()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#getProgress()">getProgress()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getR2()">getR2()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#getRelativeRates()">getRelativeRates()</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/RateMatrix.html#getRelativeRates()">getRelativeRates()</a></span> - Method in interface jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/RateMatrix.html" title="interface in jebl.evolution.substmodel">RateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getRestricted(jebl.math.OrderEnumerator, int, int)">getRestricted(OrderEnumerator, int, int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getRestrictedFactory(jebl.math.OrderEnumerator.OEFactory, int, int)">getRestrictedFactory(OrderEnumerator.OEFactory, int, int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getRootNode()">getRootNode()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getRootNode()">getRootNode()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getRootNode()">getRootNode()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">The root of the tree has the largest node height of
all nodes in the tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getRootNode()">getRootNode()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getRootNode()">getRootNode()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd>
<div class="block">The root of the tree has the largest node height of
all nodes in the tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTree.html#getRootNode()">getRootNode()</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTree.html" title="interface in jebl.evolution.trees">RootedTree</a></dt>
<dd>
<div class="block">The root of the tree has the largest node height of
all nodes in the tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getRootNode()">getRootNode()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">The root of the tree has the largest node height of
all nodes in the tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#getRootProgressListener()">getRootProgressListener()</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.html#getSampleCount()">getSampleCount()</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.html" title="interface in jebl.evolution.coalescent">IntervalList</a></dt>
<dd>
<div class="block">get the total number of sampling events.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#getSampleCount()">getSampleCount()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#getScore()">getScore()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/BartonSternberg.html#getScore()">getScore()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/BartonSternberg.html" title="class in jebl.evolution.align">BartonSternberg</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunsch.html#getScore()">getScore()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunsch.html" title="class in jebl.evolution.align">NeedlemanWunsch</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#getScore()">getScore()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html#getScore()">getScore()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#getScore()">getScore()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#getScore(jebl.evolution.sequences.Sequence, jebl.evolution.sequences.Sequence)">getScore(Sequence, Sequence)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html#getScore()">getScore()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html" title="class in jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/PairwiseAligner.html#getScore(jebl.evolution.sequences.Sequence, jebl.evolution.sequences.Sequence)">getScore(Sequence, Sequence)</a></span> - Method in interface jebl.evolution.align.<a href="./jebl/evolution/align/PairwiseAligner.html" title="interface in jebl.evolution.align">PairwiseAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoreMatrix.html#getScore(char, char)">getScore(char, char)</a></span> - Method in interface jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoreMatrix.html" title="interface in jebl.evolution.align.scores">ScoreMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Scores.html#getScore(char, char)">getScore(char, char)</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Scores.html" title="class in jebl.evolution.align.scores">Scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpace.html#getScore()">getScore()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpace.html" title="class in jebl.evolution.align">SmithWatermanLinearSpace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#getScore()">getScore()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align">SmithWatermanLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/parsimony/FitchParsimony.html#getScore(jebl.evolution.trees.Tree)">getScore(Tree)</a></span> - Method in class jebl.evolution.parsimony.<a href="./jebl/evolution/parsimony/FitchParsimony.html" title="class in jebl.evolution.parsimony">FitchParsimony</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/parsimony/ParsimonyCriterion.html#getScore(jebl.evolution.trees.Tree)">getScore(Tree)</a></span> - Method in interface jebl.evolution.parsimony.<a href="./jebl/evolution/parsimony/ParsimonyCriterion.html" title="interface in jebl.evolution.parsimony">ParsimonyCriterion</a></dt>
<dd>
<div class="block">Calculates the minimum number of steps for the parsimony reconstruction for the given tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html#getScores()">getScores()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html" title="class in jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt>
<dd>
<div class="block">The indices for these correspond to those for the getAlignments() matrix.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#getSE(jebl.evolution.taxa.Taxon)">getSE(Taxon)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeSelectionChangeEvent.html#getSelectedNodes()">getSelectedNodes()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeSelectionChangeEvent.html" title="class in jebl.evolution.trees">TreeSelectionChangeEvent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#getSequence(jebl.evolution.taxa.Taxon)">getSequence(Taxon)</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#getSequence(jebl.evolution.taxa.Taxon)">getSequence(Taxon)</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Sequences.html#getSequence(jebl.evolution.taxa.Taxon)">getSequence(Taxon)</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Sequences.html" title="interface in jebl.evolution.sequences">Sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getSequenceCharacters()">getSequenceCharacters()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd>
<div class="block">Get the sequence characters representing the sequence.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getSequenceCharacters()">getSequenceCharacters()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd>
<div class="block">Get the sequence characters representing the sequence.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Alignment.html#getSequenceList()">getSequenceList()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Alignment.html" title="interface in jebl.evolution.alignments">Alignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#getSequenceList()">getSequenceList()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#getSequenceList()">getSequenceList()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#getSequences()">getSequences()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#getSequences()">getSequences()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Sequences.html#getSequences()">getSequences()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Sequences.html" title="interface in jebl.evolution.sequences">Sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#getSequenceType()">getSequenceType()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getSequenceType()">getSequenceType()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getSequenceType()">getSequenceType()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Patterns.html#getSequenceType()">getSequenceType()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Patterns.html" title="interface in jebl.evolution.alignments">Patterns</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#getSequenceType()">getSequenceType()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getSequenceType()">getSequenceType()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getSequenceType()">getSequenceType()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getSequenceType()">getSequenceType()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#getSequenceType()">getSequenceType()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Sequence.html#getSequenceType()">getSequenceType()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences">Sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/TranslatedSequence.html#getSequenceType()">getSequenceType()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/TranslatedSequence.html" title="class in jebl.evolution.sequences">TranslatedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#getSequenceType()">getSequenceType()</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/RateMatrix.html#getSequenceType()">getSequenceType()</a></span> - Method in interface jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/RateMatrix.html" title="interface in jebl.evolution.substmodel">RateMatrix</a></dt>
<dd>
<div class="block">Get the data type of this rate matrix</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/StateClassification.Default.html#getSetName(jebl.evolution.sequences.State)">getSetName(State)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/StateClassification.Default.html" title="class in jebl.evolution.sequences">StateClassification.Default</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/StateClassification.html#getSetName(jebl.evolution.sequences.State)">getSetName(State)</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/StateClassification.html" title="interface in jebl.evolution.sequences">StateClassification</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/StateClassification.Default.html#getSetNames()">getSetNames()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/StateClassification.Default.html" title="class in jebl.evolution.sequences">StateClassification.Default</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/StateClassification.html#getSetNames()">getSetNames()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/StateClassification.html" title="interface in jebl.evolution.sequences">StateClassification</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/LogisticGrowth.html#getShape()">getShape()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent">LogisticGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getShuffled(int)">getShuffled(int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getShuffledFactory()">getShuffledFactory()</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/NumberFormatter.html#getSignificantFigures()">getSignificantFigures()</a></span> - Method in class jebl.util.<a href="./jebl/util/NumberFormatter.html" title="class in jebl.util">NumberFormatter</a></dt>
<dd>
<div class="block">Get the number of significant figures to display when formatted.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Alignment.html#getSiteCount()">getSiteCount()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Alignment.html" title="interface in jebl.evolution.alignments">Alignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#getSiteCount()">getSiteCount()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#getSiteCount()">getSiteCount()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/parsimony/FitchParsimony.html#getSiteScores(jebl.evolution.trees.Tree)">getSiteScores(Tree)</a></span> - Method in class jebl.evolution.parsimony.<a href="./jebl/evolution/parsimony/FitchParsimony.html" title="class in jebl.evolution.parsimony">FitchParsimony</a></dt>
<dd>
<div class="block">Calculates the minimum number of siteScores for the parsimony reconstruction of a
a set of character patterns on a tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/parsimony/ParsimonyCriterion.html#getSiteScores(jebl.evolution.trees.Tree)">getSiteScores(Tree)</a></span> - Method in interface jebl.evolution.parsimony.<a href="./jebl/evolution/parsimony/ParsimonyCriterion.html" title="interface in jebl.evolution.parsimony">ParsimonyCriterion</a></dt>
<dd>
<div class="block">Calculates the minimum number of steps for the parsimony reconstruction for the given tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/BasicDistanceMatrix.html#getSize()">getSize()</a></span> - Method in class jebl.evolution.distances.<a href="./jebl/evolution/distances/BasicDistanceMatrix.html" title="class in jebl.evolution.distances">BasicDistanceMatrix</a></dt>
<dd>
<div class="block">Gets the size of the matrix (which is square), i.e., number of rows or columns.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/DistanceMatrix.html#getSize()">getSize()</a></span> - Method in interface jebl.evolution.distances.<a href="./jebl/evolution/distances/DistanceMatrix.html" title="interface in jebl.evolution.distances">DistanceMatrix</a></dt>
<dd>
<div class="block">Gets the size of the matrix (which is square), i.e., number of rows or columns.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getSource()">getSource()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getSource()">getSource()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitSystem.html#getSplit(int)">getSplit(int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitSystem.html" title="class in jebl.evolution.trees">SplitSystem</a></dt>
<dd>
<div class="block">get split</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitUtils.html#getSplit(java.util.List, jebl.evolution.trees.Tree, jebl.evolution.graphs.Edge, boolean[])">getSplit(List<Taxon>, Tree, Edge, boolean[])</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitUtils.html" title="class in jebl.evolution.trees">SplitUtils</a></dt>
<dd>
<div class="block">get split for branch associated with internal node</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitSystem.html#getSplitCount()">getSplitCount()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitSystem.html" title="class in jebl.evolution.trees">SplitSystem</a></dt>
<dd>
<div class="block">get number of splits</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitUtils.html#getSplits(jebl.evolution.trees.Tree)">getSplits(Tree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitUtils.html" title="class in jebl.evolution.trees">SplitUtils</a></dt>
<dd>
<div class="block">creates a split system from a tree
(using tree-induced order of sequences)</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitUtils.html#getSplits(java.util.List, jebl.evolution.trees.Tree)">getSplits(List<Taxon>, Tree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitUtils.html" title="class in jebl.evolution.trees">SplitUtils</a></dt>
<dd>
<div class="block">creates a split system from a tree
(using a pre-specified order of sequences)</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitSystem.html#getSplitVector()">getSplitVector()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitSystem.html" title="class in jebl.evolution.trees">SplitSystem</a></dt>
<dd>
<div class="block">get split vector</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getStartCodons()">getStartCodons()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getState(int)">getState(int)</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getState(int)">getState(int)</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd>
<div class="block">Get the state for the ith taxon</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#getState(char)">getState(char)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#getState(java.lang.String)">getState(String)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#getState(int)">getState(int)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getState(int)">getState(int)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getState(int)">getState(int)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#getState(jebl.evolution.sequences.NucleotideState, jebl.evolution.sequences.NucleotideState, jebl.evolution.sequences.NucleotideState)">getState(NucleotideState, NucleotideState, NucleotideState)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#getState(java.lang.String)">getState(String)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd>
<div class="block">Gets the state object for the given code.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#getState(int)">getState(int)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getState(int)">getState(int)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#getState(int)">getState(int)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getState(char)">getState(char)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getState(java.lang.String)">getState(String)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getState(int)">getState(int)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Sequence.html#getState(int)">getState(int)</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences">Sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getState(java.lang.String)">getState(String)</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Get state corresponding to a string code</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getState(char)">getState(char)</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Get state whose code is the one-character string consisting only of code.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getState(int)">getState(int)</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Get state corresponding to a state index</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getStateCount(jebl.evolution.sequences.State)">getStateCount(State)</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd>
<div class="block">Returns the count of the given state in this pattern</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#getStateCount()">getStateCount()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#getStateCount()">getStateCount()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getStateCount()">getStateCount()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getStateCount()">getStateCount()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Get number of states including ambiguous states</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#getStateDesc()">getStateDesc()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#getStateDesc(int)">getStateDesc(int)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getStateFrequency(jebl.evolution.sequences.State)">getStateFrequency(State)</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd>
<div class="block">Returns the frequent of the given state in this pattern</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getStateIndices()">getStateIndices()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getStateIndices()">getStateIndices()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getStateIndices()">getStateIndices()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getStateIndices()">getStateIndices()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#getStateIndices()">getStateIndices()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Sequence.html#getStateIndices()">getStateIndices()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences">Sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#getStateIndices(jebl.evolution.sequences.State[])">getStateIndices(State[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getStates()">getStates()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getStates()">getStates()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/parsimony/FitchParsimony.html#getStates(jebl.evolution.trees.Tree, jebl.evolution.graphs.Node)">getStates(Tree, Node)</a></span> - Method in class jebl.evolution.parsimony.<a href="./jebl/evolution/parsimony/FitchParsimony.html" title="class in jebl.evolution.parsimony">FitchParsimony</a></dt>
<dd>
<div class="block">Returns the reconstructed character states for a given node in the tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/parsimony/ParsimonyCriterion.html#getStates(jebl.evolution.trees.Tree, jebl.evolution.graphs.Node)">getStates(Tree, Node)</a></span> - Method in interface jebl.evolution.parsimony.<a href="./jebl/evolution/parsimony/ParsimonyCriterion.html" title="interface in jebl.evolution.parsimony">ParsimonyCriterion</a></dt>
<dd>
<div class="block">Returns the reconstructed character states for a given node in the tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#getStates()">getStates()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getStates()">getStates()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getStates()">getStates()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#getStates()">getStates()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getStates()">getStates()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#getStates()">getStates()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getStates()">getStates()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Sequence.html#getStates()">getStates()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences">Sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getStates()">getStates()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Get a list of states ordered by their indices.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getStateSet()">getStateSet()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/StateClassification.Default.html#getStateSet(java.lang.String)">getStateSet(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/StateClassification.Default.html" title="class in jebl.evolution.sequences">StateClassification.Default</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/StateClassification.html#getStateSet(java.lang.String)">getStateSet(String)</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/StateClassification.html" title="interface in jebl.evolution.sequences">StateClassification</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SequenceShuffler.html#getStdev()">getStdev()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SequenceShuffler.html" title="class in jebl.evolution.align">SequenceShuffler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getStopCodonCount()">getStopCodonCount()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Returns the number of terminator amino acids.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getStopCodons()">getStopCodons()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getString()">getString()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getString()">getString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getString()">getString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getString()">getString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#getString()">getString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Sequence.html#getString()">getString()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences">Sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/BasicDistanceMatrix.html#getSubmatrix(java.util.Collection)">getSubmatrix(Collection<Taxon>)</a></span> - Method in class jebl.evolution.distances.<a href="./jebl/evolution/distances/BasicDistanceMatrix.html" title="class in jebl.evolution.distances">BasicDistanceMatrix</a></dt>
<dd>
<div class="block">Gets a sub-matrix for only those taxa in the collection (all
of which should be present in this matrix).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/DistanceMatrix.html#getSubmatrix(java.util.Collection)">getSubmatrix(Collection<Taxon>)</a></span> - Method in interface jebl.evolution.distances.<a href="./jebl/evolution/distances/DistanceMatrix.html" title="interface in jebl.evolution.distances">DistanceMatrix</a></dt>
<dd>
<div class="block">Gets a sub-matrix for only those taxa in the collection (all
of which should be present in this matrix).</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalHints.html#getSuggestedOrdering(jebl.math.OrderEnumerator)">getSuggestedOrdering(OrderEnumerator)</a></span> - Method in interface jebl.math.<a href="./jebl/math/OrthogonalHints.html" title="interface in jebl.math">OrthogonalHints</a></dt>
<dd>
<div class="block">If there is a "best" ordering to use it can be specified here,
if not should return null</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#getSum(double[])">getSum(double[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Calculate the total of an array</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ConsensusTreeBuilder.html#getSupportAttributeName()">getSupportAttributeName()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ConsensusTreeBuilder.html" title="class in jebl.evolution.trees">ConsensusTreeBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/BasicAlignment.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/BasicAlignment.html" title="class in jebl.evolution.alignments">BasicAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getTaxa()">getTaxa()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Patterns.html#getTaxa()">getTaxa()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Patterns.html" title="interface in jebl.evolution.alignments">Patterns</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/Character.html#getTaxa()">getTaxa()</a></span> - Method in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/Character.html" title="interface in jebl.evolution.characters">Character</a></dt>
<dd>
<div class="block">get a Set<Taxon> of all the taxa for this character</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/BasicDistanceMatrix.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.distances.<a href="./jebl/evolution/distances/BasicDistanceMatrix.html" title="class in jebl.evolution.distances">BasicDistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/DistanceMatrix.html#getTaxa()">getTaxa()</a></span> - Method in interface jebl.evolution.distances.<a href="./jebl/evolution/distances/DistanceMatrix.html" title="interface in jebl.evolution.distances">DistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitSystem.html#getTaxa()">getTaxa()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitSystem.html" title="class in jebl.evolution.trees">SplitSystem</a></dt>
<dd>
<div class="block">get taxon list</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Tree.html#getTaxa()">getTaxa()</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#getTaxon()">getTaxon()</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#getTaxon()">getTaxon()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#getTaxon()">getTaxon()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#getTaxon()">getTaxon()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#getTaxon()">getTaxon()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Sequence.html#getTaxon()">getTaxon()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences">Sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#getTaxon(java.lang.String)">getTaxon(String)</a></span> - Static method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd>
<div class="block">A static method that returns a Taxon object with the given name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#getTaxon(jebl.evolution.graphs.Node)">getTaxon(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#getTaxon(jebl.evolution.graphs.Node)">getTaxon(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#getTaxon(jebl.evolution.graphs.Node)">getTaxon(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#getTaxon(jebl.evolution.graphs.Node)">getTaxon(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#getTaxon(jebl.evolution.graphs.Node)">getTaxon(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#getTaxon(jebl.evolution.graphs.Node)">getTaxon(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#getTaxon(jebl.evolution.graphs.Node)">getTaxon(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Tree.html#getTaxon(jebl.evolution.graphs.Node)">getTaxon(Node)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#getTaxonomicLevel()">getTaxonomicLevel()</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd>
<div class="block">get the taxonomic level of the taxon</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/TaxonomicLevel.html#getTaxonomicLevel(java.lang.String)">getTaxonomicLevel(String)</a></span> - Static method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/TaxonomicLevel.html" title="class in jebl.evolution.taxa">TaxonomicLevel</a></dt>
<dd>
