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<a href="FeatureXMLFile_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">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</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">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Chris Bielow $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Marc Sturm, Chris Bielow, Clemens Groepl $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FORMAT_FEATUREXMLFILE_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_FEATUREXMLFILE_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="FeatureFileOptions_8h.html">OpenMS/FORMAT/OPTIONS/FeatureFileOptions.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="XMLFile_8h.html">OpenMS/FORMAT/XMLFile.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="XMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XMLHandler.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></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="preprocessor">#include <iostream></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> {</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html"> 59</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1FeatureXMLFile.html">FeatureXMLFile</a> :</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keyword">protected</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">Internal::XMLHandler</a>,</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLFile.html">Internal::XMLFile</a>,</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</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="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <a class="code" href="classOpenMS_1_1FeatureXMLFile.html">FeatureXMLFile</a>();</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  ~<a class="code" href="classOpenMS_1_1FeatureXMLFile.html">FeatureXMLFile</a>();</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordtype">void</span> load(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & feature_map);</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>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> loadSize(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename);</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keywordtype">void</span> store(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & feature_map);</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <a class="code" href="classOpenMS_1_1FeatureFileOptions.html">FeatureFileOptions</a> & getOptions();</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureFileOptions.html">FeatureFileOptions</a> & getOptions() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keywordtype">void</span> setOptions(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureFileOptions.html">FeatureFileOptions</a> &);</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> </div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="comment">// restore default state for next load/store operation</span></div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">void</span> resetMembers_();</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> endElement(<span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> qname);</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> startElement(<span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> qname, <span class="keyword">const</span> xercesc::Attributes & attributes);</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> characters(<span class="keyword">const</span> XMLCh * <span class="keyword">const</span> chars, <span class="keyword">const</span> XMLSize_t length);</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keywordtype">void</span> writeFeature_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, std::ostream & os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> & feat, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & identifier_prefix, <a class="code" href="group__Concept.html#ga5162db95dc78bdf2e3a71d73bec703e9">UInt64</a> identifier, <a class="code" href="classunsigned_01int.html">UInt</a> indentation_level);</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> </div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keywordtype">void</span> writePeptideIdentification_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, std::ostream & os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> & <span class="keywordtype">id</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & tag_name, <a class="code" href="classunsigned_01int.html">UInt</a> indentation_level);</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordtype">void</span> updateCurrentFeature_(<span class="keywordtype">bool</span> create);</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> </div>
<div class="line"><a name="l00132"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a12ef282e6aaf2af39b2efd529f8c366a"> 132</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a12ef282e6aaf2af39b2efd529f8c366a">disable_parsing_</a>;</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a name="l00135"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a5ed3baf0a9049f7413de157bc94ed214"> 135</a></span>  <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> * <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a5ed3baf0a9049f7413de157bc94ed214">current_feature_</a>;</div>
<div class="line"><a name="l00137"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a3e0c76f05a12825817a8437397efebfe"> 137</a></span>  <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<Feature></a> * <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a3e0c76f05a12825817a8437397efebfe">map_</a>;</div>
<div class="line"><a name="l00139"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#aa737b20acdbdace31394d0d052e595c4"> 139</a></span>  <a class="code" href="classOpenMS_1_1FeatureFileOptions.html">FeatureFileOptions</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#aa737b20acdbdace31394d0d052e595c4">options_</a>;</div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#acceaf354b05948d7dbe0abcc281b1e77"> 141</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#acceaf354b05948d7dbe0abcc281b1e77">size_only_</a>;</div>
<div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#afd35ebe459662ff4470a8ed425008114"> 143</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#afd35ebe459662ff4470a8ed425008114">expected_size_</a>;</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#acb2c1043367d1ab128fa399fbf58486f"> 147</a></span>  <a class="code" href="classOpenMS_1_1ModelDescription.html">ModelDescription<2></a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#acb2c1043367d1ab128fa399fbf58486f">model_desc_</a>;</div>
<div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a28c73e623c63a4fe3bfceb1ae8274f39"> 148</a></span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>;</div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#abcf2390e346a8cf1a3ba92ed7a18c0a5"> 149</a></span>  <a class="code" href="classOpenMS_1_1ConvexHull2D.html#abdcce0f11b8d73a2b4da5b1a00457d7b">ConvexHull2D::PointArrayType</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#abcf2390e346a8cf1a3ba92ed7a18c0a5">current_chull_</a>;</div>
