sbmltoolbox 4.1.0-3 / usr / share / doc / sbmltoolbox / html / convenience.html

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<h3>CONVENIENCE</h3>

<p>The Convenience folder contains a number of convenience functions for checking information or manipulating math expressions.</p>

<p>Function are:</p>

<hr>

<h4>y = CheckValidUnitKind(kind)</h4>

<p>Takes</p>

<ol>
<li>kind, a string representing a unit kind </li>
</ol>

<p>Returns </p>

<ol>
<li>y =
<ul>
<li>1 if the string represents a valid unit kind </li>
<li>0 otherwise</li>
</ul></li>
</ol>

<p><em>NOTE:</em> This is identical to the function isValidUnitKind</p>

<hr>

<h4>newArray = LoseWhiteSpace(charArray)</h4>

<p>Takes</p>

<ol>
<li>charArray, an array of characters </li>
</ol>

<p>Returns </p>

<ol>
<li>the array with any white space removed</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>     newArray = LoseWhiteSpace('     exa  mp le')

     newArray = 'example'
</code></pre>

<hr>

<h4>pairs = PairBrackets(expression)</h4>

<p>Takes</p>

<ol>
<li>expression, a string representation of a math expression</li>
</ol>

<p>Returns</p>

<ol>
<li>an array of the indices of each pair of brackets ordered from
the opening bracket index</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>     pairs = PairBrackets('(a+((b*c)/(a+b)))')

     pairs = 
                 1   17
                 4   16
                 5    9
                 11  15
</code></pre>

<hr>

<h4>output = Rearrange(expression, name)</h4>

<p>Takes</p>

<ol>
<li>expression, a string representation of a math expression</li>
<li>name, a string representing the name of a variable</li>
</ol>

<p>Returns</p>

<ol>
<li>the expression rearranged in terms of the variable</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>     output   =   Rearrange('X + Y - Z', 'X')

     output   =   '-Y+Z'
</code></pre>

<hr>

<h4>newArray = RemoveDuplicates(array)</h4>

<p>Takes</p>

<ol>
<li>array, any array</li>
</ol>

<p>Returns</p>

<ol>
<li>the array with any duplicate entries removed  </li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>          newArray = RemoveDuplicates([2, 3, 4, 3, 2, 5])
          newArray = [2, 3, 4, 5]
</code></pre>

<hr>

<h4>value = Substitute(expression, SBMLModel)</h4>

<p>Takes</p>

<ol>
<li>expression, a string representation of a math expression</li>
<li>SBMLModel, an SBML Model structure</li>
</ol>

<p>Returns</p>

<ol>
<li>the value of the expression when all variables within the model have
been substituted</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>     Consider m to be an SBMLModel containing a species with 
                id = 'g' and initialConcentration = '3' 

     value = Substitute('g*2', m)

     value = 6
</code></pre>

<hr>

<h4>newExpression = SubstituteConstants(expression, SBMLModel)</h4>

<p>Takes</p>

<ol>
<li>expression, a string representation of a math expression</li>
<li>SBMLModel, an SBML Model structure</li>
</ol>

<p>Returns</p>

<ol>
<li>the string representation of the expression when all constants within the 
model have been substituted</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>     Consider m to be an SBMLModel containing a parameter
          with id = 'g', constant = '1' and value = 3' 

     newExpression = SubstituteConstants('2 * g * S1', SBMLModel)

     newExpression = '2 * 3 * S1'
</code></pre>

<hr>

<h4>newExpression = SubstituteFunction(expression, SBMLFunctionDefinition)</h4>

<p>Takes</p>

<ol>
<li>expression, a string representation of a math expression</li>
<li>SBMLFunctionDefinition, an SBML FunctionDefinition structure</li>
</ol>