<div class="block">A static method that returns a TaxonomicLevel object with the given name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/TaxonomicLevel.html#getTaxonomicLevels()">getTaxonomicLevels()</a></span> - Static method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/TaxonomicLevel.html" title="class in jebl.evolution.taxa">TaxonomicLevel</a></dt>
<dd>
<div class="block">Returns a Set containing all the currently created taxonomic levels.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceTester.html#getTestSequence1()">getTestSequence1()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceTester.html" title="class in jebl.evolution.sequences">SequenceTester</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceTester.html#getTestSequence1(java.lang.String[])">getTestSequence1(String[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceTester.html" title="class in jebl.evolution.sequences">SequenceTester</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceTester.html#getTestSequence2()">getTestSequence2()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceTester.html" title="class in jebl.evolution.sequences">SequenceTester</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceTester.html#getTestSequence2(java.lang.String[])">getTestSequence2(String[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceTester.html" title="class in jebl.evolution.sequences">SequenceTester</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcidState.html#getThreeLetterName()">getThreeLetterName()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcidState.html" title="class in jebl.evolution.sequences">AminoAcidState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getTime()">getTime()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#getTipCount(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">getTipCount(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd>
<div class="block">Return the number of leaves under this node.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#getTipsForTaxa(jebl.evolution.trees.RootedTree, java.util.Collection)">getTipsForTaxa(RootedTree, Collection<Taxon>)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd>
<div class="block">Gets a set of external nodes that correspond to the given taxa.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#getTotal(double[], int, int)">getTotal(double[], int, int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#getTotal(double[])">getTotal(double[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.html#getTotalDuration()">getTotalDuration()</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.html" title="interface in jebl.evolution.coalescent">IntervalList</a></dt>
<dd>
<div class="block">get the total duration of these intervals.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#getTotalDuration()">getTotalDuration()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#getTransitionProbabilities(double[][])">getTransitionProbabilities(double[][])</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd>
<div class="block">A utility method for speed, transfers trans prob information quickly
into store</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/MatrixExponential.html#getTransitionProbabilities(double[][])">getTransitionProbabilities(double[][])</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/MatrixExponential.html" title="class in jebl.evolution.substmodel">MatrixExponential</a></dt>
<dd>
<div class="block">A utility method for speed, transfers trans prob information quickly
into store</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/RateMatrix.html#getTransitionProbabilities(double[][])">getTransitionProbabilities(double[][])</a></span> - Method in interface jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/RateMatrix.html" title="interface in jebl.evolution.substmodel">RateMatrix</a></dt>
<dd>
<div class="block">A utility method for speed, transfers trans prob information quickly
into store.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#getTransitionProbability(int, int)">getTransitionProbability(int, int)</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/MatrixExponential.html#getTransitionProbability(int, int)">getTransitionProbability(int, int)</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/MatrixExponential.html" title="class in jebl.evolution.substmodel">MatrixExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/RateMatrix.html#getTransitionProbability(int, int)">getTransitionProbability(int, int)</a></span> - Method in interface jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/RateMatrix.html" title="interface in jebl.evolution.substmodel">RateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getTranslation(jebl.evolution.sequences.CodonState)">getTranslation(CodonState)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Returns the state associated with AminoAcid represented by codonState.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getTranslation(jebl.evolution.sequences.NucleotideState, jebl.evolution.sequences.NucleotideState, jebl.evolution.sequences.NucleotideState)">getTranslation(NucleotideState, NucleotideState, NucleotideState)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Returns the state associated with AminoAcid represented by the three nucleotides.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#getTranslation(java.lang.String)">getTranslation(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Returns the state associated with AminoAcid represented by the three nucleotides.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeChangeEvent.html#getTree()">getTree()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeChangeEvent.html" title="class in jebl.evolution.trees">TreeChangeEvent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#getTripletCode(jebl.evolution.sequences.AminoAcidState)">getTripletCode(AminoAcidState)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/Character.html#getType()">getType()</a></span> - Method in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/Character.html" title="interface in jebl.evolution.characters">Character</a></dt>
<dd>
<div class="block">return the CharacterType of the character</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#getType()">getType()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#getType()">getType()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/RateMatrix.html#getUniqueName()">getUniqueName()</a></span> - Method in interface jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/RateMatrix.html" title="interface in jebl.evolution.substmodel">RateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/WAG.html#getUniqueName()">getUniqueName()</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/WAG.html" title="class in jebl.evolution.substmodel">WAG</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#getUnknownState()">getUnknownState()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#getUnknownState()">getUnknownState()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#getUnknownState()">getUnknownState()</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#getUnknownState()">getUnknownState()</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Get state corresponding to an unknown</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Coalescent.html#getUpperBound(int)">getUpperBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Coalescent.html" title="class in jebl.evolution.coalescent">Coalescent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#getUpperBound(int)">getUpperBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#getUpperBound(int)">getUpperBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#getUpperBound(int)">getUpperBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#getUpperBound(int)">getUpperBound(int)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">Returns the upper bound of the nth argument of this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#getUpperBound(int)">getUpperBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd>
<div class="block">Returns the upper bound of the nth argument of this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#getUpperBound(int)">getUpperBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#getUpperBound(int)">getUpperBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#getUpperBound(int)">getUpperBound(int)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateFunction.html#getUpperBound(int)">getUpperBound(int)</a></span> - Method in interface jebl.math.<a href="./jebl/math/MultivariateFunction.html" title="interface in jebl.math">MultivariateFunction</a></dt>
<dd>
<div class="block">get upper bound of argument n</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalLineFunction.html#getUpperBound()">getUpperBound()</a></span> - Method in class jebl.math.<a href="./jebl/math/OrthogonalLineFunction.html" title="class in jebl.math">OrthogonalLineFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateFunction.html#getUpperBound()">getUpperBound()</a></span> - Method in interface jebl.math.<a href="./jebl/math/UnivariateFunction.html" title="interface in jebl.math">UnivariateFunction</a></dt>
<dd>
<div class="block">get upper bound of argument</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html#getV()">getV()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/Character.html#getValue(jebl.evolution.taxa.Taxon)">getValue(Taxon)</a></span> - Method in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/Character.html" title="interface in jebl.evolution.characters">Character</a></dt>
<dd>
<div class="block">get a value for a taxon containing the character</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#getValue(jebl.evolution.taxa.Taxon)">getValue(Taxon)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#getValue(jebl.evolution.taxa.Taxon)">getValue(Taxon)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/Pattern.html#getWeight()">getWeight()</a></span> - Method in interface jebl.evolution.alignments.<a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments">Pattern</a></dt>
<dd>
<div class="block">Get the weight of this pattern</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Traceback.html#getX()">getX()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Traceback.html" title="class in jebl.evolution.align">Traceback</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Traceback.html#getY()">getY()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Traceback.html" title="class in jebl.evolution.align">Traceback</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getZero()">getZero()</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.Utils.html#getZeroFactory()">getZeroFactory()</a></span> - Static method in class jebl.math.<a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math">OrderEnumerator.Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/NumericalDerivative.html#gradient(jebl.math.MultivariateFunction, double[])">gradient(MultivariateFunction, double[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/NumericalDerivative.html" title="class in jebl.math">NumericalDerivative</a></dt>
<dd>
<div class="block">determine gradient</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/NumericalDerivative.html#gradient(jebl.math.MultivariateFunction, double[], double[])">gradient(MultivariateFunction, double[], double[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/NumericalDerivative.html" title="class in jebl.math">NumericalDerivative</a></dt>
<dd>
<div class="block">determine gradient</div>
</dd>
<dt><a href="./jebl/evolution/graphs/Graph.html" title="interface in jebl.evolution.graphs"><span class="strong">Graph</span></a> - Interface in <a href="./jebl/evolution/graphs/package-summary.html">jebl.evolution.graphs</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/graphs/Graph.NoEdgeException.html" title="class in jebl.evolution.graphs"><span class="strong">Graph.NoEdgeException</span></a> - Exception in <a href="./jebl/evolution/graphs/package-summary.html">jebl.evolution.graphs</a></dt>
<dd>
<div class="block">This class is thrown by getEdgeLength(node1, node2) if node1 and node2
are not directly connected by an edge.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Graph.NoEdgeException.html#Graph.NoEdgeException()">Graph.NoEdgeException()</a></span> - Constructor for exception jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Graph.NoEdgeException.html" title="class in jebl.evolution.graphs">Graph.NoEdgeException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/graphs/Graph.Utils.html" title="class in jebl.evolution.graphs"><span class="strong">Graph.Utils</span></a> - Class in <a href="./jebl/evolution/graphs/package-summary.html">jebl.evolution.graphs</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#guessSequenceType(java.lang.CharSequence)">guessSequenceType(CharSequence)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">Guess type of sequence from contents.</div>
</dd>
</dl>
<a name="_H_">
<!-- -->
</a>
<h2 class="title">H</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#H_STATE">H_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#H_STATE">H_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Hamming.html" title="class in jebl.evolution.align.scores"><span class="strong">Hamming</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Hamming.html#Hamming()">Hamming()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Hamming.html" title="class in jebl.evolution.align.scores">Hamming</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#hashCode()">hashCode()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#hashCode()">hashCode()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#hashCode()">hashCode()</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#hashCode()">hashCode()</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/HashPair.html#hashCode()">hashCode()</a></span> - Method in class jebl.util.<a href="./jebl/util/HashPair.html" title="class in jebl.util">HashPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#hasHeights()">hasHeights()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#hasHeights()">hasHeights()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#hasHeights()">hasHeights()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#hasHeights()">hasHeights()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#hasHeights()">hasHeights()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTree.html#hasHeights()">hasHeights()</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTree.html" title="interface in jebl.evolution.trees">RootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#hasHeights()">hasHeights()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TransformedRootedTree.html#hasHeights()">hasHeights()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TransformedRootedTree.html" title="class in jebl.evolution.trees">TransformedRootedTree</a></dt>
<dd> </dd>
<dt><a href="./jebl/util/HashPair.html" title="class in jebl.util"><span class="strong">HashPair</span></a><<a href="./jebl/util/HashPair.html" title="type parameter in HashPair">T</a>> - Class in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd>
<div class="block">A pair suitable for use in a HashMap.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/HashPair.html#HashPair(T, T)">HashPair(T, T)</a></span> - Constructor for class jebl.util.<a href="./jebl/util/HashPair.html" title="class in jebl.util">HashPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#hasIntegral()">hasIntegral()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#hasIntegral()">hasIntegral()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#hasIntegral()">hasIntegral()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#hasIntegral()">hasIntegral()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#hasIntegral()">hasIntegral()</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">returns whether an analytical expression for the integral is implemented</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#hasIntegral()">hasIntegral()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#hasIntegral()">hasIntegral()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#hasIntegral()">hasIntegral()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/LogisticGrowth.html#hasIntegral()">hasIntegral()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent">LogisticGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#hasLengths()">hasLengths()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#hasLengths()">hasLengths()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#hasLengths()">hasLengths()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#hasLengths()">hasLengths()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#hasLengths()">hasLengths()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTree.html#hasLengths()">hasLengths()</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTree.html" title="interface in jebl.evolution.trees">RootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#hasLengths()">hasLengths()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TransformedRootedTree.html#hasLengths()">hasLengths()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TransformedRootedTree.html" title="class in jebl.evolution.trees">TransformedRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.html#hasMore()">hasMore()</a></span> - Method in interface jebl.math.<a href="./jebl/math/OrderEnumerator.html" title="interface in jebl.math">OrderEnumerator</a></dt>
<dd>
<div class="block">If hasMore returns false reset should be called</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#hasNextSubtask()">hasNextSubtask()</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitSystem.html#hasSplit(boolean[])">hasSplit(boolean[])</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitSystem.html" title="class in jebl.evolution.trees">SplitSystem</a></dt>
<dd>
<div class="block">+ test whether a split is contained in this split system
(assuming the same leaf order)</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NewickImporter.html#hasTree()">hasTree()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NewickImporter.html" title="class in jebl.evolution.io">NewickImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#hasTree()">hasTree()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks
in the process if necessary.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/TreeImporter.html#hasTree()">hasTree()</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/TreeImporter.html" title="interface in jebl.evolution.io">TreeImporter</a></dt>
<dd>
<div class="block">This can be used to read one tree at a time in a loop:
<code>
List<Tree> trees = new ArrayList<Tree>();
while (hasTree()) {
trees.add(importNextTree());
}
</code>
return whether another tree is available.</div>
</dd>
<dt><a href="./jebl/evolution/distances/HKYDistanceMatrix.html" title="class in jebl.evolution.distances"><span class="strong">HKYDistanceMatrix</span></a> - Class in <a href="./jebl/evolution/distances/package-summary.html">jebl.evolution.distances</a></dt>
<dd>
<div class="block">Compute HKY corrected distance matrix</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/HKYDistanceMatrix.html#HKYDistanceMatrix(jebl.evolution.alignments.Alignment, jebl.util.ProgressListener, boolean)">HKYDistanceMatrix(Alignment, ProgressListener, boolean)</a></span> - Constructor for class jebl.evolution.distances.<a href="./jebl/evolution/distances/HKYDistanceMatrix.html" title="class in jebl.evolution.distances">HKYDistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/HKYDistanceMatrix.html#HKYDistanceMatrix(jebl.evolution.alignments.Alignment, jebl.util.ProgressListener)">HKYDistanceMatrix(Alignment, ProgressListener)</a></span> - Constructor for class jebl.evolution.distances.<a href="./jebl/evolution/distances/HKYDistanceMatrix.html" title="class in jebl.evolution.distances">HKYDistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#HYDROPATHY_CLASSIFICATION">HYDROPATHY_CLASSIFICATION</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
</dl>
<a name="_I_">
<!-- -->
</a>
<h2 class="title">I</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#I_STATE">I_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/IllegalCharacterPolicy.html" title="enum in jebl.evolution.io"><span class="strong">IllegalCharacterPolicy</span></a> - Enum in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">What to do when an imported document contains illegal characters</div>
</dd>
<dt><a href="./jebl/evolution/io/ImmediateSequenceImporter.html" title="interface in jebl.evolution.io"><span class="strong">ImmediateSequenceImporter</span></a> - Interface in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">A sequence importer sending the sequences back one by one, which makes it
possible to import larger documents if handled wisely on the other side.</div>
</dd>
<dt><a href="./jebl/evolution/io/ImmediateSequenceImporter.Callback.html" title="interface in jebl.evolution.io"><span class="strong">ImmediateSequenceImporter.Callback</span></a> - Interface in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/AlignmentImporter.html#importAlignments()">importAlignments()</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/AlignmentImporter.html" title="interface in jebl.evolution.io">AlignmentImporter</a></dt>
<dd>
<div class="block">importAlignment.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#importAlignments()">importAlignments()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Import all alignments in the input from the current position.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/DistanceMatrixImporter.html#importDistanceMatrices()">importDistanceMatrices()</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/DistanceMatrixImporter.html" title="interface in jebl.evolution.io">DistanceMatrixImporter</a></dt>
<dd>
<div class="block">importDistances.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#importDistanceMatrices()">importDistanceMatrices()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Import all distance matrices from all DISTANCES blocks in the input form the current position.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/TabDelimitedImporter.html#importDistanceMatrices()">importDistanceMatrices()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/TabDelimitedImporter.html" title="class in jebl.evolution.io">TabDelimitedImporter</a></dt>
<dd>
<div class="block">importDistances.</div>
</dd>
<dt><a href="./jebl/evolution/io/ImportException.html" title="class in jebl.evolution.io"><span class="strong">ImportException</span></a> - Exception in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.html#ImportException()">ImportException()</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.html" title="class in jebl.evolution.io">ImportException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.html#ImportException(java.lang.String)">ImportException(String)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.html" title="class in jebl.evolution.io">ImportException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.html#ImportException(java.lang.String, java.lang.Throwable)">ImportException(String, Throwable)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.html" title="class in jebl.evolution.io">ImportException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/ImportException.BadFormatException.html" title="class in jebl.evolution.io"><span class="strong">ImportException.BadFormatException</span></a> - Exception in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.BadFormatException.html#ImportException.BadFormatException()">ImportException.BadFormatException()</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.BadFormatException.html" title="class in jebl.evolution.io">ImportException.BadFormatException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.BadFormatException.html#ImportException.BadFormatException(java.lang.String)">ImportException.BadFormatException(String)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.BadFormatException.html" title="class in jebl.evolution.io">ImportException.BadFormatException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/ImportException.DuplicateFieldException.html" title="class in jebl.evolution.io"><span class="strong">ImportException.DuplicateFieldException</span></a> - Exception in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.DuplicateFieldException.html#ImportException.DuplicateFieldException()">ImportException.DuplicateFieldException()</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.DuplicateFieldException.html" title="class in jebl.evolution.io">ImportException.DuplicateFieldException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.DuplicateFieldException.html#ImportException.DuplicateFieldException(java.lang.String)">ImportException.DuplicateFieldException(String)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.DuplicateFieldException.html" title="class in jebl.evolution.io">ImportException.DuplicateFieldException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/ImportException.DuplicateTaxaException.html" title="class in jebl.evolution.io"><span class="strong">ImportException.DuplicateTaxaException</span></a> - Exception in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.DuplicateTaxaException.html#ImportException.DuplicateTaxaException()">ImportException.DuplicateTaxaException()</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.DuplicateTaxaException.html" title="class in jebl.evolution.io">ImportException.DuplicateTaxaException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.DuplicateTaxaException.html#ImportException.DuplicateTaxaException(java.lang.String)">ImportException.DuplicateTaxaException(String)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.DuplicateTaxaException.html" title="class in jebl.evolution.io">ImportException.DuplicateTaxaException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/ImportException.MissingFieldException.html" title="class in jebl.evolution.io"><span class="strong">ImportException.MissingFieldException</span></a> - Exception in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.MissingFieldException.html#ImportException.MissingFieldException()">ImportException.MissingFieldException()</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.MissingFieldException.html" title="class in jebl.evolution.io">ImportException.MissingFieldException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.MissingFieldException.html#ImportException.MissingFieldException(java.lang.String)">ImportException.MissingFieldException(String)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.MissingFieldException.html" title="class in jebl.evolution.io">ImportException.MissingFieldException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/ImportException.ShortSequenceException.html" title="class in jebl.evolution.io"><span class="strong">ImportException.ShortSequenceException</span></a> - Exception in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.ShortSequenceException.html#ImportException.ShortSequenceException()">ImportException.ShortSequenceException()</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.ShortSequenceException.html" title="class in jebl.evolution.io">ImportException.ShortSequenceException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.ShortSequenceException.html#ImportException.ShortSequenceException(java.lang.String)">ImportException.ShortSequenceException(String)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.ShortSequenceException.html" title="class in jebl.evolution.io">ImportException.ShortSequenceException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/ImportException.TooFewTaxaException.html" title="class in jebl.evolution.io"><span class="strong">ImportException.TooFewTaxaException</span></a> - Exception in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.TooFewTaxaException.html#ImportException.TooFewTaxaException()">ImportException.TooFewTaxaException()</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.TooFewTaxaException.html" title="class in jebl.evolution.io">ImportException.TooFewTaxaException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.TooFewTaxaException.html#ImportException.TooFewTaxaException(java.lang.String)">ImportException.TooFewTaxaException(String)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.TooFewTaxaException.html" title="class in jebl.evolution.io">ImportException.TooFewTaxaException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/ImportException.UnknownTaxonException.html" title="class in jebl.evolution.io"><span class="strong">ImportException.UnknownTaxonException</span></a> - Exception in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.UnknownTaxonException.html#ImportException.UnknownTaxonException()">ImportException.UnknownTaxonException()</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.UnknownTaxonException.html" title="class in jebl.evolution.io">ImportException.UnknownTaxonException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.UnknownTaxonException.html#ImportException.UnknownTaxonException(java.lang.String)">ImportException.UnknownTaxonException(String)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.UnknownTaxonException.html" title="class in jebl.evolution.io">ImportException.UnknownTaxonException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/ImportException.UnparsableDataException.html" title="class in jebl.evolution.io"><span class="strong">ImportException.UnparsableDataException</span></a> - Exception in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.UnparsableDataException.html#ImportException.UnparsableDataException()">ImportException.UnparsableDataException()</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.UnparsableDataException.html" title="class in jebl.evolution.io">ImportException.UnparsableDataException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.UnparsableDataException.html#ImportException.UnparsableDataException(java.lang.String)">ImportException.UnparsableDataException(String)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.UnparsableDataException.html" title="class in jebl.evolution.io">ImportException.UnparsableDataException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io"><span class="strong">ImportHelper</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">A helper class for phylogenetic file format importers</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#ImportHelper(java.io.Reader)">ImportHelper(Reader)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">ATTENTION: The ImportHelper never closes the reader passed to the constructor.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#ImportHelper(java.io.Reader, java.io.Writer)">ImportHelper(Reader, Writer)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NewickImporter.html#importNextTree()">importNextTree()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NewickImporter.html" title="class in jebl.evolution.io">NewickImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#importNextTree()">importNextTree()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks
