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<a href="_sam_read_group_dictionary_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// ***************************************************************************</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// SamReadGroupDictionary.h (c) 2010 Derek Barnett</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// Marth Lab, Department of Biology, Boston College</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// Last modified: 16 October 2011 (DB)</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// Provides methods for operating on a collection of SamReadGroup entries.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// ***************************************************************************</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> </div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#ifndef SAM_READGROUP_DICTIONARY_H</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#define SAM_READGROUP_DICTIONARY_H</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> </div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include "<a class="code" href="api__global_8h.html">api/api_global.h</a>"</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include "<a class="code" href="_sam_read_group_8h.html">api/SamReadGroup.h</a>"</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include <map></span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="keyword">namespace </span><a class="code" href="namespace_bam_tools.html">BamTools</a> {</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> </div><div class="line"><a name="l00021"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a65d72324945d02c05115772904745e92"> 21</a></span> <span class="keyword">typedef</span> std::vector<SamReadGroup> <a class="code" href="namespace_bam_tools.html#a65d72324945d02c05115772904745e92">SamReadGroupContainer</a>;</div><div class="line"><a name="l00022"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#aa01a6a0367d3a90968ae9065ecf5bb2a"> 22</a></span> <span class="keyword">typedef</span> SamReadGroupContainer::iterator <a class="code" href="namespace_bam_tools.html#aa01a6a0367d3a90968ae9065ecf5bb2a">SamReadGroupIterator</a>;</div><div class="line"><a name="l00023"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a13213686975a6efa187f21595507724e"> 23</a></span> <span class="keyword">typedef</span> SamReadGroupContainer::const_iterator <a class="code" href="namespace_bam_tools.html#a13213686975a6efa187f21595507724e">SamReadGroupConstIterator</a>;</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div><div class="line"><a name="l00025"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_sam_read_group_dictionary.html"> 25</a></span> <span class="keyword">class </span><a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <a class="code" href="class_bam_tools_1_1_sam_read_group_dictionary.html">SamReadGroupDictionary</a> {</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> </div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <span class="comment">// ctor & dtor</span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <a class="code" href="class_bam_tools_1_1_sam_read_group_dictionary.html">SamReadGroupDictionary</a>(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <a class="code" href="class_bam_tools_1_1_sam_read_group_dictionary.html">SamReadGroupDictionary</a>(<span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_sam_read_group_dictionary.html">SamReadGroupDictionary</a>& other);</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  ~<a class="code" href="class_bam_tools_1_1_sam_read_group_dictionary.html">SamReadGroupDictionary</a>(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> </div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="comment">// query/modify read group data</span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="comment">// adds a read group</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keywordtype">void</span> Add(<span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_sam_read_group.html">SamReadGroup</a>& readGroup);</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordtype">void</span> Add(<span class="keyword">const</span> std::string& readGroupId);</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="comment">// adds multiple read groups</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keywordtype">void</span> Add(<span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_sam_read_group_dictionary.html">SamReadGroupDictionary</a>& readGroups);</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordtype">void</span> Add(<span class="keyword">const</span> std::vector<SamReadGroup>& readGroups);</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordtype">void</span> Add(<span class="keyword">const</span> std::vector<std::string>& readGroupIds);</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="comment">// clears all read group entries</span></div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordtype">void</span> Clear(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="comment">// returns true if dictionary contains this read group</span></div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keywordtype">bool</span> Contains(<span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_sam_read_group.html">SamReadGroup</a>& readGroup) <span class="keyword">const</span>;</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordtype">bool</span> Contains(<span class="keyword">const</span> std::string& readGroupId) <span class="keyword">const</span>;</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="comment">// returns true if dictionary is empty</span></div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordtype">bool</span> IsEmpty(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="comment">// removes