<p>Returns</p>

<ol>
<li>newExpression
<ul>
<li>the string representation of the expression when any instances of the 
functionDefinition have been substituted</li>
<li>an empty string if the functiondefinition is not in the original
expression</li>
</ul></li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>     Consider fD to be an SBMLFunctionDefinition 
          with id = 'g' and math = 'lambda(x,x+0.5)' 

     formula = SubstituteFormula('g(y)', fD)

     formula = 'y+0.5'


     formula = SubstituteFormula('h(y)', fD)

     formula = ''
</code></pre>

<hr>

<h4>y = isIntegralNumber(number)</h4>

<p>Takes</p>

<ol>
<li>number, any number</li>
</ol>

<p>Returns</p>

<ol>
<li>y = </li>
<li>1 if the number represents an integer </li>
<li>0 otherwise </li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>          y = isIntegralNumber(int32(3))
          y = 1

          y = isIntegralNumber(double(3.2))
          y = 0

          y = isIntegralNumber(double(3))
          y = 1
</code></pre>

<p><em>NOTE:</em> The inbuilt 'isinteger' function only returns true if the number 
 has been declared as having an integer type, whereas the default type for numbers 
 in MATLAB is double. This function will return '1' if the number
 represents an integer.</p>

<hr>

<h4>y = isValidUnitKind(kind)</h4>

<p>Takes</p>

<ol>
<li>kind, a string representing a unit kind </li>
</ol>

<p>returns </p>

<ol>
<li>y =
<ul>
<li>1 if the string represents a valid unit kind </li>
<li>0 otherwise</li>
</ul></li>
</ol>

<p><em>NOTE:</em> This is identical to the function CheckValidUnitKind</p>

<hr>

<h4>index = matchFunctionName(expression, name)</h4>

<p>Takes</p>

<ol>
<li>expression, a string representation of a math expression</li>
<li>name, a string representing the name of a function</li>
</ol>

<p>Returns</p>

<ol>
<li>the index of the starting point of 'name' in the 'expression'</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>     index = matchFunctionName('f*g', 'g')

     index = []


     index = matchFunctionName('add(d,g_1)', 'add')

     index = 0


     index = matchFunctionName('add(add(a,b), c)', 'add')

     index = [1, 5]
</code></pre>

<p><em>NOTE:</em> This differs from the 'strfind' function in that it checks
      that the name is used as a function call.</p>

<hr>

<h4>index = matchName(expression, name)</h4>

<p>Takes</p>

<ol>
<li>expression, a string representation of a math expression</li>
<li>name, a string representing the name of a variable</li>
</ol>

<p>Returns</p>

<ol>
<li>the index of the starting point of 'name' in the 'expression'</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>     index = matchName('f*g', 'g')

     index = 3


     index = matchName('f*g_1', 'g')

     index = []


     index = matchName('f*g(a,g)', 'g')

     index = 7
</code></pre>

<p><em>NOTE:</em> This differs from the 'strfind' function in that it checks
      that the name is used as a variable.</p>

<hr>

<h4>value = piecewise(value1, test, value2)</h4>

<p>Takes</p>

<ol>
<li>value1, the value to return if the test is true</li>
<li>test, a boolean test that will return true or false</li>
<li>value2, the value to return if the test is false</li>
</ol>

<p>Returns</p>

<ol>
<li>value = 
<ul>
<li>value1, if test returns true</li>
<li>value2, if test returns false</li>
</ul></li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>          value = piecewise(3, 1&lt;2, 4)
          value = 3

          value = piecewise(3, 1&gt;2, 4)
          value = 4
</code></pre>

<p><em>NOTE:</em> This function provides the functionality of the MathML 'piecewise' function.</p>

<hr>

<h4>y = testmember(value, array)</h4>

<p>Takes</p>

<ol>
<li>value, any number/string</li>
<li>array, an array of objects </li>
</ol>

<p>Returns </p>

<ol>
<li>y = 
<ul>
<li>1 if value is a member of the array </li>
<li>0 otherwise</li>
</ul></li>
</ol>

<p><em>NOTE:</em> this function is necessary for octave to emulate the MATLAB
      functionality of the 'ismember' function</p>

<hr>