in the process if necessary.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/TreeImporter.html#importNextTree()">importNextTree()</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/TreeImporter.html" title="interface in jebl.evolution.io">TreeImporter</a></dt>
<dd>
<div class="block">Import a single tree</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/FastaImporter.html#importSequences()">importSequences()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/FastaImporter.html" title="class in jebl.evolution.io">FastaImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/FastaImporter.html#importSequences(jebl.evolution.io.ImmediateSequenceImporter.Callback, jebl.util.ProgressListener)">importSequences(ImmediateSequenceImporter.Callback, ProgressListener)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/FastaImporter.html" title="class in jebl.evolution.io">FastaImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImmediateSequenceImporter.html#importSequences(jebl.evolution.io.ImmediateSequenceImporter.Callback, jebl.util.ProgressListener)">importSequences(ImmediateSequenceImporter.Callback, ProgressListener)</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/ImmediateSequenceImporter.html" title="interface in jebl.evolution.io">ImmediateSequenceImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#importSequences()">importSequences()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Import all sequences in the input from the current position</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/PhylipSequentialImporter.html#importSequences()">importSequences()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/PhylipSequentialImporter.html" title="class in jebl.evolution.io">PhylipSequentialImporter</a></dt>
<dd>
<div class="block">importSequences.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/SequenceImporter.html#importSequences()">importSequences()</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/SequenceImporter.html" title="interface in jebl.evolution.io">SequenceImporter</a></dt>
<dd>
<div class="block">importSequences.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NewickImporter.html#importTrees()">importTrees()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NewickImporter.html" title="class in jebl.evolution.io">NewickImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#importTrees()">importTrees()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Import all trees in the file from the current position.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/TreeImporter.html#importTrees()">importTrees()</a></span> - Method in interface jebl.evolution.io.<a href="./jebl/evolution/io/TreeImporter.html" title="interface in jebl.evolution.io">TreeImporter</a></dt>
<dd>
<div class="block">Import all the trees</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Scores.html#includeAdditionalCharacters(jebl.evolution.align.scores.Scores, java.lang.String)">includeAdditionalCharacters(Scores, String)</a></span> - Static method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Scores.html" title="class in jebl.evolution.align.scores">Scores</a></dt>
<dd>
<div class="block">includes additional characters in the score matrix which will all have scored zero when compared to other
characters.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Scores.html#includeGaps(jebl.evolution.align.scores.Scores, float, float)">includeGaps(Scores, float, float)</a></span> - Static method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Scores.html" title="class in jebl.evolution.align.scores">Scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/GammaFunction.html#incompleteGammaP(double, double)">incompleteGammaP(double, double)</a></span> - Static method in class jebl.math.<a href="./jebl/math/GammaFunction.html" title="class in jebl.math">GammaFunction</a></dt>
<dd>
<div class="block">Incomplete Gamma function P(a,x) = 1-Q(a,x)
(a cleanroom implementation of Numerical Recipes gammp(a,x);
in Mathematica this function is 1-GammaRegularized)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/GammaFunction.html#incompleteGammaP(double, double, double)">incompleteGammaP(double, double, double)</a></span> - Static method in class jebl.math.<a href="./jebl/math/GammaFunction.html" title="class in jebl.math">GammaFunction</a></dt>
<dd>
<div class="block">Incomplete Gamma function P(a,x) = 1-Q(a,x)
(a cleanroom implementation of Numerical Recipes gammp(a,x);
in Mathematica this function is 1-GammaRegularized)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/GammaFunction.html#incompleteGammaQ(double, double)">incompleteGammaQ(double, double)</a></span> - Static method in class jebl.math.<a href="./jebl/math/GammaFunction.html" title="class in jebl.math">GammaFunction</a></dt>
<dd>
<div class="block">Incomplete Gamma function Q(a,x)
(a cleanroom implementation of Numerical Recipes gammq(a,x);
in Mathematica this function is called GammaRegularized)</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#INDICATOR">INDICATOR</a></span> - Variable in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#init(jebl.evolution.alignments.Alignment, int[])">init(Alignment, int[])</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd>
<div class="block">Setup resampled alignment.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#innerProduct(double[], double[], int)">innerProduct(double[], double[], int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">innerProdect
calculates inner product of two vectors from i down</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/IllegalCharacterPolicy.html#instanceOf(java.lang.String)">instanceOf(String)</a></span> - Static method in enum jebl.evolution.io.<a href="./jebl/evolution/io/IllegalCharacterPolicy.html" title="enum in jebl.evolution.io">IllegalCharacterPolicy</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#intersect(jebl.util.FixedBitSet)">intersect(FixedBitSet)</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#intersectCardinality(jebl.util.FixedBitSet)">intersectCardinality(FixedBitSet)</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/treesimulation/IntervalGenerator.html" title="interface in jebl.evolution.treesimulation"><span class="strong">IntervalGenerator</span></a> - Interface in <a href="./jebl/evolution/treesimulation/package-summary.html">jebl.evolution.treesimulation</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/coalescent/IntervalList.html" title="interface in jebl.evolution.coalescent"><span class="strong">IntervalList</span></a> - Interface in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">An interface for a set of coalescent intevals.</div>
</dd>
<dt><a href="./jebl/evolution/coalescent/IntervalList.IntervalType.html" title="enum in jebl.evolution.coalescent"><span class="strong">IntervalList.IntervalType</span></a> - Enum in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/coalescent/IntervalList.Utils.html" title="class in jebl.evolution.coalescent"><span class="strong">IntervalList.Utils</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent"><span class="strong">Intervals</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">A concrete class for a set of coalescent intevals.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#Intervals(jebl.evolution.trees.RootedTree)">Intervals(RootedTree)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#Intervals(int)">Intervals(int)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#INVERTEBRATE_MT">INVERTEBRATE_MT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Utils.html#isAcyclical(jebl.evolution.graphs.Graph)">isAcyclical(Graph)</a></span> - Method in class jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Utils.html" title="class in jebl.evolution.graphs">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#isAllGaps()">isAllGaps()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#isAmbiguous()">isAmbiguous()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isATstate(jebl.evolution.sequences.State)">isATstate(State)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#isBinary(jebl.evolution.trees.RootedTree)">isBinary(RootedTree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#isBinary(jebl.evolution.trees.RootedTree)">isBinary(RootedTree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.html#isBinaryCoalescent()">isBinaryCoalescent()</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.html" title="interface in jebl.evolution.coalescent">IntervalList</a></dt>
<dd>
<div class="block">Checks whether this set of coalescent intervals is fully resolved
(i.e.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#isBinaryCoalescent()">isBinaryCoalescent()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/BasicProgressListener.html#isCanceled()">isCanceled()</a></span> - Method in class jebl.util.<a href="./jebl/util/BasicProgressListener.html" title="class in jebl.util">BasicProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Cancelable.html#isCanceled()">isCanceled()</a></span> - Method in interface jebl.util.<a href="./jebl/util/Cancelable.html" title="interface in jebl.util">Cancelable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#isCanceled()">isCanceled()</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#isCanceled()">isCanceled()</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">This method must be implemented by all subclasses.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.Wrapper.html#isCanceled()">isCanceled()</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.Wrapper.html" title="class in jebl.util">ProgressListener.Wrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ByteBuilder.html#isCharacterAscii(char)">isCharacterAscii(char)</a></span> - Static method in class jebl.evolution.io.<a href="./jebl/evolution/io/ByteBuilder.html" title="class in jebl.evolution.io">ByteBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.html#isCoalescentOnly()">isCoalescentOnly()</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.html" title="interface in jebl.evolution.coalescent">IntervalList</a></dt>
<dd>
<div class="block">Checks whether this set of coalescent intervals coalescent only
(i.e.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#isCoalescentOnly()">isCoalescentOnly()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Utils.html#isConnected(jebl.evolution.graphs.Graph)">isConnected(Graph)</a></span> - Method in class jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Utils.html" title="class in jebl.evolution.graphs">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#isContains(java.lang.String[], java.lang.String)">isContains(String[], String)</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">Test if a string occurs within a set</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#isExternal(jebl.evolution.graphs.Node)">isExternal(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#isExternal(jebl.evolution.graphs.Node)">isExternal(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#isExternal(jebl.evolution.graphs.Node)">isExternal(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#isExternal(jebl.evolution.graphs.Node)">isExternal(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#isExternal(jebl.evolution.graphs.Node)">isExternal(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#isExternal(jebl.evolution.graphs.Node)">isExternal(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#isExternal(jebl.evolution.graphs.Node)">isExternal(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#isExternal(jebl.evolution.graphs.Edge)">isExternal(Edge)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Tree.html#isExternal(jebl.evolution.graphs.Node)">isExternal(Node)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#isGap(jebl.evolution.sequences.AminoAcidState)">isGap(AminoAcidState)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcidState.html#isGap()">isGap()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcidState.html" title="class in jebl.evolution.sequences">AminoAcidState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#isGap(jebl.evolution.sequences.CodonState)">isGap(CodonState)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonState.html#isGap()">isGap()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonState.html" title="class in jebl.evolution.sequences">CodonState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isGap(jebl.evolution.sequences.NucleotideState)">isGap(NucleotideState)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/NucleotideState.html#isGap()">isGap()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/NucleotideState.html" title="class in jebl.evolution.sequences">NucleotideState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#isGap(jebl.evolution.sequences.State)">isGap(State)</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#isGap()">isGap()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isGCstate(jebl.evolution.sequences.State)">isGCstate(State)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#isGeneratedTreeName(java.lang.String)">isGeneratedTreeName(String)</a></span> - Static method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/BasicProgressListener.html#isIndeterminate()">isIndeterminate()</a></span> - Method in class jebl.util.<a href="./jebl/util/BasicProgressListener.html" title="class in jebl.util">BasicProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#isMonophyletic(jebl.evolution.trees.RootedTree, java.util.Set)">isMonophyletic(RootedTree, Set<Node>)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd>
<div class="block">Performs the a monophyly test on a set of tip nodes.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#isOrdered()">isOrdered()</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isPossibleTransition(char, char)">isPossibleTransition(char, char)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isPossibleTransition(jebl.evolution.sequences.State, jebl.evolution.sequences.State)">isPossibleTransition(State, State)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isPossibleTransversion(char, char)">isPossibleTransversion(char, char)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isPossibleTransversion(jebl.evolution.sequences.State, jebl.evolution.sequences.State)">isPossibleTransversion(State, State)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#isPredominantlyRNA(java.lang.CharSequence, int)">isPredominantlyRNA(CharSequence, int)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">Is the given NucleotideSequence predominantly RNA?
(i.e the more occurrences of "U" than "T")</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isPurine(jebl.evolution.sequences.State)">isPurine(State)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isPyrimidine(jebl.evolution.sequences.State)">isPyrimidine(State)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#isRoot(jebl.evolution.graphs.Node)">isRoot(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#isRoot(jebl.evolution.graphs.Node)">isRoot(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#isRoot(jebl.evolution.graphs.Node)">isRoot(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#isRoot(jebl.evolution.graphs.Node)">isRoot(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#isRoot(jebl.evolution.graphs.Node)">isRoot(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTree.html#isRoot(jebl.evolution.graphs.Node)">isRoot(Node)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTree.html" title="interface in jebl.evolution.trees">RootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#isRoot(jebl.evolution.graphs.Node)">isRoot(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.html#isRootedMethod(jebl.evolution.trees.TreeBuilderFactory.Method)">isRootedMethod(TreeBuilderFactory.Method)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.html" title="class in jebl.evolution.trees">TreeBuilderFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitUtils.html#isSame(boolean[], boolean[])">isSame(boolean[], boolean[])</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitUtils.html" title="class in jebl.evolution.trees">SplitUtils</a></dt>
<dd>
<div class="block">Checks two splits for identity.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#isStartCodon(jebl.evolution.sequences.CodonState)">isStartCodon(CodonState)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#isStartCodonString(java.lang.String)">isStartCodonString(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Checks whether all possible disambiguations of a given nucleotide triplet
string represents a start codon.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcidState.html#isStop()">isStop()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcidState.html" title="class in jebl.evolution.sequences">AminoAcidState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#isStopCodon(jebl.evolution.sequences.CodonState)">isStopCodon(CodonState)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#isStopCodonString(java.lang.String)">isStopCodonString(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Checks whether a given String represents a stop codon.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ConsensusTreeBuilder.html#isSupportAsPercent()">isSupportAsPercent()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ConsensusTreeBuilder.html" title="class in jebl.evolution.trees">ConsensusTreeBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isTransition(jebl.evolution.sequences.State, jebl.evolution.sequences.State)">isTransition(State, State)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isTransversion(jebl.evolution.sequences.State, jebl.evolution.sequences.State)">isTransversion(State, State)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/graphs/Utils.html#isTree(jebl.evolution.graphs.Graph)">isTree(Graph)</a></span> - Method in class jebl.evolution.graphs.<a href="./jebl/evolution/graphs/Utils.html" title="class in jebl.evolution.graphs">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#isUltrametric(jebl.evolution.trees.RootedTree, double)">isUltrametric(RootedTree, double)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#isUltrametric(jebl.evolution.trees.RootedTree)">isUltrametric(RootedTree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#isUnknown(jebl.evolution.sequences.AminoAcidState)">isUnknown(AminoAcidState)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#isUnknown(jebl.evolution.sequences.CodonState)">isUnknown(CodonState)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#isUnknown(jebl.evolution.sequences.NucleotideState)">isUnknown(NucleotideState)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#isUnknown(jebl.evolution.sequences.State)">isUnknown(State)</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NewickImporter.html#iterator()">iterator()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NewickImporter.html" title="class in jebl.evolution.io">NewickImporter</a></dt>
<dd>
<div class="block">Returns an iterator over a set of elements of type T.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#iterator()">iterator()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#IUB">IUB</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
</dl>
<a name="_J_">
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</a>
<h2 class="title">J</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#J_STATE">J_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/alignments/JackknifedAlignment.html" title="class in jebl.evolution.alignments"><span class="strong">JackknifedAlignment</span></a> - Class in <a href="./jebl/evolution/alignments/package-summary.html">jebl.evolution.alignments</a></dt>
<dd>
<div class="block">Date: 17/01/2006
Time: 08:18:32</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/JackknifedAlignment.html#JackknifedAlignment(jebl.evolution.alignments.Alignment, double)">JackknifedAlignment(Alignment, double)</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/JackknifedAlignment.html" title="class in jebl.evolution.alignments">JackknifedAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/JackknifedAlignment.html#JackknifedAlignment(jebl.evolution.alignments.Alignment, double, long)">JackknifedAlignment(Alignment, double, long)</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/JackknifedAlignment.html" title="class in jebl.evolution.alignments">JackknifedAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/JackknifedAlignment.html#JackknifedAlignment(jebl.evolution.alignments.Alignment, double, java.util.Random)">JackknifedAlignment(Alignment, double, Random)</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/JackknifedAlignment.html" title="class in jebl.evolution.alignments">JackknifedAlignment</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a> - package jebl.evolution.align</dt>
<dd>
<div class="block">Provides classes and interfaces for pairwise alignment of two sequences.</div>
</dd>
<dt><a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a> - package jebl.evolution.align.scores</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/aligners/package-summary.html">jebl.evolution.aligners</a> - package jebl.evolution.aligners</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/alignments/package-summary.html">jebl.evolution.alignments</a> - package jebl.evolution.alignments</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/characters/package-summary.html">jebl.evolution.characters</a> - package jebl.evolution.characters</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a> - package jebl.evolution.coalescent</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/distances/package-summary.html">jebl.evolution.distances</a> - package jebl.evolution.distances</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/graphs/package-summary.html">jebl.evolution.graphs</a> - package jebl.evolution.graphs</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a> - package jebl.evolution.io</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/parsimony/package-summary.html">jebl.evolution.parsimony</a> - package jebl.evolution.parsimony</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a> - package jebl.evolution.sequences</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/substmodel/package-summary.html">jebl.evolution.substmodel</a> - package jebl.evolution.substmodel</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/taxa/package-summary.html">jebl.evolution.taxa</a> - package jebl.evolution.taxa</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/treemetrics/package-summary.html">jebl.evolution.treemetrics</a> - package jebl.evolution.treemetrics</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a> - package jebl.evolution.trees</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/treesimulation/package-summary.html">jebl.evolution.treesimulation</a> - package jebl.evolution.treesimulation</dt>
<dd> </dd>
<dt><a href="./jebl/math/package-summary.html">jebl.math</a> - package jebl.math</dt>
<dd> </dd>
<dt><a href="./jebl/util/package-summary.html">jebl.util</a> - package jebl.util</dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/JukesCantor.html" title="class in jebl.evolution.align.scores"><span class="strong">JukesCantor</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd>
<div class="block">Jukes Cantor assumes equal substitution frequencies and equal nucleotide
equilibrium frequencies.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/JukesCantor.html#JukesCantor(float)">JukesCantor(float)</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/JukesCantor.html" title="class in jebl.evolution.align.scores">JukesCantor</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/distances/JukesCantorDistanceMatrix.html" title="class in jebl.evolution.distances"><span class="strong">JukesCantorDistanceMatrix</span></a> - Class in <a href="./jebl/evolution/distances/package-summary.html">jebl.evolution.distances</a></dt>
<dd>
<div class="block">Compute jukes-cantor corrected distance matrix for a set of aligned sequences.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/JukesCantorDistanceMatrix.html#JukesCantorDistanceMatrix(jebl.evolution.alignments.Alignment, jebl.util.ProgressListener)">JukesCantorDistanceMatrix(Alignment, ProgressListener)</a></span> - Constructor for class jebl.evolution.distances.<a href="./jebl/evolution/distances/JukesCantorDistanceMatrix.html" title="class in jebl.evolution.distances">JukesCantorDistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/JukesCantorDistanceMatrix.html#JukesCantorDistanceMatrix(jebl.evolution.alignments.Alignment, jebl.util.ProgressListener, boolean)">JukesCantorDistanceMatrix(Alignment, ProgressListener, boolean)</a></span> - Constructor for class jebl.evolution.distances.<a href="./jebl/evolution/distances/JukesCantorDistanceMatrix.html" title="class in jebl.evolution.distances">JukesCantorDistanceMatrix</a></dt>
<dd> </dd>
</dl>
<a name="_K_">
<!-- -->
</a>
<h2 class="title">K</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#K_STATE">K_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#K_STATE">K_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
</dl>
<a name="_L_">
<!-- -->
</a>
<h2 class="title">L</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#L_STATE">L_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#leftNb(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">leftNb(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd>
<div class="block">Left Neighbour of a tip (taxon).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ByteBuilder.html#length()">length()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ByteBuilder.html" title="class in jebl.evolution.io">ByteBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/GammaFunction.html#lnGamma(double)">lnGamma(double)</a></span> - Static method in class jebl.math.<a href="./jebl/math/GammaFunction.html" title="class in jebl.math">GammaFunction</a></dt>
<dd>
<div class="block">log Gamma function: ln(gamma(alpha)) for alpha>0, accurate to 10 decimal places</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#loadTrees(int, int)">loadTrees(int, int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent"><span class="strong">LogisticGrowth</span></a> - Class in <a href="./jebl/evolution/coalescent/package-summary.html">jebl.evolution.coalescent</a></dt>
<dd>
<div class="block">This class models logistic growth.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/LogisticGrowth.html#LogisticGrowth()">LogisticGrowth()</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent">LogisticGrowth</a></dt>
<dd>
<div class="block">Construct demographic model with default settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/LogisticGrowth.html#LogisticGrowth(double, double, double)">LogisticGrowth(double, double, double)</a></span> - Constructor for class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent">LogisticGrowth</a></dt>
<dd>