read group, if found</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordtype">void</span> Remove(<span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_sam_read_group.html">SamReadGroup</a>& readGroup);</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordtype">void</span> Remove(<span class="keyword">const</span> std::string& readGroupId);</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="comment">// removes multiple read groups</span></div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordtype">void</span> Remove(<span class="keyword">const</span> std::vector<SamReadGroup>& readGroups);</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordtype">void</span> Remove(<span class="keyword">const</span> std::vector<std::string>& readGroupIds);</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="comment">// returns number of read groups in dictionary</span></div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordtype">int</span> Size(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="comment">// retrieves a modifiable reference to the SamReadGroup object associated with this ID</span></div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <a class="code" href="struct_bam_tools_1_1_sam_read_group.html">SamReadGroup</a>& operator[](<span class="keyword">const</span> std::string& readGroupId);</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="comment">// retrieve STL-compatible iterators</span></div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  SamReadGroupIterator Begin(<span class="keywordtype">void</span>); <span class="comment">// returns iterator to begin()</span></div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  SamReadGroupConstIterator Begin(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns const_iterator to begin()</span></div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  SamReadGroupConstIterator ConstBegin(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns const_iterator to begin()</span></div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  SamReadGroupIterator End(<span class="keywordtype">void</span>); <span class="comment">// returns iterator to end()</span></div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  SamReadGroupConstIterator End(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns const_iterator to end()</span></div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  SamReadGroupConstIterator ConstEnd(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns const_iterator to end()</span></div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="comment">// data members</span></div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keyword">private</span>:</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  SamReadGroupContainer m_data;</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  std::map<std::string, size_t> m_lookupData;</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> };</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> } <span class="comment">// namespace BamTools</span></div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="preprocessor">#endif // SAM_READGROUP_DICTIONARY_H</span></div><div class="ttc" id="_sam_read_group_8h_html"><div class="ttname"><a href="_sam_read_group_8h.html">SamReadGroup.h</a></div></div>
<div class="ttc" id="namespace_bam_tools_html_a13213686975a6efa187f21595507724e"><div class="ttname"><a href="namespace_bam_tools.html#a13213686975a6efa187f21595507724e">BamTools::SamReadGroupConstIterator</a></div><div class="ttdeci">SamReadGroupContainer::const_iterator SamReadGroupConstIterator</div><div class="ttdef"><b>Definition:</b> SamReadGroupDictionary.h:23</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_read_group_html"><div class="ttname"><a href="struct_bam_tools_1_1_sam_read_group.html">BamTools::SamReadGroup</a></div><div class="ttdoc">Represents a SAM read group entry. </div><div class="ttdef"><b>Definition:</b> SamReadGroup.h:20</div></div>
<div class="ttc" id="api__global_8h_html_a5e3652cae8b48c1ad174f0b06bbd06d0"><div class="ttname"><a href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a></div><div class="ttdeci">#define API_EXPORT</div><div class="ttdef"><b>Definition:</b> api_global.h:18</div></div>
<div class="ttc" id="class_bam_tools_1_1_sam_read_group_dictionary_html"><div class="ttname"><a href="class_bam_tools_1_1_sam_read_group_dictionary.html">BamTools::SamReadGroupDictionary</a></div><div class="ttdoc">Container of SamReadGroup entries. </div><div class="ttdef"><b>Definition:</b> SamReadGroupDictionary.h:25</div></div>
<div class="ttc" id="namespace_bam_tools_html_aa01a6a0367d3a90968ae9065ecf5bb2a"><div class="ttname"><a href="namespace_bam_tools.html#aa01a6a0367d3a90968ae9065ecf5bb2a">BamTools::SamReadGroupIterator</a></div><div class="ttdeci">SamReadGroupContainer::iterator SamReadGroupIterator</div><div class="ttdef"><b>Definition:</b> SamReadGroupDictionary.h:22</div></div>
<div class="ttc" id="namespace_bam_tools_html_a65d72324945d02c05115772904745e92"><div class="ttname"><a href="namespace_bam_tools.html#a65d72324945d02c05115772904745e92">BamTools::SamReadGroupContainer</a></div><div class="ttdeci">std::vector< SamReadGroup > SamReadGroupContainer</div><div class="ttdef"><b>Definition:</b> SamReadGroupDictionary.h:21</div></div>
<div class="ttc" id="namespace_bam_tools_html"><div class="ttname"><a href="namespace_bam_tools.html">BamTools</a></div><div class="ttdoc">Contains all BamTools classes & methods. </div><div class="ttdef"><b>Definition:</b> Sort.h:24</div></div>
<div class="ttc" id="api__global_8h_html"><div class="ttname"><a href="api__global_8h.html">api_global.h</a></div></div>
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