<div class="block">Construct demographic model with given settings</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#lowerSolve(double[][], double[], double)">lowerSolve(double[][], double[], double)</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">lower Solve
forward elimination with (optional) default diagonal value</div>
</dd>
</dl>
<a name="_M_">
<!-- -->
</a>
<h2 class="title">M</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#M_STATE">M_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#M_STATE">M_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/MachineAccuracy.html" title="class in jebl.math"><span class="strong">MachineAccuracy</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">determines machine accuracy</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MachineAccuracy.html#MachineAccuracy()">MachineAccuracy()</a></span> - Constructor for class jebl.math.<a href="./jebl/math/MachineAccuracy.html" title="class in jebl.math">MachineAccuracy</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignCommand.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/AlignCommand.html" title="class in jebl.evolution.align">AlignCommand</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/BartonSternberg.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/BartonSternberg.html" title="class in jebl.evolution.align">BartonSternberg</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treesimulation/TreeSimulator.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class jebl.evolution.treesimulation.<a href="./jebl/evolution/treesimulation/TreeSimulator.html" title="class in jebl.evolution.treesimulation">TreeSimulator</a></dt>
<dd>
<div class="block">A main() to test the tree simulation classes.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#makeIntoAllowableIdentifier(java.lang.String)">makeIntoAllowableIdentifier(String)</a></span> - Static method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/MatrixCalc.html" title="class in jebl.math"><span class="strong">MatrixCalc</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#MatrixCalc()">MatrixCalc()</a></span> - Constructor for class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/MatrixCalcException.html" title="class in jebl.math"><span class="strong">MatrixCalcException</span></a> - Exception in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalcException.html#MatrixCalcException()">MatrixCalcException()</a></span> - Constructor for exception jebl.math.<a href="./jebl/math/MatrixCalcException.html" title="class in jebl.math">MatrixCalcException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalcException.html#MatrixCalcException(java.lang.String)">MatrixCalcException(String)</a></span> - Constructor for exception jebl.math.<a href="./jebl/math/MatrixCalcException.html" title="class in jebl.math">MatrixCalcException</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/MatrixCalcException.NotSquareMatrixException.html" title="class in jebl.math"><span class="strong">MatrixCalcException.NotSquareMatrixException</span></a> - Exception in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalcException.NotSquareMatrixException.html#MatrixCalcException.NotSquareMatrixException()">MatrixCalcException.NotSquareMatrixException()</a></span> - Constructor for exception jebl.math.<a href="./jebl/math/MatrixCalcException.NotSquareMatrixException.html" title="class in jebl.math">MatrixCalcException.NotSquareMatrixException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalcException.NotSquareMatrixException.html#MatrixCalcException.NotSquareMatrixException(java.lang.String)">MatrixCalcException.NotSquareMatrixException(String)</a></span> - Constructor for exception jebl.math.<a href="./jebl/math/MatrixCalcException.NotSquareMatrixException.html" title="class in jebl.math">MatrixCalcException.NotSquareMatrixException</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/MatrixCalcException.PositiveDefiniteException.html" title="class in jebl.math"><span class="strong">MatrixCalcException.PositiveDefiniteException</span></a> - Exception in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalcException.PositiveDefiniteException.html#MatrixCalcException.PositiveDefiniteException()">MatrixCalcException.PositiveDefiniteException()</a></span> - Constructor for exception jebl.math.<a href="./jebl/math/MatrixCalcException.PositiveDefiniteException.html" title="class in jebl.math">MatrixCalcException.PositiveDefiniteException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalcException.PositiveDefiniteException.html#MatrixCalcException.PositiveDefiniteException(java.lang.String)">MatrixCalcException.PositiveDefiniteException(String)</a></span> - Constructor for exception jebl.math.<a href="./jebl/math/MatrixCalcException.PositiveDefiniteException.html" title="class in jebl.math">MatrixCalcException.PositiveDefiniteException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/substmodel/MatrixExponential.html" title="class in jebl.evolution.substmodel"><span class="strong">MatrixExponential</span></a> - Class in <a href="./jebl/evolution/substmodel/package-summary.html">jebl.evolution.substmodel</a></dt>
<dd>
<div class="block">compute matrix exponential and, subsequently, transition probabilities
for a given rate matrix</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/MatrixExponential.html#MatrixExponential(int)">MatrixExponential(int)</a></span> - Constructor for class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/MatrixExponential.html" title="class in jebl.evolution.substmodel">MatrixExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/MatrixExponential.html#MatrixExponential(jebl.evolution.substmodel.RateMatrix)">MatrixExponential(RateMatrix)</a></span> - Constructor for class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/MatrixExponential.html" title="class in jebl.evolution.substmodel">MatrixExponential</a></dt>
<dd>
<div class="block">create module</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#MAX_ROW_LENGTH">MAX_ROW_LENGTH</a></span> - Static variable in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#maxFun">maxFun</a></span> - Variable in class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd>
<div class="block">maxFun is the maximum number of calls to fun allowed.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#maxFun">maxFun</a></span> - Variable in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">maximum number of function evaluations
(default 0 indicates no limit on calls)</div>
</dd>
<dt><a href="./jebl/evolution/align/MaximalSegmentPair.html" title="class in jebl.evolution.align"><span class="strong">MaximalSegmentPair</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/MaximalSegmentPair.html#MaximalSegmentPair(jebl.evolution.align.scores.Scores)">MaximalSegmentPair(Scores)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/MaximalSegmentPair.html" title="class in jebl.evolution.align">MaximalSegmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#maxLevels(jebl.evolution.trees.RootedTree)">maxLevels(RootedTree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><a href="./jebl/util/MaybeBoolean.html" title="enum in jebl.util"><span class="strong">MaybeBoolean</span></a> - Enum in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd>
<div class="block">A tri-state boolean value that can also be "Maybe" besides True and False.</div>
</dd>
<dt><a href="./jebl/evolution/io/MEGAExporter.html" title="class in jebl.evolution.io"><span class="strong">MEGAExporter</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">* Export to MEGA.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/MEGAExporter.html#MEGAExporter(java.io.Writer, java.lang.String)">MEGAExporter(Writer, String)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/MEGAExporter.html" title="class in jebl.evolution.io">MEGAExporter</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/MinimiserMonitor.html" title="interface in jebl.math"><span class="strong">MinimiserMonitor</span></a> - Interface in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">interface for a classes that wish to monitor the progress of a Minimiser</div>
</dd>
<dt><a href="./jebl/math/MinimiserMonitor.Utils.html" title="class in jebl.math"><span class="strong">MinimiserMonitor.Utils</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#minx">minx</a></span> - Variable in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">last minimum</div>
</dd>
<dt><a href="./jebl/evolution/taxa/MissingTaxonException.html" title="class in jebl.evolution.taxa"><span class="strong">MissingTaxonException</span></a> - Class in <a href="./jebl/evolution/taxa/package-summary.html">jebl.evolution.taxa</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/MissingTaxonException.html#MissingTaxonException(jebl.evolution.taxa.Taxon)">MissingTaxonException(Taxon)</a></span> - Constructor for class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/MissingTaxonException.html" title="class in jebl.evolution.taxa">MissingTaxonException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/distances/ModelBasedDistanceMatrix.html" title="class in jebl.evolution.distances"><span class="strong">ModelBasedDistanceMatrix</span></a> - Class in <a href="./jebl/evolution/distances/package-summary.html">jebl.evolution.distances</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/ModelBasedDistanceMatrix.html#ModelBasedDistanceMatrix()">ModelBasedDistanceMatrix()</a></span> - Constructor for class jebl.evolution.distances.<a href="./jebl/evolution/distances/ModelBasedDistanceMatrix.html" title="class in jebl.evolution.distances">ModelBasedDistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#MOLD_PROTOZOAN_MT">MOLD_PROTOZOAN_MT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/MostProbableTopology.html" title="class in jebl.evolution.trees"><span class="strong">MostProbableTopology</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Given a set of trees determine the most probable trees, i.e.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MostProbableTopology.html#MostProbableTopology(java.util.Collection)">MostProbableTopology(Collection<? extends Tree>)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/MostProbableTopology.html" title="class in jebl.evolution.trees">MostProbableTopology</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/MultipleAligner.html" title="interface in jebl.evolution.align"><span class="strong">MultipleAligner</span></a> - Interface in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/MultivariateFunction.html" title="interface in jebl.math"><span class="strong">MultivariateFunction</span></a> - Interface in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">interface for a function of several variables</div>
</dd>
<dt><a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math"><span class="strong">MultivariateMinimum</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">abstract base class for minimisation of a multivariate function</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#MultivariateMinimum()">MultivariateMinimum()</a></span> - Constructor for class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/MultivariateMinimum.Factory.html" title="interface in jebl.math"><span class="strong">MultivariateMinimum.Factory</span></a> - Interface in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">A factory interface for MultivariateMinimums (because they aren't statefree)</div>
</dd>
<dt><a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees"><span class="strong">MutableRootedTree</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A simple rooted tree providing some ability to manipulate the tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#MutableRootedTree(jebl.evolution.trees.Tree, jebl.evolution.graphs.Node)">MutableRootedTree(Tree, Node)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">Construct a rooted tree from unrooted.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#MutableRootedTree(jebl.evolution.trees.RootedTree)">MutableRootedTree(RootedTree)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">Construct a rooted tree from an immutable rooted tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#MYCOPLASMA">MYCOPLASMA</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
</dl>
<a name="_N_">
<!-- -->
</a>
<h2 class="title">N</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#N_STATE">N_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#N_STATE">N_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#NAME">NAME</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#NAME">NAME</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#NAME">NAME</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/NeedlemanWunsch.html" title="class in jebl.evolution.align"><span class="strong">NeedlemanWunsch</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunsch.html#NeedlemanWunsch(jebl.evolution.align.scores.Scores, float)">NeedlemanWunsch(Scores, float)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunsch.html" title="class in jebl.evolution.align">NeedlemanWunsch</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align"><span class="strong">NeedlemanWunschAffine</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#NeedlemanWunschAffine(jebl.evolution.align.scores.Scores, float, float)">NeedlemanWunschAffine(Scores, float, float)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html" title="class in jebl.evolution.align"><span class="strong">NeedlemanWunschLinearSpace</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html#NeedlemanWunschLinearSpace(jebl.evolution.align.scores.Scores, float)">NeedlemanWunschLinearSpace(Scores, float)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpace</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align"><span class="strong">NeedlemanWunschLinearSpaceAffine</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#NeedlemanWunschLinearSpaceAffine(jebl.evolution.align.scores.Scores, float, float)">NeedlemanWunschLinearSpaceAffine(Scores, float, float)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#NeedlemanWunschLinearSpaceAffine(jebl.evolution.align.scores.Scores, float, float, boolean)">NeedlemanWunschLinearSpaceAffine(Scores, float, float, boolean)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#NeedlemanWunschLinearSpaceAffine(jebl.evolution.align.scores.Scores, float, float, boolean, boolean)">NeedlemanWunschLinearSpaceAffine(Scores, float, float, boolean, boolean)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/NeighborJoiningTreeBuilder.html" title="class in jebl.evolution.trees"><span class="strong">NeighborJoiningTreeBuilder</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Constructs an unrooted tree by neighbor-joining using pairwise distances.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/NeighborJoiningTreeBuilder.html#NeighborJoiningTreeBuilder(jebl.evolution.distances.DistanceMatrix)">NeighborJoiningTreeBuilder(DistanceMatrix)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/NeighborJoiningTreeBuilder.html" title="class in jebl.evolution.trees">NeighborJoiningTreeBuilder</a></dt>
<dd>
<div class="block">construct NJ tree</div>
</dd>
<dt><a href="./jebl/evolution/io/NewickExporter.html" title="class in jebl.evolution.io"><span class="strong">NewickExporter</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NewickExporter.html#NewickExporter(java.io.Writer)">NewickExporter(Writer)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/NewickExporter.html" title="class in jebl.evolution.io">NewickExporter</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/NewickImporter.html" title="class in jebl.evolution.io"><span class="strong">NewickImporter</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NewickImporter.html#NewickImporter(java.io.Reader, boolean)">NewickImporter(Reader, boolean)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/NewickImporter.html" title="class in jebl.evolution.io">NewickImporter</a></dt>
<dd>
<div class="block">Constructor</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MinimiserMonitor.html#newMinimum(double, double[], jebl.math.MultivariateFunction)">newMinimum(double, double[], MultivariateFunction)</a></span> - Method in interface jebl.math.<a href="./jebl/math/MinimiserMonitor.html" title="interface in jebl.math">MinimiserMonitor</a></dt>
<dd>
<div class="block">Inform monitor of a new minimum, along with the current arguments.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/TracebackPlotter.html#newTraceBack(java.lang.String, java.lang.String)">newTraceBack(String, String)</a></span> - Method in interface jebl.evolution.align.<a href="./jebl/evolution/align/TracebackPlotter.html" title="interface in jebl.evolution.align">TracebackPlotter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#next(jebl.evolution.align.Traceback)">next(Traceback)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd>
<div class="block">Get the next state in the traceback</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/MaximalSegmentPair.html#next(jebl.evolution.align.Traceback)">next(Traceback)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/MaximalSegmentPair.html" title="class in jebl.evolution.align">MaximalSegmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#next()">next()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextBoolean()">nextBoolean()</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextByte()">nextByte()</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextBytes(byte[])">nextBytes(byte[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextChar()">nextChar()</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#nextCharacter()">nextCharacter()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextDouble()">nextDouble()</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextFloat()">nextFloat()</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextGaussian()">nextGaussian()</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextInt()">nextInt()</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextInt(int)">nextInt(int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextLong()">nextLong()</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#nextOnBit(int)">nextOnBit(int)</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd>
<div class="block">Iteration helper.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#nextShort()">nextShort()</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io"><span class="strong">NexusExporter</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Export sequences and trees to Nexus format.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#NexusExporter(java.io.Writer)">NexusExporter(Writer)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#NexusExporter(java.io.Writer, boolean)">NexusExporter(Writer, boolean)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#NexusExporter(java.io.Writer, boolean, boolean)">NexusExporter(Writer, boolean, boolean)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io"><span class="strong">NexusImporter</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Class for importing NEXUS file format.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#NexusImporter(java.io.Reader, long)">NexusImporter(Reader, long)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#NexusImporter(java.io.Reader)">NexusImporter(Reader)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#NexusImporter(java.io.Reader, boolean, long)">NexusImporter(Reader, boolean, long)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#NexusImporter(java.io.Reader, boolean)">NexusImporter(Reader, boolean)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use NexusImporter(Reader reader, boolean compactTrees, long expectedInputLength)</i></div>
</div>
</dd>
<dt><a href="./jebl/evolution/io/NexusImporter.MissingBlockException.html" title="class in jebl.evolution.io"><span class="strong">NexusImporter.MissingBlockException</span></a> - Exception in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Thrown when a block is missing that is required for importing a particular type of data from the nexus input.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.MissingBlockException.html#NexusImporter.MissingBlockException()">NexusImporter.MissingBlockException()</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.MissingBlockException.html" title="class in jebl.evolution.io">NexusImporter.MissingBlockException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.MissingBlockException.html#NexusImporter.MissingBlockException(java.lang.String)">NexusImporter.MissingBlockException(String)</a></span> - Constructor for exception jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.MissingBlockException.html" title="class in jebl.evolution.io">NexusImporter.MissingBlockException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/NexusImporter.NexusBlock.html" title="enum in jebl.evolution.io"><span class="strong">NexusImporter.NexusBlock</span></a> - Enum in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Represents the block types used in the nexus format</div>
</dd>
<dt><a href="./jebl/evolution/graphs/Node.html" title="interface in jebl.evolution.graphs"><span class="strong">Node</span></a> - Interface in <a href="./jebl/evolution/graphs/package-summary.html">jebl.evolution.graphs</a></dt>
<dd>
<div class="block">Represents a node in a graph or tree.</div>
</dd>
<dt><a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html" title="class in jebl.evolution.align"><span class="strong">NonOverlapMultipleLocalAffine</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd>
<div class="block">Performs recursive local alignments.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html#NonOverlapMultipleLocalAffine(jebl.evolution.align.scores.Scores, float, float, int)">NonOverlapMultipleLocalAffine(Scores, float, float, int)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html" title="class in jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#NUCLEOTIDE">NUCLEOTIDE</a></span> - Static variable in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#NUCLEOTIDE_51_PERCENT_SIMILARITY">NUCLEOTIDE_51_PERCENT_SIMILARITY</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#NUCLEOTIDE_65_PERCENT_SIMILARITY">NUCLEOTIDE_65_PERCENT_SIMILARITY</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#NUCLEOTIDE_70_PERCENT_SIMILARITY">NUCLEOTIDE_70_PERCENT_SIMILARITY</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#NUCLEOTIDE_93_PERCENT_SIMILARITY">NUCLEOTIDE_93_PERCENT_SIMILARITY</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences"><span class="strong">Nucleotides</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd>
<div class="block">Uninstantiable utility class with only static methods.</div>
</dd>
<dt><a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores"><span class="strong">NucleotideScores</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#NucleotideScores(jebl.evolution.align.scores.NucleotideScores)">NucleotideScores(NucleotideScores)</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#NucleotideScores(float, float)">NucleotideScores(float, float)</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#NucleotideScores(float, float, float)">NucleotideScores(float, float, float)</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#NucleotideScores(java.lang.String, float, float)">NucleotideScores(String, float, float)</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#NucleotideScores(java.lang.String, float, float, float)">NucleotideScores(String, float, float, float)</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#NucleotideScores(java.lang.String, float, float, float, float, boolean)">NucleotideScores(String, float, float, float, float, boolean)</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#NucleotideScores(jebl.evolution.align.scores.Scores, double)">NucleotideScores(Scores, double)</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/NucleotideState.html" title="class in jebl.evolution.sequences"><span class="strong">NucleotideState</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><a href="./jebl/util/NumberFormatter.html" title="class in jebl.util"><span class="strong">NumberFormatter</span></a> - Class in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd>
<div class="block">An interface for a numerical column in a log.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/NumberFormatter.html#NumberFormatter(int)">NumberFormatter(int)</a></span> - Constructor for class jebl.util.<a href="./jebl/util/NumberFormatter.html" title="class in jebl.util">NumberFormatter</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/NumericalDerivative.html" title="class in jebl.math"><span class="strong">NumericalDerivative</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">approximates numerically the first and second derivatives of a
function of a single variable and approximates gradient and
diagonal of Hessian for multivariate functions</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/NumericalDerivative.html#NumericalDerivative()">NumericalDerivative()</a></span> - Constructor for class jebl.math.<a href="./jebl/math/NumericalDerivative.html" title="class in jebl.math">NumericalDerivative</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#numFun">numFun</a></span> - Variable in class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd>
<div class="block">total number of function evaluations necessary</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#numFun">numFun</a></span> - Variable in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">total number of function evaluations neccessary</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#numFuncStops">numFuncStops</a></span> - Variable in class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd>
<div class="block">numFuncStops is the number of consecutive positive
evaluations of the stop criterion based on function evaluation
necessary to cause the abortion of the optimization
(default is 4)</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#numRateBoxes">numRateBoxes</a></span> - Variable in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#numTimeBoxes">numTimeBoxes</a></span> - Variable in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
</dl>
<a name="_O_">
<!-- -->
</a>
<h2 class="title">O</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#O_STATE">O_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/SimpleListener.html#objectChanged()">objectChanged()</a></span> - Method in interface jebl.util.<a href="./jebl/util/SimpleListener.html" title="interface in jebl.util">SimpleListener</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/OldNeedlemanWunschAffine.html" title="class in jebl.evolution.align"><span class="strong">OldNeedlemanWunschAffine</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/OldNeedlemanWunschAffine.html#OldNeedlemanWunschAffine(jebl.evolution.align.scores.Scores, float, float)">OldNeedlemanWunschAffine(Scores, float, float)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/OldNeedlemanWunschAffine.html" title="class in jebl.evolution.align">OldNeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#optimize(jebl.math.MultivariateFunction, double[], double, double)">optimize(MultivariateFunction, double[], double, double)</a></span> - Method in class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd>
<div class="block">The actual optimization routine
(needs to be implemented in a subclass of MultivariateMinimum).</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#optimize(jebl.math.MultivariateFunction, double[], double, double, jebl.math.MinimiserMonitor)">optimize(MultivariateFunction, double[], double, double, MinimiserMonitor)</a></span> - Method in class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd>
<div class="block">The actual optimization routine
It finds a minimum close to vector x when the
absolute tolerance for each parameter is specified.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalSearch.html#optimize(jebl.math.MultivariateFunction, double[], double, double)">optimize(MultivariateFunction, double[], double, double)</a></span> - Method in class jebl.math.<a href="./jebl/math/OrthogonalSearch.html" title="class in jebl.math">OrthogonalSearch</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalSearch.html#optimize(jebl.math.MultivariateFunction, double[], double, double, jebl.math.MinimiserMonitor)">optimize(MultivariateFunction, double[], double, double, MinimiserMonitor)</a></span> - Method in class jebl.math.<a href="./jebl/math/OrthogonalSearch.html" title="class in jebl.math">OrthogonalSearch</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#optimize(jebl.math.UnivariateFunction, double, double, double)">optimize(UnivariateFunction, double, double, double)</a></span> - Method in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">The actual optimization routine (Brent's golden section method)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#optimize(jebl.math.UnivariateFunction, double)">optimize(UnivariateFunction, double)</a></span> - Method in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">The actual optimization routine (Brent's golden section method)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#optimize(double, jebl.math.UnivariateFunction, double, double, double)">optimize(double, UnivariateFunction, double, double, double)</a></span> - Method in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">The actual optimization routine (Brent's golden section method)</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#optimize(double, jebl.math.UnivariateFunction, double)">optimize(double, UnivariateFunction, double)</a></span> - Method in class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd>
<div class="block">The actual optimization routine (Brent's golden section method)</div>
</dd>
<dt><a href="./jebl/math/OrderEnumerator.html" title="interface in jebl.math"><span class="strong">OrderEnumerator</span></a> - Interface in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">A means for describing odering information, and Utilities for creating such Orderings</div>
</dd>
<dt><a href="./jebl/math/OrderEnumerator.OEFactory.html" title="interface in jebl.math"><span class="strong">OrderEnumerator.OEFactory</span></a> - Interface in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/OrderEnumerator.Utils.html" title="class in jebl.math"><span class="strong">OrderEnumerator.Utils</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/OrthogonalHints.html" title="interface in jebl.math"><span class="strong">OrthogonalHints</span></a> - Interface in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum)
hints about the function that may alow it to optimise better.</div>
</dd>
<dt><a href="./jebl/math/OrthogonalHints.Utils.html" title="class in jebl.math"><span class="strong">OrthogonalHints.Utils</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/OrthogonalLineFunction.html" title="class in jebl.math"><span class="strong">OrthogonalLineFunction</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">converts a multivariate function into a univariate function
by keeping all but one argument constant</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalLineFunction.html#OrthogonalLineFunction(jebl.math.MultivariateFunction)">OrthogonalLineFunction(MultivariateFunction)</a></span> - Constructor for class jebl.math.<a href="./jebl/math/OrthogonalLineFunction.html" title="class in jebl.math">OrthogonalLineFunction</a></dt>
<dd>
<div class="block">construct univariate function from multivariate function</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalLineFunction.html#OrthogonalLineFunction(jebl.math.MultivariateFunction, int, double[])">OrthogonalLineFunction(MultivariateFunction, int, double[])</a></span> - Constructor for class jebl.math.<a href="./jebl/math/OrthogonalLineFunction.html" title="class in jebl.math">OrthogonalLineFunction</a></dt>
<dd>
<div class="block">construct univariate function from multivariate function</div>
</dd>
<dt><a href="./jebl/math/OrthogonalSearch.html" title="class in jebl.math"><span class="strong">OrthogonalSearch</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">minimization of a real-valued function of
several variables without using derivatives, using the simple
strategy of optimizing variables one by one.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalSearch.html#OrthogonalSearch()">OrthogonalSearch()</a></span> - Constructor for class jebl.math.<a href="./jebl/math/OrthogonalSearch.html" title="class in jebl.math">OrthogonalSearch</a></dt>
<dd>
<div class="block">Initialization</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalSearch.html#OrthogonalSearch(boolean)">OrthogonalSearch(boolean)</a></span> - Constructor for class jebl.math.<a href="./jebl/math/OrthogonalSearch.html" title="class in jebl.math">OrthogonalSearch</a></dt>
<dd>
<div class="block">Initialization</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalSearch.html#OrthogonalSearch(jebl.math.OrderEnumerator.OEFactory)">OrthogonalSearch(OrderEnumerator.OEFactory)</a></span> - Constructor for class jebl.math.<a href="./jebl/math/OrthogonalSearch.html" title="class in jebl.math">OrthogonalSearch</a></dt>
<dd>
<div class="block">Initialization</div>
</dd>
<dt><a href="./jebl/evolution/align/Output.html" title="class in jebl.evolution.align"><span class="strong">Output</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Output.html#Output()">Output()</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/Output.html" title="class in jebl.evolution.align">Output</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/OverlapAlign.html" title="class in jebl.evolution.align"><span class="strong">OverlapAlign</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/OverlapAlign.html#OverlapAlign(jebl.evolution.align.scores.Scores, float)">OverlapAlign(Scores, float)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/OverlapAlign.html" title="class in jebl.evolution.align">OverlapAlign</a></dt>
<dd> </dd>
</dl>
<a name="_P_">
<!-- -->
</a>
<h2 class="title">P</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#P_STATE">P_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/PairwiseAligner.html" title="interface in jebl.evolution.align"><span class="strong">PairwiseAligner</span></a> - Interface in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/PairwiseAligner.Result.html" title="class in jebl.evolution.align"><span class="strong">PairwiseAligner.Result</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam100.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam100</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam100.html#Pam100()">Pam100()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam100.html" title="class in jebl.evolution.align.scores">Pam100</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam110.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam110</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam110.html#Pam110()">Pam110()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam110.html" title="class in jebl.evolution.align.scores">Pam110</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam120.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam120</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam120.html#Pam120()">Pam120()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam120.html" title="class in jebl.evolution.align.scores">Pam120</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam130.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam130</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam130.html#Pam130()">Pam130()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam130.html" title="class in jebl.evolution.align.scores">Pam130</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam140.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam140</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam140.html#Pam140()">Pam140()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam140.html" title="class in jebl.evolution.align.scores">Pam140</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam150.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam150</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam150.html#Pam150()">Pam150()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam150.html" title="class in jebl.evolution.align.scores">Pam150</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam160.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam160</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam160.html#Pam160()">Pam160()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam160.html" title="class in jebl.evolution.align.scores">Pam160</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam170.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam170</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam170.html#Pam170()">Pam170()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam170.html" title="class in jebl.evolution.align.scores">Pam170</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam180.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam180</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam180.html#Pam180()">Pam180()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam180.html" title="class in jebl.evolution.align.scores">Pam180</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam190.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam190</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam190.html#Pam190()">Pam190()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam190.html" title="class in jebl.evolution.align.scores">Pam190</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam200.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam200</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam200.html#Pam200()">Pam200()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam200.html" title="class in jebl.evolution.align.scores">Pam200</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam210.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam210</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam210.html#Pam210()">Pam210()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam210.html" title="class in jebl.evolution.align.scores">Pam210</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam220.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam220</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam220.html#Pam220()">Pam220()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam220.html" title="class in jebl.evolution.align.scores">Pam220</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam230.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam230</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam230.html#Pam230()">Pam230()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam230.html" title="class in jebl.evolution.align.scores">Pam230</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam240.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam240</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam240.html#Pam240()">Pam240()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam240.html" title="class in jebl.evolution.align.scores">Pam240</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Pam250.html" title="class in jebl.evolution.align.scores"><span class="strong">Pam250</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Pam250.html#Pam250()">Pam250()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Pam250.html" title="class in jebl.evolution.align.scores">Pam250</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_100">PAM_100</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_110">PAM_110</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_120">PAM_120</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_130">PAM_130</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_140">PAM_140</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_150">PAM_150</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_160">PAM_160</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_170">PAM_170</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_180">PAM_180</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_190">PAM_190</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_200">PAM_200</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_210">PAM_210</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_220">PAM_220</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_230">PAM_230</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_240">PAM_240</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#PAM_250">PAM_250</a></span> - Static variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#parseCharactersBlock(java.util.List)">parseCharactersBlock(List<Taxon>)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Parse the next 'CHARACTERS' block encountered in the input.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#parseDataBlock(java.util.List)">parseDataBlock(List<Taxon>)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Parse the next 'DATA' block encountered in the input.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#parseDistancesBlock(java.util.List)">parseDistancesBlock(List<Taxon>)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Parse the next 'DISTANCES' block encountered in the input.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#parseTaxaBlock()">parseTaxaBlock()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Parse the next 'TAXA' block encountered in the input.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#parseTreesBlock(java.util.List)">parseTreesBlock(List<Taxon>)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Parse the next 'TREES' block encountered in the input.</div>
</dd>
<dt><a href="./jebl/evolution/parsimony/ParsimonyCriterion.html" title="interface in jebl.evolution.parsimony"><span class="strong">ParsimonyCriterion</span></a> - Interface in <a href="./jebl/evolution/parsimony/package-summary.html">jebl.evolution.parsimony</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/alignments/Pattern.html" title="interface in jebl.evolution.alignments"><span class="strong">Pattern</span></a> - Interface in <a href="./jebl/evolution/alignments/package-summary.html">jebl.evolution.alignments</a></dt>
<dd>
<div class="block">An interface representing a list of states for a list of taxa
(e.g.</div>
</dd>
<dt><a href="./jebl/evolution/alignments/Patterns.html" title="interface in jebl.evolution.alignments"><span class="strong">Patterns</span></a> - Interface in <a href="./jebl/evolution/alignments/package-summary.html">jebl.evolution.alignments</a></dt>
<dd>
<div class="block">An interface representing a set of site patterns.</div>
</dd>
<dt><a href="./jebl/evolution/io/PHYLIPExporter.html" title="class in jebl.evolution.io"><span class="strong">PHYLIPExporter</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Export alignment to Phylip format.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/PHYLIPExporter.html#PHYLIPExporter(java.io.Writer)">PHYLIPExporter(Writer)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/PHYLIPExporter.html" title="class in jebl.evolution.io">PHYLIPExporter</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/PhylipSequentialImporter.html" title="class in jebl.evolution.io"><span class="strong">PhylipSequentialImporter</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Class for importing PHYLIP sequential file format</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/PhylipSequentialImporter.html#PhylipSequentialImporter(java.io.Reader, jebl.evolution.sequences.SequenceType, int)">PhylipSequentialImporter(Reader, SequenceType, int)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/PhylipSequentialImporter.html" title="class in jebl.evolution.io">PhylipSequentialImporter</a></dt>
<dd>
<div class="block">Constructor</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#possiblyEqual(jebl.evolution.sequences.State)">possiblyEqual(State)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#prepareAlignment(java.lang.String, java.lang.String)">prepareAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd>
<div class="block">Initialises the matrices for the alignment.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschAffine.html#prepareAlignment(java.lang.String, java.lang.String)">prepareAlignment(String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschAffine.html" title="class in jebl.evolution.align">NeedlemanWunschAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Output.html#print(java.lang.String)">print(String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Output.html" title="class in jebl.evolution.align">Output</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#print()">print()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SystemOut.html#print(java.lang.String)">print(String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SystemOut.html" title="class in jebl.evolution.align">SystemOut</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#printf(jebl.evolution.align.Output)">printf(Output)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd>
<div class="block">Print the matrix (matrices) used to compute the alignment</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html#printf(jebl.evolution.align.Output)">printf(Output)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html" title="class in jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt>
<dd>
<div class="block">Print matrix used to calculate this alignment.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Output.html#println(java.lang.String)">println(String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Output.html" title="class in jebl.evolution.align">Output</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Output.html#println()">println()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Output.html" title="class in jebl.evolution.align">Output</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SystemOut.html#println(java.lang.String)">println(String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SystemOut.html" title="class in jebl.evolution.align">SystemOut</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SystemOut.html#println()">println()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SystemOut.html" title="class in jebl.evolution.align">SystemOut</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align"><span class="strong">ProfileCharacter</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#ProfileCharacter(int)">ProfileCharacter(int)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><a href="./jebl/util/ProgressListener.html" title="class in jebl.util"><span class="strong">ProgressListener</span></a> - Class in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#ProgressListener()">ProgressListener()</a></span> - Constructor for class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd> </dd>
<dt><a href="./jebl/util/ProgressListener.Wrapper.html" title="class in jebl.util"><span class="strong">ProgressListener.Wrapper</span></a> - Class in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd>
<div class="block">A decorator progress listener which delegates all method calls to an internal progress listener.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.Wrapper.html#ProgressListener.Wrapper(jebl.util.ProgressListener)">ProgressListener.Wrapper(ProgressListener)</a></span> - Constructor for class jebl.util.<a href="./jebl/util/ProgressListener.Wrapper.html" title="class in jebl.util">ProgressListener.Wrapper</a></dt>
<dd> </dd>
</dl>
<a name="_Q_">
<!-- -->
</a>
<h2 class="title">Q</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#Q_STATE">Q_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
</dl>
<a name="_R_">
<!-- -->
</a>
<h2 class="title">R</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#R_STATE">R_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#R_STATE">R_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><a href="./jebl/math/Random.html" title="class in jebl.math"><span class="strong">Random</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">Random number generation.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#randomChoice(double[])">randomChoice(double[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CalculateSplitRates.html#RATE">RATE</a></span> - Variable in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CalculateSplitRates.html" title="class in jebl.evolution.trees">CalculateSplitRates</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/substmodel/RateMatrix.html" title="interface in jebl.evolution.substmodel"><span class="strong">RateMatrix</span></a> - Interface in <a href="./jebl/evolution/substmodel/package-summary.html">jebl.evolution.substmodel</a></dt>
<dd>
<div class="block">abstract base class for all rate matrices</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#read()">read()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">All read attempts pass through this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readCharacter()">readCharacter()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readDouble()">readDouble()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Attempts to read and parse a double delimited by whitespace.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readDouble(java.lang.String)">readDouble(String)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Attempts to read and parse a double delimited by whitespace or by
any character in delimiters.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readInteger()">readInteger()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Attempts to read and parse an integer delimited by whitespace.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readInteger(java.lang.String)">readInteger(String)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Attempts to read and parse an integer delimited by whitespace or by
any character in delimiters.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readLine()">readLine()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Reads a line, skipping over any comments.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readSequence(java.lang.StringBuilder, jebl.evolution.sequences.SequenceType, java.lang.String, int, java.lang.String, java.lang.String, java.lang.String, java.lang.String)">readSequence(StringBuilder, SequenceType, String, int, String, String, String, String)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readSequence(java.lang.StringBuilder, jebl.evolution.sequences.SequenceType, java.lang.String, int, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean)">readSequence(StringBuilder, SequenceType, String, int, String, String, String, String, boolean)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readSequence(java.lang.StringBuilder, jebl.evolution.sequences.SequenceType, java.lang.String, int, java.lang.String, java.lang.String, java.lang.String, java.lang.String, jebl.util.ProgressListener)">readSequence(StringBuilder, SequenceType, String, int, String, String, String, String, ProgressListener)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readSequence(java.lang.StringBuilder, jebl.evolution.sequences.SequenceType, java.lang.String, int, java.lang.String, java.lang.String, java.lang.String, java.lang.String, jebl.util.ProgressListener, boolean)">readSequence(StringBuilder, SequenceType, String, int, String, String, String, String, ProgressListener, boolean)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Reads sequence, skipping over any comments and filtering using sequenceType.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceTester.html#readSequence(java.lang.String)">readSequence(String)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceTester.html" title="class in jebl.evolution.sequences">SequenceTester</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readSequenceLine(java.lang.StringBuffer, jebl.evolution.sequences.SequenceType, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String)">readSequenceLine(StringBuffer, SequenceType, String, String, String, String, String)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Reads a line of sequence, skipping over any comments and filtering using sequenceType.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readToken()">readToken()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Reads a token stopping when any whitespace or a comment is found.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#readToken(java.lang.String)">readToken(String)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Reads a token stopping when any whitespace, a comment or when any character
in delimiters is found.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#rebuild()">rebuild()</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html#recurseAlignment(java.lang.String, int)">recurseAlignment(String, int)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NonOverlapMultipleLocalAffine.html" title="class in jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#refineNode(jebl.evolution.graphs.Node, int[])">refineNode(Node, int[])</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseEdge.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseEdge.html" title="class in jebl.evolution.trees">BaseEdge</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseNode.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseNode.html" title="class in jebl.evolution.trees">BaseNode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Attributable.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in interface jebl.util.<a href="./jebl/util/Attributable.html" title="interface in jebl.util">Attributable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/AttributableHelper.html#removeAttribute(java.lang.String)">removeAttribute(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/AttributableHelper.html" title="class in jebl.util">AttributableHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#removeFeedbackAction(java.lang.String)">removeFeedbackAction(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#removeFeedbackAction(java.lang.String)">removeFeedbackAction(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">Removes a feedback action previously added using
<a href="./jebl/util/ProgressListener.html#addFeedbackAction(java.lang.String, jebl.util.SimpleListener)"><code>ProgressListener.addFeedbackAction(String, jebl.util.SimpleListener)</code></a>.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.Wrapper.html#removeFeedbackAction(java.lang.String)">removeFeedbackAction(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.Wrapper.html" title="class in jebl.util">ProgressListener.Wrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#removeInternalNode(jebl.evolution.graphs.Node)">removeInternalNode(Node)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">Remove internal node.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#removeProfileCharacter(jebl.evolution.align.ProfileCharacter)">removeProfileCharacter(ProfileCharacter)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/aligners/Aligner.html#removeProgressListener(jebl.util.ProgressListener)">removeProgressListener(ProgressListener)</a></span> - Method in interface jebl.evolution.aligners.<a href="./jebl/evolution/aligners/Aligner.html" title="interface in jebl.evolution.aligners">Aligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ClusteringTreeBuilder.html#removeProgressListener(jebl.util.ProgressListener)">removeProgressListener(ProgressListener)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ClusteringTreeBuilder.html" title="class in jebl.evolution.trees">ClusteringTreeBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ConsensusTreeBuilder.html#removeProgressListener(jebl.util.ProgressListener)">removeProgressListener(ProgressListener)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/ConsensusTreeBuilder.html" title="class in jebl.evolution.trees">ConsensusTreeBuilder</a></dt>
<dd>
<div class="block">Stops a ProgressListener from receiving progress.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilder.html#removeProgressListener(jebl.util.ProgressListener)">removeProgressListener(ProgressListener)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilder.html" title="interface in jebl.evolution.trees">TreeBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#renameTaxa(jebl.evolution.taxa.Taxon, jebl.evolution.taxa.Taxon)">renameTaxa(Taxon, Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#renameTaxa(jebl.evolution.taxa.Taxon, jebl.evolution.taxa.Taxon)">renameTaxa(Taxon, Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#renameTaxa(jebl.evolution.taxa.Taxon, jebl.evolution.taxa.Taxon)">renameTaxa(Taxon, Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#renameTaxa(jebl.evolution.taxa.Taxon, jebl.evolution.taxa.Taxon)">renameTaxa(Taxon, Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#renameTaxa(jebl.evolution.taxa.Taxon, jebl.evolution.taxa.Taxon)">renameTaxa(Taxon, Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#renameTaxa(jebl.evolution.taxa.Taxon, jebl.evolution.taxa.Taxon)">renameTaxa(Taxon, Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#renameTaxa(jebl.evolution.taxa.Taxon, jebl.evolution.taxa.Taxon)">renameTaxa(Taxon, Taxon)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Tree.html#renameTaxa(jebl.evolution.taxa.Taxon, jebl.evolution.taxa.Taxon)">renameTaxa(Taxon, Taxon)</a></span> - Method in interface jebl.evolution.trees.<a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/ReRootedTree.html" title="class in jebl.evolution.trees"><span class="strong">ReRootedTree</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ReRootedTree.html#ReRootedTree(jebl.evolution.trees.RootedTree, jebl.evolution.trees.ReRootedTree.RootingType)">ReRootedTree(RootedTree, ReRootedTree.RootingType)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/ReRootedTree.html" title="class in jebl.evolution.trees">ReRootedTree</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/ReRootedTree.RootingType.html" title="enum in jebl.evolution.trees"><span class="strong">ReRootedTree.RootingType</span></a> - Enum in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#reRootWithOutgroup(jebl.evolution.graphs.Node, java.util.Set)">reRootWithOutgroup(Node, Set<String>)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd>
<div class="block">Re-root tree using an outgroup.</div>
</dd>
<dt><a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments"><span class="strong">ResampledAlignment</span></a> - Class in <a href="./jebl/evolution/alignments/package-summary.html">jebl.evolution.alignments</a></dt>
<dd>
<div class="block">Date: 17/01/2006
Time: 08:08:44</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ResampledAlignment.html#ResampledAlignment()">ResampledAlignment()</a></span> - Constructor for class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ResampledAlignment.html" title="class in jebl.evolution.alignments">ResampledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrderEnumerator.html#reset()">reset()</a></span> - Method in interface jebl.math.<a href="./jebl/math/OrderEnumerator.html" title="interface in jebl.math">OrderEnumerator</a></dt>
<dd>
<div class="block">Reset back to starting state, may have a differnet number of values, and a different ordering after a reset!</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Intervals.html#resetEvents()">resetEvents()</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Intervals.html" title="class in jebl.evolution.coalescent">Intervals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#reverse(jebl.evolution.sequences.State[])">reverse(State[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#reverseComplement(java.lang.String)">reverseComplement(String)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#reverseComplement(jebl.evolution.sequences.NucleotideState[])">reverseComplement(NucleotideState[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#reverseComplementWithGaps(java.lang.String)">reverseComplementWithGaps(String)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#reverseMatrix(double[][])">reverseMatrix(double[][])</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">reverse a matrix</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#reverseVector(double[])">reverseVector(double[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">reverse a vector</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#rightNb(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">rightNb(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd>
<div class="block">Right Neighbour of a tip (taxon).</div>
</dd>
<dt><a href="./jebl/evolution/treemetrics/RobinsonsFouldMetric.html" title="class in jebl.evolution.treemetrics"><span class="strong">RobinsonsFouldMetric</span></a> - Class in <a href="./jebl/evolution/treemetrics/package-summary.html">jebl.evolution.treemetrics</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treemetrics/RobinsonsFouldMetric.html#RobinsonsFouldMetric()">RobinsonsFouldMetric()</a></span> - Constructor for class jebl.evolution.treemetrics.<a href="./jebl/evolution/treemetrics/RobinsonsFouldMetric.html" title="class in jebl.evolution.treemetrics">RobinsonsFouldMetric</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treemetrics/RobinsonsFouldMetric.html#RobinsonsFouldMetric(java.util.List)">RobinsonsFouldMetric(List<Taxon>)</a></span> - Constructor for class jebl.evolution.treemetrics.<a href="./jebl/evolution/treemetrics/RobinsonsFouldMetric.html" title="class in jebl.evolution.treemetrics">RobinsonsFouldMetric</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees"><span class="strong">RootedFromUnrooted</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Root an unrooted tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#RootedFromUnrooted(jebl.evolution.trees.Tree, jebl.evolution.graphs.Node, boolean)">RootedFromUnrooted(Tree, Node, boolean)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd>
<div class="block">Root tree at some internal node.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#RootedFromUnrooted(jebl.evolution.trees.Tree, jebl.evolution.graphs.Node, jebl.evolution.graphs.Node, double)">RootedFromUnrooted(Tree, Node, Node, double)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd>
<div class="block">Root source by creating a new internal node whose children are (the adjacent) left and right.</div>
</dd>
<dt><a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees"><span class="strong">RootedSubtree</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A simple, immutable rooted tree implementation that is a subtree of an existing tree
subtending a specified set of taxa..</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#RootedSubtree(jebl.evolution.trees.RootedTree, java.util.Set)">RootedSubtree(RootedTree, Set<Taxon>)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd>
<div class="block">Make a copy of the given rooted tree</div>
</dd>
<dt><a href="./jebl/evolution/trees/RootedTree.html" title="interface in jebl.evolution.trees"><span class="strong">RootedTree</span></a> - Interface in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A tree with a root (node with maximum height).</div>
</dd>
<dt><a href="./jebl/evolution/treemetrics/RootedTreeMetric.html" title="interface in jebl.evolution.treemetrics"><span class="strong">RootedTreeMetric</span></a> - Interface in <a href="./jebl/evolution/treemetrics/package-summary.html">jebl.evolution.treemetrics</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees"><span class="strong">RootedTreeUtils</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Static utility functions for rooted trees.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#rootTheTree(jebl.evolution.trees.Tree)">rootTheTree(Tree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd>
<div class="block">Return a rooted tree from any tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#rootTreeAtCenter(jebl.evolution.trees.Tree)">rootTreeAtCenter(Tree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd>
<div class="block">Root any tree by locating the "center" of tree and adding a new root node at that point
<p/>
for any point on the tree x let D(x) = Max{distance between x and t : for all tips t}
The "center" c is the point with the smallest distance, i.e.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#roundDouble(double, int)">roundDouble(double, int)</a></span> - Static method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
</dl>
<a name="_S_">
<!-- -->
</a>
<h2 class="title">S</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#S_STATE">S_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#S_STATE">S_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#safeNodeHeight(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">safeNodeHeight(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MachineAccuracy.html#same(double, double)">same(double, double)</a></span> - Static method in class jebl.math.<a href="./jebl/math/MachineAccuracy.html" title="class in jebl.math">MachineAccuracy</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#scale(double)">scale(double)</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/PairwiseAligner.Result.html#score">score</a></span> - Variable in class jebl.evolution.align.<a href="./jebl/evolution/align/PairwiseAligner.Result.html" title="class in jebl.evolution.align">PairwiseAligner.Result</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#score(jebl.evolution.align.ProfileCharacter, jebl.evolution.align.ProfileCharacter, jebl.evolution.align.scores.Scores)">score(ProfileCharacter, ProfileCharacter, Scores)</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Scores.html#score">score</a></span> - Variable in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Scores.html" title="class in jebl.evolution.align.scores">Scores</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/ScoreMatrix.html" title="interface in jebl.evolution.align.scores"><span class="strong">ScoreMatrix</span></a> - Interface in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/Scores.html" title="class in jebl.evolution.align.scores"><span class="strong">Scores</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd>
<div class="block">Base class for all score matrices in the package.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Scores.html#Scores()">Scores()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Scores.html" title="class in jebl.evolution.align.scores">Scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#scoreSelf(jebl.evolution.align.ProfileCharacter, jebl.evolution.align.scores.Scores)">scoreSelf(ProfileCharacter, Scores)</a></span> - Static method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores"><span class="strong">ScoresFactory</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/ScoresFactory.html#ScoresFactory()">ScoresFactory()</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/ScoresFactory.html" title="class in jebl.evolution.align.scores">ScoresFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/HashPair.html#second">second</a></span> - Variable in class jebl.util.<a href="./jebl/util/HashPair.html" title="class in jebl.util">HashPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/NumericalDerivative.html#secondDerivative(jebl.math.UnivariateFunction, double)">secondDerivative(UnivariateFunction, double)</a></span> - Static method in class jebl.math.<a href="./jebl/math/NumericalDerivative.html" title="class in jebl.math">NumericalDerivative</a></dt>
<dd>
<div class="block">determine second derivative</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalLineFunction.html#selectArgument(int)">selectArgument(int)</a></span> - Method in class jebl.math.<a href="./jebl/math/OrthogonalLineFunction.html" title="class in jebl.math">OrthogonalLineFunction</a></dt>
<dd>
<div class="block">use only the specified argument in the
constructed univariate function
and keep all others constant</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeChangeListener.html#selectionChanged(jebl.evolution.trees.TreeSelectionChangeEvent)">selectionChanged(TreeSelectionChangeEvent)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeChangeListener.html" title="class in jebl.evolution.trees">TreeChangeListener</a></dt>
<dd>
<div class="block">The selected nodes in the tree have changed.</div>
</dd>
<dt><a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences"><span class="strong">Sequence</span></a> - Interface in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd>
<div class="block">A biomolecular sequence.</div>
</dd>
<dt><a href="./jebl/evolution/align/SequenceAlignmentsDistanceMatrix.html" title="class in jebl.evolution.align"><span class="strong">SequenceAlignmentsDistanceMatrix</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd>
<div class="block">Builds a distance matrix by performing a series of pairwise alignments between the
specified sequences (unlike the methods in jebl.evolution.distances, which
extract the pairwise distances from a multiple sequence alignment).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SequenceAlignmentsDistanceMatrix.html#SequenceAlignmentsDistanceMatrix(java.util.List, jebl.evolution.align.PairwiseAligner, jebl.util.ProgressListener)">SequenceAlignmentsDistanceMatrix(List<Sequence>, PairwiseAligner, ProgressListener)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/SequenceAlignmentsDistanceMatrix.html" title="class in jebl.evolution.align">SequenceAlignmentsDistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SequenceAlignmentsDistanceMatrix.html#SequenceAlignmentsDistanceMatrix(java.util.List, jebl.evolution.align.PairwiseAligner, jebl.util.ProgressListener, jebl.evolution.trees.TreeBuilderFactory.DistanceModel)">SequenceAlignmentsDistanceMatrix(List<Sequence>, PairwiseAligner, ProgressListener, TreeBuilderFactory.DistanceModel)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/SequenceAlignmentsDistanceMatrix.html" title="class in jebl.evolution.align">SequenceAlignmentsDistanceMatrix</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/SequenceExporter.html" title="interface in jebl.evolution.io"><span class="strong">SequenceExporter</span></a> - Interface in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/SequenceImporter.html" title="interface in jebl.evolution.io"><span class="strong">SequenceImporter</span></a> - Interface in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Interface for importers that do sequences</div>
</dd>
<dt><a href="./jebl/evolution/sequences/Sequences.html" title="interface in jebl.evolution.sequences"><span class="strong">Sequences</span></a> - Interface in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd>
<div class="block">A set of sequence objects.</div>
</dd>
<dt><a href="./jebl/evolution/align/SequenceShuffler.html" title="class in jebl.evolution.align"><span class="strong">SequenceShuffler</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd>
<div class="block">Shuffles a sequence and aligns it again multiple times to give mean and variance of
alignments on random sequences.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SequenceShuffler.html#SequenceShuffler()">SequenceShuffler()</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/SequenceShuffler.html" title="class in jebl.evolution.align">SequenceShuffler</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/SequenceStateException.html" title="class in jebl.evolution.sequences"><span class="strong">SequenceStateException</span></a> - Exception in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceStateException.html#SequenceStateException(java.lang.String)">SequenceStateException(String)</a></span> - Constructor for exception jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceStateException.html" title="class in jebl.evolution.sequences">SequenceStateException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/SequenceTester.html" title="class in jebl.evolution.sequences"><span class="strong">SequenceTester</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceTester.html#SequenceTester()">SequenceTester()</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceTester.html" title="class in jebl.evolution.sequences">SequenceTester</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences"><span class="strong">SequenceType</span></a> - Interface in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd>
<div class="block">Interface for sequences data types.</div>
</dd>
<dt><a href="./jebl/evolution/sequences/SequenceType.Utils.html" title="class in jebl.evolution.sequences"><span class="strong">SequenceType.Utils</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#set(int)">set(int)</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalLineFunction.html#setAllArguments(double[])">setAllArguments(double[])</a></span> - Method in class jebl.math.<a href="./jebl/math/OrthogonalLineFunction.html" title="class in jebl.math">OrthogonalLineFunction</a></dt>
<dd>
<div class="block">set (change) values of all arguments (start values)</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#setArgument(int, double)">setArgument(int, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#setArgument(int, double)">setArgument(int, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#setArgument(int, double)">setArgument(int, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.html#setArgument(int, double)">setArgument(int, double)</a></span> - Method in interface jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.html" title="interface in jebl.evolution.coalescent">DemographicFunction</a></dt>
<dd>
<div class="block">Sets the value of the nth argument of this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html#setArgument(int, double)">setArgument(int, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/EmpiricalDemographicFunction.html" title="class in jebl.evolution.coalescent">EmpiricalDemographicFunction</a></dt>
<dd>
<div class="block">Sets the value of the nth argument of this function.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#setArgument(int, double)">setArgument(int, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#setArgument(int, double)">setArgument(int, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#setArgument(int, double)">setArgument(int, double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalLineFunction.html#setArgument(double)">setArgument(double)</a></span> - Method in class jebl.math.<a href="./jebl/math/OrthogonalLineFunction.html" title="class in jebl.math">OrthogonalLineFunction</a></dt>
<dd>
<div class="block">set (change) value of a single argument
(the one currently active)</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/alignments/ConsensusSequence.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.alignments.<a href="./jebl/evolution/alignments/ConsensusSequence.html" title="class in jebl.evolution.alignments">ConsensusSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseEdge.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseEdge.html" title="class in jebl.evolution.trees">BaseEdge</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/BaseNode.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/BaseNode.html" title="class in jebl.evolution.trees">BaseNode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/FilteredRootedTree.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/FilteredRootedTree.html" title="class in jebl.evolution.trees">FilteredRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedFromUnrooted.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedFromUnrooted.html" title="class in jebl.evolution.trees">RootedFromUnrooted</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Attributable.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in interface jebl.util.<a href="./jebl/util/Attributable.html" title="interface in jebl.util">Attributable</a></dt>
<dd>
<div class="block">Sets an named attribute for this object.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/AttributableHelper.html#setAttribute(java.lang.String, java.lang.Object)">setAttribute(String, Object)</a></span> - Method in class jebl.util.<a href="./jebl/util/AttributableHelper.html" title="class in jebl.util">AttributableHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#setCataclysmTime(double)">setCataclysmTime(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#setCommentDelimiters(char)">setCommentDelimiters(char)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#setCommentDelimiters(char, char)">setCommentDelimiters(char, char)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#setCommentDelimiters(char, char, char)">setCommentDelimiters(char, char, char)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#setCommentDelimiters(char, char, char, char, char)">setCommentDelimiters(char, char, char, char, char)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#setCommentWriter(java.io.Writer)">setCommentWriter(Writer)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#setComplete()">setComplete()</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/CompactRootedTree.html#setConceptuallyUnrooted(boolean)">setConceptuallyUnrooted(boolean)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/CompactRootedTree.html" title="class in jebl.evolution.trees">CompactRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#setConceptuallyUnrooted(boolean)">setConceptuallyUnrooted(boolean)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#setConceptuallyUnrooted(boolean)">setConceptuallyUnrooted(boolean)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#setConceptuallyUnrooted(boolean)">setConceptuallyUnrooted(boolean)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#setDebug(boolean)">setDebug(boolean)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/NumberFormatter.html#setDecimalPlaces(int)">setDecimalPlaces(int)</a></span> - Method in class jebl.util.<a href="./jebl/util/NumberFormatter.html" title="class in jebl.util">NumberFormatter</a></dt>
<dd>
<div class="block">Set the number of decimal places to display when formatted.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#setDeclineRate(double)">setDeclineRate(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd>
<div class="block">sets the decline rate.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/Character.html#setDesc(java.lang.String)">setDesc(String)</a></span> - Method in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/Character.html" title="interface in jebl.evolution.characters">Character</a></dt>
<dd>
<div class="block">set the description of the character</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#setDesc(java.lang.String)">setDesc(String)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#setDesc(java.lang.String)">setDesc(String)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#setDistance(double)">setDistance(double)</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd>
<div class="block">Sets the distance (such as time/branch length) used when calculating
the probabilities.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/MatrixExponential.html#setDistance(double)">setDistance(double)</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/MatrixExponential.html" title="class in jebl.evolution.substmodel">MatrixExponential</a></dt>
<dd>
<div class="block">compute transition probabilities for a expected distance
using the prespecified rate matrix</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/RateMatrix.html#setDistance(double)">setDistance(double)</a></span> - Method in interface jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/RateMatrix.html" title="interface in jebl.evolution.substmodel">RateMatrix</a></dt>
<dd>
<div class="block">Sets the distance (such as time/branch length) used when calculating
the probabilities.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#setDistanceTranspose(double)">setDistanceTranspose(double)</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd>
<div class="block">Sets the distance (such as time/branch length) used when calculating
the probabilities.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/MatrixExponential.html#setDistanceTranspose(double)">setDistanceTranspose(double)</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/MatrixExponential.html" title="class in jebl.evolution.substmodel">MatrixExponential</a></dt>
<dd>
<div class="block">compute transition probabilities for a expected distance
using the prespecified rate matrix.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#setDoublingTime(double)">setDoublingTime(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd>
<div class="block">An alternative parameterization of this model.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#setEdgeLength(jebl.evolution.graphs.Node, jebl.evolution.graphs.Node, double)">setEdgeLength(Node, Node, double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">Set edge distance between two adjacent nodes.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#setEdgeLength(jebl.evolution.graphs.Edge, double)">setEdgeLength(Edge, double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">Change length of an existing edge.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#setExpectedInputLength(long)">setExpectedInputLength(long)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#setGapOpen(float)">setGapOpen(float)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialGrowth.html#setGrowthRate(double)">setGrowthRate(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialGrowth.html" title="class in jebl.evolution.coalescent">ExponentialGrowth</a></dt>
<dd>
<div class="block">sets growth rate.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#setHeight(jebl.evolution.graphs.Node, double)">setHeight(Node, double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#setHeight(jebl.evolution.graphs.Node, double)">setHeight(Node, double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#setHeight(jebl.evolution.graphs.Node, double)">setHeight(Node, double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalSearch.html#setIgnoreNonMinimalUnivariateMinimisations(boolean)">setIgnoreNonMinimalUnivariateMinimisations(boolean)</a></span> - Method in class jebl.math.<a href="./jebl/math/OrthogonalSearch.html" title="class in jebl.math">OrthogonalSearch</a></dt>
<dd>
<div class="block">Should we ignore new minisations that are not as minimal as the current one?</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/FastaImporter.html#setIllegalCharacterPolicy(jebl.evolution.io.IllegalCharacterPolicy)">setIllegalCharacterPolicy(IllegalCharacterPolicy)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/FastaImporter.html" title="class in jebl.evolution.io">FastaImporter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#setImage(java.awt.Image)">setImage(Image)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">Set an image associated with the current progress.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#setInclusion(jebl.util.FixedBitSet)">setInclusion(FixedBitSet)</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#setIndeterminateProgress()">setIndeterminateProgress()</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">Sets indefinite progress (i.e.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#setIsOrdered(boolean)">setIsOrdered(boolean)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/MutableRootedTree.html#setLength(jebl.evolution.graphs.Node, double)">setLength(Node, double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/MutableRootedTree.html" title="class in jebl.evolution.trees">MutableRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedSubtree.html#setLength(jebl.evolution.graphs.Node, double)">setLength(Node, double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedSubtree.html" title="class in jebl.evolution.trees">RootedSubtree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#setLength(jebl.evolution.graphs.Node, double)">setLength(Node, double)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/MatrixExponential.html#setMatrix(jebl.evolution.substmodel.RateMatrix)">setMatrix(RateMatrix)</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/MatrixExponential.html" title="class in jebl.evolution.substmodel">MatrixExponential</a></dt>
<dd>
<div class="block">update rate matrix used in present module</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#setMessage(java.lang.String)">setMessage(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">Set visible user message.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#setMinus(jebl.util.FixedBitSet)">setMinus(FixedBitSet)</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstantPopulation.html#setN0(double)">setN0(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstantPopulation.html" title="class in jebl.evolution.coalescent">ConstantPopulation</a></dt>
<dd>
<div class="block">sets initial population size.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#setN1(double)">setN1(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstLogistic.html#setN1(double)">setN1(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstLogistic.html" title="class in jebl.evolution.coalescent">ConstLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#setN1(double)">setN1(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/Character.html#setName(java.lang.String)">setName(String)</a></span> - Method in interface jebl.evolution.characters.<a href="./jebl/evolution/characters/Character.html" title="interface in jebl.evolution.characters">Character</a></dt>
<dd>
<div class="block">set the name of the character</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/ContinuousCharacter.html#setName(java.lang.String)">setName(String)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/ContinuousCharacter.html" title="class in jebl.evolution.characters">ContinuousCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#setName(java.lang.String)">setName(String)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#setNumOfStates(int)">setNumOfStates(int)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/AbstractRateMatrix.html#setParametersNoScale(double[])">setParametersNoScale(double[])</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/AbstractRateMatrix.html" title="class in jebl.evolution.substmodel">AbstractRateMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#setProgress(double)">setProgress(double)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#setProgress(int, int)">setProgress(int, int)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">Same as calling <a href="./jebl/util/ProgressListener.html#setProgress(double)"><code>setProgress(((double)currentStep)/numberOfSteps)</code></a></div>
</dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#setProgress(long, long)">setProgress(long, long)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">Same as calling <a href="./jebl/util/ProgressListener.html#setProgress(double)"><code>setProgress(((double)currentStep)/numberOfSteps)</code></a></div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SequenceShuffler.html#setProgressMonitor(javax.swing.ProgressMonitor)">setProgressMonitor(ProgressMonitor)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SequenceShuffler.html" title="class in jebl.evolution.align">SequenceShuffler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ConstExponential.html#setProportion(double)">setProportion(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ConstExponential.html" title="class in jebl.evolution.coalescent">ConstExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/Expansion.html#setProportion(double)">setProportion(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/Expansion.html" title="class in jebl.evolution.coalescent">Expansion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#setR2(double)">setR2(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#setScores(jebl.evolution.align.scores.Scores)">setScores(Scores)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#setSeed(long)">setSeed(long)</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Access a default instance of this class, access is synchronized</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/LogisticGrowth.html#setShape(double)">setShape(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent">LogisticGrowth</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/NumberFormatter.html#setSignificantFigures(int)">setSignificantFigures(int)</a></span> - Method in class jebl.util.<a href="./jebl/util/NumberFormatter.html" title="class in jebl.util">NumberFormatter</a></dt>
<dd>
<div class="block">Set the number of significant figures to display when formatted.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/CataclysmicDemographic.html#setSpikeFactor(double)">setSpikeFactor(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/CataclysmicDemographic.html" title="class in jebl.evolution.coalescent">CataclysmicDemographic</a></dt>
<dd>
<div class="block">An alternative parameterization of this model.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/characters/DiscreteCharacter.html#setStateDesc(java.util.Map)">setStateDesc(Map<Integer, String>)</a></span> - Method in class jebl.evolution.characters.<a href="./jebl/evolution/characters/DiscreteCharacter.html" title="class in jebl.evolution.characters">DiscreteCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/ExponentialLogistic.html#setTime(double)">setTime(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/ExponentialLogistic.html" title="class in jebl.evolution.coalescent">ExponentialLogistic</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/LogisticGrowth.html#setTime50(double)">setTime50(double)</a></span> - Method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/LogisticGrowth.html" title="class in jebl.evolution.coalescent">LogisticGrowth</a></dt>
<dd>
<div class="block">An alternative parameterization of this model.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/CompositeProgressListener.html#setTitle(java.lang.String)">setTitle(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/CompositeProgressListener.html" title="class in jebl.util">CompositeProgressListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.html#setTitle(java.lang.String)">setTitle(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.html" title="class in jebl.util">ProgressListener</a></dt>
<dd>
<div class="block">Sets a title associated with whatever is being done.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/ProgressListener.Wrapper.html#setTitle(java.lang.String)">setTitle(String)</a></span> - Method in class jebl.util.<a href="./jebl/util/ProgressListener.Wrapper.html" title="class in jebl.util">ProgressListener.Wrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/OrthogonalSearch.html#setUseCurrentInUnivariateMinimisation(boolean)">setUseCurrentInUnivariateMinimisation(boolean)</a></span> - Method in class jebl.math.<a href="./jebl/math/OrthogonalSearch.html" title="class in jebl.math">OrthogonalSearch</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SequenceShuffler.html#shuffle(jebl.evolution.align.Align, java.lang.String, java.lang.String, int)">shuffle(Align, String, String, int)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SequenceShuffler.html" title="class in jebl.evolution.align">SequenceShuffler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#shuffle(int[])">shuffle(int[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Shuffles an array.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#shuffle(int[], int)">shuffle(int[], int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Shuffles an array.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/Random.html#shuffled(int)">shuffled(int)</a></span> - Static method in class jebl.math.<a href="./jebl/math/Random.html" title="class in jebl.math">Random</a></dt>
<dd>
<div class="block">Returns an array of shuffled indices of length l.</div>
</dd>
<dt><a href="./jebl/util/SimpleListener.html" title="interface in jebl.util"><span class="strong">SimpleListener</span></a> - Interface in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees"><span class="strong">SimpleRootedTree</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A simple, and initially immutable rooted tree implementation.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#SimpleRootedTree()">SimpleRootedTree()</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#SimpleRootedTree(jebl.evolution.trees.RootedTree)">SimpleRootedTree(RootedTree)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Make a copy of the given rooted tree</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#SimpleRootedTree(jebl.evolution.trees.RootedTree, java.util.Map)">SimpleRootedTree(RootedTree, Map<Node, Node>)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Make a copy of the given rooted tree</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#SimpleRootedTree(jebl.evolution.trees.Tree, jebl.evolution.graphs.Node, jebl.evolution.graphs.Node, double)">SimpleRootedTree(Tree, Node, Node, double)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd>
<div class="block">Make a copy of the given unrooted tree</div>
</dd>
<dt><a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees"><span class="strong">SimpleTree</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A basic implementation on an unrooted tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#SimpleTree()">SimpleTree()</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">Tree (to be constructed by subsequent calls).</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleTree.html#SimpleTree(jebl.evolution.trees.Tree)">SimpleTree(Tree)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleTree.html" title="class in jebl.evolution.trees">SimpleTree</a></dt>
<dd>
<div class="block">Duplicate a tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/treesimulation/TreeSimulator.html#simulate(jebl.evolution.treesimulation.IntervalGenerator)">simulate(IntervalGenerator)</a></span> - Method in class jebl.evolution.treesimulation.<a href="./jebl/evolution/treesimulation/TreeSimulator.html" title="class in jebl.evolution.treesimulation">TreeSimulator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treesimulation/TreeSimulator.html#simulate(jebl.evolution.treesimulation.IntervalGenerator, boolean)">simulate(IntervalGenerator, boolean)</a></span> - Method in class jebl.evolution.treesimulation.<a href="./jebl/evolution/treesimulation/TreeSimulator.html" title="class in jebl.evolution.treesimulation">TreeSimulator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#skipCharacters(java.lang.String)">skipCharacters(String)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Skips over any contiguous characters in skip.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#skipSpace()">skipSpace()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Skips over any space (plus tabs and returns) in the file.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#skipToEndOfLine()">skipToEndOfLine()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Skips to the end of the line.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#skipUntil(java.lang.String)">skipUntil(String)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Skips over the file until a character from delimiters is found.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#skipWhile(java.lang.String)">skipWhile(String)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd>
<div class="block">Skips char any contiguous characters in skip.</div>
</dd>
<dt><a href="./jebl/evolution/align/SmithWaterman.html" title="class in jebl.evolution.align"><span class="strong">SmithWaterman</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWaterman.html#SmithWaterman(jebl.evolution.align.scores.Scores, float)">SmithWaterman(Scores, float)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWaterman.html" title="class in jebl.evolution.align">SmithWaterman</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/SmithWatermanLinearSpace.html" title="class in jebl.evolution.align"><span class="strong">SmithWatermanLinearSpace</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpace.html#SmithWatermanLinearSpace(jebl.evolution.align.scores.Scores, float)">SmithWatermanLinearSpace(Scores, float)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpace.html" title="class in jebl.evolution.align">SmithWatermanLinearSpace</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align"><span class="strong">SmithWatermanLinearSpaceAffine</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#SmithWatermanLinearSpaceAffine(jebl.evolution.align.scores.Scores, float, float)">SmithWatermanLinearSpaceAffine(Scores, float, float)</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align">SmithWatermanLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/SortedRootedTree.html" title="class in jebl.evolution.trees"><span class="strong">SortedRootedTree</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SortedRootedTree.html#SortedRootedTree(jebl.evolution.trees.RootedTree, jebl.evolution.trees.SortedRootedTree.BranchOrdering)">SortedRootedTree(RootedTree, SortedRootedTree.BranchOrdering)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/SortedRootedTree.html" title="class in jebl.evolution.trees">SortedRootedTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SortedRootedTree.html#SortedRootedTree(jebl.evolution.trees.RootedTree, java.util.Comparator)">SortedRootedTree(RootedTree, Comparator<Node>)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/SortedRootedTree.html" title="class in jebl.evolution.trees">SortedRootedTree</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/SortedRootedTree.BranchOrdering.html" title="enum in jebl.evolution.trees"><span class="strong">SortedRootedTree.BranchOrdering</span></a> - Enum in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/SplitSystem.html" title="class in jebl.evolution.trees"><span class="strong">SplitSystem</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">data structure for a set of splits</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitSystem.html#SplitSystem(java.util.Collection, int)">SplitSystem(Collection<Taxon>, int)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitSystem.html" title="class in jebl.evolution.trees">SplitSystem</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/SplitUtils.html" title="class in jebl.evolution.trees"><span class="strong">SplitUtils</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">utilities for split systems</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MachineAccuracy.html#SQRT_EPSILON">SQRT_EPSILON</a></span> - Static variable in class jebl.math.<a href="./jebl/math/MachineAccuracy.html" title="class in jebl.math">MachineAccuracy</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MachineAccuracy.html#SQRT_SQRT_EPSILON">SQRT_SQRT_EPSILON</a></span> - Static variable in class jebl.math.<a href="./jebl/math/MachineAccuracy.html" title="class in jebl.math">MachineAccuracy</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.html#startReadingTrees()">startReadingTrees()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.html" title="class in jebl.evolution.io">NexusImporter</a></dt>
<dd>
<div class="block">Read nexus blocks until the next TREES block (or the end of the input) is encountered.</div>
</dd>
<dt><a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences"><span class="strong">State</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#STATE_COUNT">STATE_COUNT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#STATE_COUNT">STATE_COUNT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#STATE_COUNT">STATE_COUNT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/StateClassification.html" title="interface in jebl.evolution.sequences"><span class="strong">StateClassification</span></a> - Interface in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/sequences/StateClassification.Default.html" title="class in jebl.evolution.sequences"><span class="strong">StateClassification.Default</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/StateClassification.Default.html#StateClassification.Default(java.lang.String, java.lang.String[], jebl.evolution.sequences.State[][])">StateClassification.Default(String, String[], State[][])</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/StateClassification.Default.html" title="class in jebl.evolution.sequences">StateClassification.Default</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#STATES">STATES</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#STATES">STATES</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#STATES">STATES</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#STOP_STATE">STOP_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MultivariateMinimum.html#stopCondition(double, double[], double, double, boolean)">stopCondition(double, double[], double, double, boolean)</a></span> - Method in class jebl.math.<a href="./jebl/math/MultivariateMinimum.html" title="class in jebl.math">MultivariateMinimum</a></dt>
<dd>
<div class="block">Checks whether optimization should stop</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#stripGaps(jebl.evolution.sequences.State[])">stripGaps(State[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ByteBuilder.html#subSequence(int, int)">subSequence(int, int)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ByteBuilder.html" title="class in jebl.evolution.io">ByteBuilder</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/scores/SubstScoreMatrix.html" title="class in jebl.evolution.align.scores"><span class="strong">SubstScoreMatrix</span></a> - Class in <a href="./jebl/evolution/align/scores/package-summary.html">jebl.evolution.align.scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/SubstScoreMatrix.html#SubstScoreMatrix(jebl.evolution.substmodel.RateMatrix)">SubstScoreMatrix(RateMatrix)</a></span> - Constructor for class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/SubstScoreMatrix.html" title="class in jebl.evolution.align.scores">SubstScoreMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#sumVector(double[])">sumVector(double[])</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">sum a vector</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SimpleRootedTree.html#swapNodes(jebl.evolution.graphs.Node, int, int)">swapNodes(Node, int, int)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SimpleRootedTree.html" title="class in jebl.evolution.trees">SimpleRootedTree</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/SystemOut.html" title="class in jebl.evolution.align"><span class="strong">SystemOut</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SystemOut.html#SystemOut()">SystemOut()</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/SystemOut.html" title="class in jebl.evolution.align">SystemOut</a></dt>
<dd> </dd>
</dl>
<a name="_T_">
<!-- -->
</a>
<h2 class="title">T</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#T_STATE">T_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#T_STATE">T_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/TabDelimitedImporter.html" title="class in jebl.evolution.io"><span class="strong">TabDelimitedImporter</span></a> - Class in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/TabDelimitedImporter.html#TabDelimitedImporter(java.io.Reader, jebl.evolution.io.DistanceMatrixImporter.Triangle, boolean, boolean, boolean)">TabDelimitedImporter(Reader, DistanceMatrixImporter.Triangle, boolean, boolean, boolean)</a></span> - Constructor for class jebl.evolution.io.<a href="./jebl/evolution/io/TabDelimitedImporter.html" title="class in jebl.evolution.io">TabDelimitedImporter</a></dt>
<dd>
<div class="block">Constructor</div>
</dd>
<dt><a href="./jebl/evolution/distances/TamuraNeiDistanceMatrix.html" title="class in jebl.evolution.distances"><span class="strong">TamuraNeiDistanceMatrix</span></a> - Class in <a href="./jebl/evolution/distances/package-summary.html">jebl.evolution.distances</a></dt>
<dd>
<div class="block">Date: 22/01/2006
Time: 17:28:59</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/TamuraNeiDistanceMatrix.html#TamuraNeiDistanceMatrix(jebl.evolution.alignments.Alignment, jebl.util.ProgressListener, boolean)">TamuraNeiDistanceMatrix(Alignment, ProgressListener, boolean)</a></span> - Constructor for class jebl.evolution.distances.<a href="./jebl/evolution/distances/TamuraNeiDistanceMatrix.html" title="class in jebl.evolution.distances">TamuraNeiDistanceMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/distances/TamuraNeiDistanceMatrix.html#TamuraNeiDistanceMatrix(jebl.evolution.alignments.Alignment, jebl.util.ProgressListener)">TamuraNeiDistanceMatrix(Alignment, ProgressListener)</a></span> - Constructor for class jebl.evolution.distances.<a href="./jebl/evolution/distances/TamuraNeiDistanceMatrix.html" title="class in jebl.evolution.distances">TamuraNeiDistanceMatrix</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa"><span class="strong">Taxon</span></a> - Class in <a href="./jebl/evolution/taxa/package-summary.html">jebl.evolution.taxa</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/taxa/TaxonomicLevel.html" title="class in jebl.evolution.taxa"><span class="strong">TaxonomicLevel</span></a> - Class in <a href="./jebl/evolution/taxa/package-summary.html">jebl.evolution.taxa</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/DemographicFunction.Utils.html#testConsistency(jebl.evolution.coalescent.DemographicFunction, int, double)">testConsistency(DemographicFunction, int, double)</a></span> - Static method in class jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/DemographicFunction.Utils.html" title="class in jebl.evolution.coalescent">DemographicFunction.Utils</a></dt>
<dd>
<div class="block">This function tests the consistency of the
getIntensity and getInverseIntensity methods
of this demographic model.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#toNewick(jebl.evolution.trees.RootedTree)">toNewick(RootedTree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#toNucleotides(jebl.evolution.sequences.CodonState)">toNucleotides(CodonState)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#toStateArray(java.lang.String)">toStateArray(String)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#toStateArray(byte[])">toStateArray(byte[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#toStateArray(java.lang.String)">toStateArray(String)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#toStateArray(byte[])">toStateArray(byte[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#toStateArray(java.lang.String)">toStateArray(String)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#toStateArray(byte[])">toStateArray(byte[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#toStateArray(java.lang.String)">toStateArray(String)</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Converts a string of state codes into an array of State objects for this SequenceType</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/SequenceType.html#toStateArray(byte[])">toStateArray(byte[])</a></span> - Method in interface jebl.evolution.sequences.<a href="./jebl/evolution/sequences/SequenceType.html" title="interface in jebl.evolution.sequences">SequenceType</a></dt>
<dd>
<div class="block">Converts an array of state indices into an array of State objects for this SequenceType</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/ProfileCharacter.html#toString()">toString()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/ProfileCharacter.html" title="class in jebl.evolution.align">ProfileCharacter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Hamming.html#toString()">toString()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Hamming.html" title="class in jebl.evolution.align.scores">Hamming</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/NucleotideScores.html#toString()">toString()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/NucleotideScores.html" title="class in jebl.evolution.align.scores">NucleotideScores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/scores/Scores.html#toString()">toString()</a></span> - Method in class jebl.evolution.align.scores.<a href="./jebl/evolution/align/scores/Scores.html" title="class in jebl.evolution.align.scores">Scores</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Traceback.html#toString()">toString()</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Traceback.html" title="class in jebl.evolution.align">Traceback</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.IntervalType.html#toString()">toString()</a></span> - Method in enum jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.IntervalType.html" title="enum in jebl.evolution.coalescent">IntervalList.IntervalType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ByteBuilder.html#toString()">toString()</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ByteBuilder.html" title="class in jebl.evolution.io">ByteBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/IllegalCharacterPolicy.html#toString()">toString()</a></span> - Method in enum jebl.evolution.io.<a href="./jebl/evolution/io/IllegalCharacterPolicy.html" title="enum in jebl.evolution.io">IllegalCharacterPolicy</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/BasicSequence.html#toString()">toString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/BasicSequence.html" title="class in jebl.evolution.sequences">BasicSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CanonicalSequence.html#toString()">toString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CanonicalSequence.html" title="class in jebl.evolution.sequences">CanonicalSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/CodonSequence.html#toString()">toString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/CodonSequence.html" title="class in jebl.evolution.sequences">CodonSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/FilteredSequence.html#toString()">toString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/FilteredSequence.html" title="class in jebl.evolution.sequences">FilteredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#toString()">toString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd>
<div class="block">Same as getDescription() (so that GeneticCode objects can be used e.g.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/State.html#toString()">toString()</a></span> - Method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/State.html" title="class in jebl.evolution.sequences">State</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#toString(jebl.evolution.sequences.State[])">toString(State[])</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/taxa/Taxon.html#toString()">toString()</a></span> - Method in class jebl.evolution.taxa.<a href="./jebl/evolution/taxa/Taxon.html" title="class in jebl.evolution.taxa">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ConsensusTreeBuilder.Method.html#toString()">toString()</a></span> - Method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/ConsensusTreeBuilder.Method.html" title="enum in jebl.evolution.trees">ConsensusTreeBuilder.Method</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ReRootedTree.RootingType.html#toString()">toString()</a></span> - Method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/ReRootedTree.RootingType.html" title="enum in jebl.evolution.trees">ReRootedTree.RootingType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SortedRootedTree.BranchOrdering.html#toString()">toString()</a></span> - Method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/SortedRootedTree.BranchOrdering.html" title="enum in jebl.evolution.trees">SortedRootedTree.BranchOrdering</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SplitSystem.html#toString()">toString()</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/SplitSystem.html" title="class in jebl.evolution.trees">SplitSystem</a></dt>
<dd>
<div class="block">print split system</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TransformedRootedTree.Transform.html#toString()">toString()</a></span> - Method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TransformedRootedTree.Transform.html" title="enum in jebl.evolution.trees">TransformedRootedTree.Transform</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.Method.html#toString()">toString()</a></span> - Method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.Method.html" title="enum in jebl.evolution.trees">TreeBuilderFactory.Method</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#toString()">toString()</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#toString(double[], int)">toString(double[], int)</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">A simple toString method for an array of doubles.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#toString(java.lang.Object[], int)">toString(Object[], int)</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">A simple toString method for an array of objects.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#toString(java.lang.Object[], java.lang.String)">toString(Object[], String)</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">A simple toString method for an array of objects.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#toString(java.lang.Object[], java.lang.String, int)">toString(Object[], String, int)</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">A simple toString method for an array of objects.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#toString(java.lang.Object[])">toString(Object[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">A simple toString method for an array of doubles.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#toString(double[])">toString(double[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">A simple toString method for an array of doubles.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#toString(int[])">toString(int[])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">A simple toString method for an array of ints.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#toString(int[], int)">toString(int[], int)</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#toString(double[][])">toString(double[][])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">A simple toString method for an array of doubles.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/Utils.html#toString(int[][])">toString(int[][])</a></span> - Static method in class jebl.util.<a href="./jebl/util/Utils.html" title="class in jebl.util">Utils</a></dt>
<dd>
<div class="block">A simple toString method for an array of ints.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#toUniqueNewick(jebl.evolution.trees.RootedTree)">toUniqueNewick(RootedTree)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd>
<div class="block">Constructs a unique newick representation of a tree</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/Utils.html#toUniqueNewickByAttribute(jebl.evolution.trees.RootedTree, java.lang.String)">toUniqueNewickByAttribute(RootedTree, String)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees">Utils</a></dt>
<dd>
<div class="block">Constructs a unique newick representation of a tree print only an attribute</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Align.html#traceback(jebl.evolution.align.TracebackPlotter)">traceback(TracebackPlotter)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/Align.html" title="class in jebl.evolution.align">Align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html#traceback(jebl.evolution.align.TracebackPlotter)">traceback(TracebackPlotter)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html#traceback(jebl.evolution.align.TracebackPlotter, int, int, java.lang.String, java.lang.String)">traceback(TracebackPlotter, int, int, String, String)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/NeedlemanWunschLinearSpace.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpace.html#traceback(jebl.evolution.align.TracebackPlotter)">traceback(TracebackPlotter)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpace.html" title="class in jebl.evolution.align">SmithWatermanLinearSpace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#traceback(jebl.evolution.align.TracebackPlotter)">traceback(TracebackPlotter)</a></span> - Method in class jebl.evolution.align.<a href="./jebl/evolution/align/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align">SmithWatermanLinearSpaceAffine</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/Traceback.html" title="class in jebl.evolution.align"><span class="strong">Traceback</span></a> - Class in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/Traceback.html#Traceback()">Traceback()</a></span> - Constructor for class jebl.evolution.align.<a href="./jebl/evolution/align/Traceback.html" title="class in jebl.evolution.align">Traceback</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/TracebackPlotter.html#traceBack(jebl.evolution.align.Traceback)">traceBack(Traceback)</a></span> - Method in interface jebl.evolution.align.<a href="./jebl/evolution/align/TracebackPlotter.html" title="interface in jebl.evolution.align">TracebackPlotter</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/align/TracebackPlotter.html" title="interface in jebl.evolution.align"><span class="strong">TracebackPlotter</span></a> - Interface in <a href="./jebl/evolution/align/package-summary.html">jebl.evolution.align</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/TransformedRootedTree.html" title="class in jebl.evolution.trees"><span class="strong">TransformedRootedTree</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">This RootedTree class wraps another RootedTree and transforms
the branch lengths and node heights using various functions.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TransformedRootedTree.html#TransformedRootedTree(jebl.evolution.trees.RootedTree, jebl.evolution.trees.TransformedRootedTree.Transform)">TransformedRootedTree(RootedTree, TransformedRootedTree.Transform)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/TransformedRootedTree.html" title="class in jebl.evolution.trees">TransformedRootedTree</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/TransformedRootedTree.Transform.html" title="enum in jebl.evolution.trees"><span class="strong">TransformedRootedTree.Transform</span></a> - Enum in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#translate(jebl.evolution.sequences.Sequence, jebl.evolution.sequences.GeneticCode)">translate(Sequence, GeneticCode)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">Translates a given <a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences"><code>Sequence</code></a> to a corresponding <a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences"><code>Sequence</code></a> under the given genetic code.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#translate(jebl.evolution.sequences.Sequence, jebl.evolution.sequences.GeneticCode, int)">translate(Sequence, GeneticCode, int)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">Translates a given <a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences"><code>Sequence</code></a> to a corresponding <a href="./jebl/evolution/sequences/Sequence.html" title="interface in jebl.evolution.sequences"><code>Sequence</code></a> under the given genetic code.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#translate(jebl.evolution.sequences.State[], jebl.evolution.sequences.GeneticCode)">translate(State[], GeneticCode)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">Translates each of a given sequence of <a href="./jebl/evolution/sequences/NucleotideState.html" title="class in jebl.evolution.sequences"><code>NucleotideState</code></a>s or <a href="./jebl/evolution/sequences/CodonState.html" title="class in jebl.evolution.sequences"><code>CodonState</code></a>s
to the <a href="./jebl/evolution/sequences/AminoAcidState.html" title="class in jebl.evolution.sequences"><code>AminoAcidState</code></a> corresponding to it under the given genetic code.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#translate(jebl.evolution.sequences.State[], jebl.evolution.sequences.GeneticCode, int)">translate(State[], GeneticCode, int)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">Translates each of a given sequence of <a href="./jebl/evolution/sequences/NucleotideState.html" title="class in jebl.evolution.sequences"><code>NucleotideState</code></a>s or <a href="./jebl/evolution/sequences/CodonState.html" title="class in jebl.evolution.sequences"><code>CodonState</code></a>s
to the <a href="./jebl/evolution/sequences/AminoAcidState.html" title="class in jebl.evolution.sequences"><code>AminoAcidState</code></a> corresponding to it under the given genetic code.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#translate(java.lang.String, jebl.evolution.sequences.GeneticCode)">translate(String, GeneticCode)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">A wrapper for <a href="./jebl/evolution/sequences/Utils.html#translateCharSequence(java.lang.CharSequence, jebl.evolution.sequences.GeneticCode)"><code>Utils.translateCharSequence(CharSequence,GeneticCode)</code></a>
that takes a nucleotide sequence as a String only rather than a
CharSequence.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Utils.html#translateCharSequence(java.lang.CharSequence, jebl.evolution.sequences.GeneticCode)">translateCharSequence(CharSequence, GeneticCode)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences">Utils</a></dt>
<dd>
<div class="block">Translates the given nucleotideSequence into an amino acid sequence
string, using the given geneticCode.</div>
</dd>
<dt><a href="./jebl/evolution/sequences/TranslatedSequence.html" title="class in jebl.evolution.sequences"><span class="strong">TranslatedSequence</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/TranslatedSequence.html#TranslatedSequence(jebl.evolution.sequences.Sequence, jebl.evolution.sequences.GeneticCode)">TranslatedSequence(Sequence, GeneticCode)</a></span> - Constructor for class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/TranslatedSequence.html" title="class in jebl.evolution.sequences">TranslatedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.Result.html#tree">tree</a></span> - Variable in class jebl.evolution.align.<a href="./jebl/evolution/align/AlignmentTreeBuilderFactory.Result.html" title="class in jebl.evolution.align">AlignmentTreeBuilderFactory.Result</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees"><span class="strong">Tree</span></a> - Interface in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A rooted or unrooted tree.</div>
</dd>
<dt><a href="./jebl/evolution/trees/TreeBiPartitionInfo.html" title="class in jebl.evolution.trees"><span class="strong">TreeBiPartitionInfo</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Work in progress</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBiPartitionInfo.html#TreeBiPartitionInfo(jebl.evolution.trees.RootedTree, java.util.List)">TreeBiPartitionInfo(RootedTree, List<Taxon>)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBiPartitionInfo.html" title="class in jebl.evolution.trees">TreeBiPartitionInfo</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/TreeBiPartitionInfo.DistanceNorm.html" title="enum in jebl.evolution.trees"><span class="strong">TreeBiPartitionInfo.DistanceNorm</span></a> - Enum in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/TreeBuilder.html" title="interface in jebl.evolution.trees"><span class="strong">TreeBuilder</span></a><<a href="./jebl/evolution/trees/TreeBuilder.html" title="type parameter in TreeBuilder">T</a> extends <a href="./jebl/evolution/trees/Tree.html" title="interface in jebl.evolution.trees">Tree</a>> - Interface in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/TreeBuilderFactory.html" title="class in jebl.evolution.trees"><span class="strong">TreeBuilderFactory</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A meeting point for tree building from sequence data.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.html#TreeBuilderFactory()">TreeBuilderFactory()</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.html" title="class in jebl.evolution.trees">TreeBuilderFactory</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/TreeBuilderFactory.ConsensusMethod.html" title="enum in jebl.evolution.trees"><span class="strong">TreeBuilderFactory.ConsensusMethod</span></a> - Enum in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Supported consensus methods.</div>
</dd>
<dt><a href="./jebl/evolution/trees/TreeBuilderFactory.DistanceModel.html" title="enum in jebl.evolution.trees"><span class="strong">TreeBuilderFactory.DistanceModel</span></a> - Enum in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Supported pairwise distance methods</div>
</dd>
<dt><a href="./jebl/evolution/trees/TreeBuilderFactory.Method.html" title="enum in jebl.evolution.trees"><span class="strong">TreeBuilderFactory.Method</span></a> - Enum in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Supported methods for tree building</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeChangeListener.html#treeChanged(jebl.evolution.trees.TreeChangeEvent)">treeChanged(TreeChangeEvent)</a></span> - Method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeChangeListener.html" title="class in jebl.evolution.trees">TreeChangeListener</a></dt>
<dd>
<div class="block">The tree has changed.</div>
</dd>
<dt><a href="./jebl/evolution/trees/TreeChangeEvent.html" title="class in jebl.evolution.trees"><span class="strong">TreeChangeEvent</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Represents a change to a tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeChangeEvent.html#TreeChangeEvent(jebl.evolution.trees.Tree)">TreeChangeEvent(Tree)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeChangeEvent.html" title="class in jebl.evolution.trees">TreeChangeEvent</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/TreeChangeListener.html" title="class in jebl.evolution.trees"><span class="strong">TreeChangeListener</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A listener for notifying about changes to a tree or to the selected nodes in a tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeChangeListener.html#TreeChangeListener()">TreeChangeListener()</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeChangeListener.html" title="class in jebl.evolution.trees">TreeChangeListener</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/TreeExporter.html" title="interface in jebl.evolution.io"><span class="strong">TreeExporter</span></a> - Interface in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/io/TreeImporter.html" title="interface in jebl.evolution.io"><span class="strong">TreeImporter</span></a> - Interface in <a href="./jebl/evolution/io/package-summary.html">jebl.evolution.io</a></dt>
<dd>
<div class="block">Interface for importers that do trees</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusExporter.html#treeNameAttributeKey">treeNameAttributeKey</a></span> - Static variable in class jebl.evolution.io.<a href="./jebl/evolution/io/NexusExporter.html" title="class in jebl.evolution.io">NexusExporter</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/TreeSelectionChangeEvent.html" title="class in jebl.evolution.trees"><span class="strong">TreeSelectionChangeEvent</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">Represents a change to the selected nodes in a tree.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeSelectionChangeEvent.html#TreeSelectionChangeEvent(java.util.Set)">TreeSelectionChangeEvent(Set<Node>)</a></span> - Constructor for class jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeSelectionChangeEvent.html" title="class in jebl.evolution.trees">TreeSelectionChangeEvent</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/treesimulation/TreeSimulator.html" title="class in jebl.evolution.treesimulation"><span class="strong">TreeSimulator</span></a> - Class in <a href="./jebl/evolution/treesimulation/package-summary.html">jebl.evolution.treesimulation</a></dt>
<dd>
<div class="block">This class provides the framework for (backwards-through-time) tree simulation.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/treesimulation/TreeSimulator.html#TreeSimulator(java.lang.String, int)">TreeSimulator(String, int)</a></span> - Constructor for class jebl.evolution.treesimulation.<a href="./jebl/evolution/treesimulation/TreeSimulator.html" title="class in jebl.evolution.treesimulation">TreeSimulator</a></dt>
<dd>
<div class="block">A constructor for a given number of taxa, all sampled at the same time</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/treesimulation/TreeSimulator.html#TreeSimulator(java.lang.String, double[])">TreeSimulator(String, double[])</a></span> - Constructor for class jebl.evolution.treesimulation.<a href="./jebl/evolution/treesimulation/TreeSimulator.html" title="class in jebl.evolution.treesimulation">TreeSimulator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treesimulation/TreeSimulator.html#TreeSimulator(java.lang.String, int[], double[])">TreeSimulator(String, int[], double[])</a></span> - Constructor for class jebl.evolution.treesimulation.<a href="./jebl/evolution/treesimulation/TreeSimulator.html" title="class in jebl.evolution.treesimulation">TreeSimulator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/treesimulation/TreeSimulator.html#TreeSimulator(java.util.Collection, java.lang.String)">TreeSimulator(Collection<Taxon>, String)</a></span> - Constructor for class jebl.evolution.treesimulation.<a href="./jebl/evolution/treesimulation/TreeSimulator.html" title="class in jebl.evolution.treesimulation">TreeSimulator</a></dt>
<dd>
<div class="block">A constructor for a given collection of taxa.</div>
</dd>
</dl>
<a name="_U_">
<!-- -->
</a>
<h2 class="title">U</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#U_STATE">U_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/util/FixedBitSet.html#union(jebl.util.FixedBitSet)">union(FixedBitSet)</a></span> - Method in class jebl.util.<a href="./jebl/util/FixedBitSet.html" title="class in jebl.util">FixedBitSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/RootedTreeUtils.html#uniqueNewick(jebl.evolution.trees.RootedTree, jebl.evolution.graphs.Node)">uniqueNewick(RootedTree, Node)</a></span> - Static method in class jebl.evolution.trees.<a href="./jebl/evolution/trees/RootedTreeUtils.html" title="class in jebl.evolution.trees">RootedTreeUtils</a></dt>
<dd>
<div class="block">Recursive function for constructing a newick tree representation in the given buffer.</div>
</dd>
<dt><a href="./jebl/math/UnivariateFunction.html" title="interface in jebl.math"><span class="strong">UnivariateFunction</span></a> - Interface in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">interface for a function of one variable</div>
</dd>
<dt><a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math"><span class="strong">UnivariateMinimum</span></a> - Class in <a href="./jebl/math/package-summary.html">jebl.math</a></dt>
<dd>
<div class="block">minimization of a real-valued function of one variable
without using derivatives.</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/UnivariateMinimum.html#UnivariateMinimum()">UnivariateMinimum()</a></span> - Constructor for class jebl.math.<a href="./jebl/math/UnivariateMinimum.html" title="class in jebl.math">UnivariateMinimum</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#UNIVERSAL">UNIVERSAL</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#UNKNOWN_STATE">UNKNOWN_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Codons.html#UNKNOWN_STATE">UNKNOWN_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Codons.html" title="class in jebl.evolution.sequences">Codons</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#UNKNOWN_STATE">UNKNOWN_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportHelper.html#unreadCharacter(char)">unreadCharacter(char)</a></span> - Method in class jebl.evolution.io.<a href="./jebl/evolution/io/ImportHelper.html" title="class in jebl.evolution.io">ImportHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/MatrixExponential.html#updateByRelativeRates(double[][])">updateByRelativeRates(double[][])</a></span> - Method in class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/MatrixExponential.html" title="class in jebl.evolution.substmodel">MatrixExponential</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/math/MinimiserMonitor.html#updateProgress(double)">updateProgress(double)</a></span> - Method in interface jebl.math.<a href="./jebl/math/MinimiserMonitor.html" title="interface in jebl.math">MinimiserMonitor</a></dt>
<dd>
<div class="block">Inform monitor of current progress (as a number between 0 and 1), or -1 to reset</div>
</dd>
<dt><span class="strong"><a href="./jebl/math/MatrixCalc.html#upperSolve(double[][], double[], double)">upperSolve(double[][], double[], double)</a></span> - Static method in class jebl.math.<a href="./jebl/math/MatrixCalc.html" title="class in jebl.math">MatrixCalc</a></dt>
<dd>
<div class="block">upperSolve
back substitution with optional over-riding diagonal</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.MissingFieldException.html#userMessage()">userMessage()</a></span> - Method in exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.MissingFieldException.html" title="class in jebl.evolution.io">ImportException.MissingFieldException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.ShortSequenceException.html#userMessage()">userMessage()</a></span> - Method in exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.ShortSequenceException.html" title="class in jebl.evolution.io">ImportException.ShortSequenceException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.TooFewTaxaException.html#userMessage()">userMessage()</a></span> - Method in exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.TooFewTaxaException.html" title="class in jebl.evolution.io">ImportException.TooFewTaxaException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/io/ImportException.html#userMessage()">userMessage()</a></span> - Method in exception jebl.evolution.io.<a href="./jebl/evolution/io/ImportException.html" title="class in jebl.evolution.io">ImportException</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/graphs/Utils.html" title="class in jebl.evolution.graphs"><span class="strong">Utils</span></a> - Class in <a href="./jebl/evolution/graphs/package-summary.html">jebl.evolution.graphs</a></dt>
<dd>
<div class="block">A collection of utility functions for graphs.</div>
</dd>
<dt><a href="./jebl/evolution/sequences/Utils.html" title="class in jebl.evolution.sequences"><span class="strong">Utils</span></a> - Class in <a href="./jebl/evolution/sequences/package-summary.html">jebl.evolution.sequences</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/trees/Utils.html" title="class in jebl.evolution.trees"><span class="strong">Utils</span></a> - Class in <a href="./jebl/evolution/trees/package-summary.html">jebl.evolution.trees</a></dt>
<dd>
<div class="block">A collection of utility functions for trees.</div>
</dd>
<dt><a href="./jebl/util/Utils.html" title="class in jebl.util"><span class="strong">Utils</span></a> - Class in <a href="./jebl/util/package-summary.html">jebl.util</a></dt>
<dd>
<div class="block">Provides some miscellaneous methods.</div>
</dd>
</dl>
<a name="_V_">
<!-- -->
</a>
<h2 class="title">V</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#V_STATE">V_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#V_STATE">V_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.IntervalType.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.IntervalType.html" title="enum in jebl.evolution.coalescent">IntervalList.IntervalType</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/DistanceMatrixImporter.Triangle.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.io.<a href="./jebl/evolution/io/DistanceMatrixImporter.Triangle.html" title="enum in jebl.evolution.io">DistanceMatrixImporter.Triangle</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/IllegalCharacterPolicy.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.io.<a href="./jebl/evolution/io/IllegalCharacterPolicy.html" title="enum in jebl.evolution.io">IllegalCharacterPolicy</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.NexusBlock.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.NexusBlock.html" title="enum in jebl.evolution.io">NexusImporter.NexusBlock</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#valueOf(int)">valueOf(int)</a></span> - Static method in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ConsensusTreeBuilder.Method.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/ConsensusTreeBuilder.Method.html" title="enum in jebl.evolution.trees">ConsensusTreeBuilder.Method</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ReRootedTree.RootingType.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/ReRootedTree.RootingType.html" title="enum in jebl.evolution.trees">ReRootedTree.RootingType</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SortedRootedTree.BranchOrdering.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/SortedRootedTree.BranchOrdering.html" title="enum in jebl.evolution.trees">SortedRootedTree.BranchOrdering</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TransformedRootedTree.Transform.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TransformedRootedTree.Transform.html" title="enum in jebl.evolution.trees">TransformedRootedTree.Transform</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBiPartitionInfo.DistanceNorm.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBiPartitionInfo.DistanceNorm.html" title="enum in jebl.evolution.trees">TreeBiPartitionInfo.DistanceNorm</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.ConsensusMethod.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.ConsensusMethod.html" title="enum in jebl.evolution.trees">TreeBuilderFactory.ConsensusMethod</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.DistanceModel.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.DistanceModel.html" title="enum in jebl.evolution.trees">TreeBuilderFactory.DistanceModel</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.Method.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.Method.html" title="enum in jebl.evolution.trees">TreeBuilderFactory.Method</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/MaybeBoolean.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum jebl.util.<a href="./jebl/util/MaybeBoolean.html" title="enum in jebl.util">MaybeBoolean</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/MaybeBoolean.html#valueOf(boolean)">valueOf(boolean)</a></span> - Static method in enum jebl.util.<a href="./jebl/util/MaybeBoolean.html" title="enum in jebl.util">MaybeBoolean</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/coalescent/IntervalList.IntervalType.html#values()">values()</a></span> - Static method in enum jebl.evolution.coalescent.<a href="./jebl/evolution/coalescent/IntervalList.IntervalType.html" title="enum in jebl.evolution.coalescent">IntervalList.IntervalType</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/DistanceMatrixImporter.Triangle.html#values()">values()</a></span> - Static method in enum jebl.evolution.io.<a href="./jebl/evolution/io/DistanceMatrixImporter.Triangle.html" title="enum in jebl.evolution.io">DistanceMatrixImporter.Triangle</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/IllegalCharacterPolicy.html#values()">values()</a></span> - Static method in enum jebl.evolution.io.<a href="./jebl/evolution/io/IllegalCharacterPolicy.html" title="enum in jebl.evolution.io">IllegalCharacterPolicy</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/io/NexusImporter.NexusBlock.html#values()">values()</a></span> - Static method in enum jebl.evolution.io.<a href="./jebl/evolution/io/NexusImporter.NexusBlock.html" title="enum in jebl.evolution.io">NexusImporter.NexusBlock</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ConsensusTreeBuilder.Method.html#values()">values()</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/ConsensusTreeBuilder.Method.html" title="enum in jebl.evolution.trees">ConsensusTreeBuilder.Method</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/ReRootedTree.RootingType.html#values()">values()</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/ReRootedTree.RootingType.html" title="enum in jebl.evolution.trees">ReRootedTree.RootingType</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/SortedRootedTree.BranchOrdering.html#values()">values()</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/SortedRootedTree.BranchOrdering.html" title="enum in jebl.evolution.trees">SortedRootedTree.BranchOrdering</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TransformedRootedTree.Transform.html#values()">values()</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TransformedRootedTree.Transform.html" title="enum in jebl.evolution.trees">TransformedRootedTree.Transform</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBiPartitionInfo.DistanceNorm.html#values()">values()</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBiPartitionInfo.DistanceNorm.html" title="enum in jebl.evolution.trees">TreeBiPartitionInfo.DistanceNorm</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.ConsensusMethod.html#values()">values()</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.ConsensusMethod.html" title="enum in jebl.evolution.trees">TreeBuilderFactory.ConsensusMethod</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.DistanceModel.html#values()">values()</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.DistanceModel.html" title="enum in jebl.evolution.trees">TreeBuilderFactory.DistanceModel</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/trees/TreeBuilderFactory.Method.html#values()">values()</a></span> - Static method in enum jebl.evolution.trees.<a href="./jebl/evolution/trees/TreeBuilderFactory.Method.html" title="enum in jebl.evolution.trees">TreeBuilderFactory.Method</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/util/MaybeBoolean.html#values()">values()</a></span> - Static method in enum jebl.util.<a href="./jebl/util/MaybeBoolean.html" title="enum in jebl.util">MaybeBoolean</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#VERTEBRATE_MT">VERTEBRATE_MT</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#VOLUME_CLASSIFICATION">VOLUME_CLASSIFICATION</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
</dl>
<a name="_W_">
<!-- -->
</a>
<h2 class="title">W</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#W_STATE">W_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#W_STATE">W_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><a href="./jebl/evolution/substmodel/WAG.html" title="class in jebl.evolution.substmodel"><span class="strong">WAG</span></a> - Class in <a href="./jebl/evolution/substmodel/package-summary.html">jebl.evolution.substmodel</a></dt>
<dd>
<div class="block">WAG model of amino acid evolution (S.</div>
</dd>
<dt><span class="strong"><a href="./jebl/evolution/substmodel/WAG.html#WAG(double[])">WAG(double[])</a></span> - Constructor for class jebl.evolution.substmodel.<a href="./jebl/evolution/substmodel/WAG.html" title="class in jebl.evolution.substmodel">WAG</a></dt>
<dd>
<div class="block">constructor</div>
</dd>
</dl>
<a name="_X_">
<!-- -->
</a>
<h2 class="title">X</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#X_STATE">X_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
</dl>
<a name="_Y_">
<!-- -->
</a>
<h2 class="title">Y</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#Y_STATE">Y_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/Nucleotides.html#Y_STATE">Y_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/Nucleotides.html" title="class in jebl.evolution.sequences">Nucleotides</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./jebl/evolution/sequences/GeneticCode.html#YEAST">YEAST</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/GeneticCode.html" title="class in jebl.evolution.sequences">GeneticCode</a></dt>
<dd> </dd>
</dl>
<a name="_Z_">
<!-- -->
</a>
<h2 class="title">Z</h2>
<dl>
<dt><span class="strong"><a href="./jebl/evolution/sequences/AminoAcids.html#Z_STATE">Z_STATE</a></span> - Static variable in class jebl.evolution.sequences.<a href="./jebl/evolution/sequences/AminoAcids.html" title="class in jebl.evolution.sequences">AminoAcids</a></dt>
<dd> </dd>
</dl>
<a href="#_A_">A</a> <a href="#_B_">B</a> <a href="#_C_">C</a> <a href="#_D_">D</a> <a href="#_E_">E</a> <a href="#_F_">F</a> <a href="#_G_">G</a> <a href="#_H_">H</a> <a href="#_I_">I</a> <a href="#_J_">J</a> <a href="#_K_">K</a> <a href="#_L_">L</a> <a href="#_M_">M</a> <a href="#_N_">N</a> <a href="#_O_">O</a> <a href="#_P_">P</a> <a href="#_Q_">Q</a> <a href="#_R_">R</a> <a href="#_S_">S</a> <a href="#_T_">T</a> <a href="#_U_">U</a> <a href="#_V_">V</a> <a href="#_W_">W</a> <a href="#_X_">X</a> <a href="#_Y_">Y</a> <a href="#_Z_">Z</a> </div>
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