<div class="line"><a name="l00150"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a13f7d99438428a09180ecb8dcc150eea"> 150</a></span>  <a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a13f7d99438428a09180ecb8dcc150eea">hull_position_</a>;</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a name="l00154"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#ab5aad57e2888d802c723198751fb316c"> 154</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#ab5aad57e2888d802c723198751fb316c">dim_</a>;</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span> </div>
<div class="line"><a name="l00157"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#aec4ba30d606de78e435df3c5ff9329d0"> 157</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#aec4ba30d606de78e435df3c5ff9329d0">in_description_</a>;</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> </div>
<div class="line"><a name="l00160"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a8601bf4da7f6183ac9dc6251893dd9d6"> 160</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a8601bf4da7f6183ac9dc6251893dd9d6">subordinate_feature_level_</a>;</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> </div>
<div class="line"><a name="l00163"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a23a7355f9a0e61f3990a763f0fa7c528"> 163</a></span>  <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a> * <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a23a7355f9a0e61f3990a763f0fa7c528">last_meta_</a>;</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> </div>
<div class="line"><a name="l00166"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a5e548fc9726de1f64e315fa215f4de19"> 166</a></span>  <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a5e548fc9726de1f64e315fa215f4de19">prot_id_</a>;</div>
<div class="line"><a name="l00168"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#ab59916b51e0840799c0a78ed04d7f859"> 168</a></span>  <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#ab59916b51e0840799c0a78ed04d7f859">pep_id_</a>;</div>
<div class="line"><a name="l00170"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a855d1cd159f5a8295c3d6be4327a1542"> 170</a></span>  <a class="code" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a855d1cd159f5a8295c3d6be4327a1542">prot_hit_</a>;</div>
<div class="line"><a name="l00172"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a963bc7db375d58bd099601271cc7a011"> 172</a></span>  <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a963bc7db375d58bd099601271cc7a011">pep_hit_</a>;</div>
<div class="line"><a name="l00174"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#ad23fa42c762a035786d56a07e2f1ea16"> 174</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<String, String></a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#ad23fa42c762a035786d56a07e2f1ea16">proteinid_to_accession_</a>;</div>
<div class="line"><a name="l00176"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a15e5e3bc144b437972738bf1d168b741"> 176</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<String, Size></a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a15e5e3bc144b437972738bf1d168b741">accession_to_id_</a>;</div>
<div class="line"><a name="l00178"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a65fe117944045e89e6add20e3f7ba912"> 178</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<String, String></a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a65fe117944045e89e6add20e3f7ba912">identifier_id_</a>;</div>
<div class="line"><a name="l00180"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a3b0075b28e6591f39fafa2720002c5d6"> 180</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<String, String></a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a3b0075b28e6591f39fafa2720002c5d6">id_identifier_</a>;</div>
<div class="line"><a name="l00182"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureXMLFile.html#a22cfe808d1f3b2c6b9f97ccde38e6ec4"> 182</a></span>  <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">ProteinIdentification::SearchParameters</a> <a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a22cfe808d1f3b2c6b9f97ccde38e6ec4">search_param_</a>;</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span> </div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  };</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span> </div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> </div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span> <span class="preprocessor">#endif // OPENMS_FORMAT_FeatureXMLFile_H</span></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a13f7d99438428a09180ecb8dcc150eea"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a13f7d99438428a09180ecb8dcc150eea">OpenMS::FeatureXMLFile::hull_position_</a></div><div class="ttdeci">DPosition< 2 > hull_position_</div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:150</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html">OpenMS::ProteinIdentification</a></div><div class="ttdoc">Representation of a protein identification run. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:61</div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a5ed3baf0a9049f7413de157bc94ed214"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a5ed3baf0a9049f7413de157bc94ed214">OpenMS::FeatureXMLFile::current_feature_</a></div><div class="ttdeci">Feature * current_feature_</div><div class="ttdoc">points to the last open &lt;feature&gt; tag (possibly a subordinate feature) </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:135</div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a22cfe808d1f3b2c6b9f97ccde38e6ec4"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a22cfe808d1f3b2c6b9f97ccde38e6ec4">OpenMS::FeatureXMLFile::search_param_</a></div><div class="ttdeci">ProteinIdentification::SearchParameters search_param_</div><div class="ttdoc">Temporary search parameters file. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:182</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap<></a></div></div>
<div class="ttc" id="classOpenMS_1_1ConvexHull2D_html_abdcce0f11b8d73a2b4da5b1a00457d7b"><div class="ttname"><a href="classOpenMS_1_1ConvexHull2D.html#abdcce0f11b8d73a2b4da5b1a00457d7b">OpenMS::ConvexHull2D::PointArrayType</a></div><div class="ttdeci">std::vector< PointType > PointArrayType</div><div class="ttdef"><b>Definition:</b> ConvexHull2D.h:79</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html">OpenMS::Internal::XMLHandler</a></div><div class="ttdoc">Base class for XML handlers. </div><div class="ttdef"><b>Definition:</b> XMLHandler.h:89</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a12ef282e6aaf2af39b2efd529f8c366a"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a12ef282e6aaf2af39b2efd529f8c366a">OpenMS::FeatureXMLFile::disable_parsing_</a></div><div class="ttdeci">Int disable_parsing_</div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:132</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_acceaf354b05948d7dbe0abcc281b1e77"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#acceaf354b05948d7dbe0abcc281b1e77">OpenMS::FeatureXMLFile::size_only_</a></div><div class="ttdeci">bool size_only_</div><div class="ttdoc">only parse until &quot;count&quot; tag is reached (used in loadSize()) </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:141</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">OpenMS::ProteinIdentification::SearchParameters</a></div><div class="ttdoc">Search parameters of the DB search. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:115</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_ad23fa42c762a035786d56a07e2f1ea16"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#ad23fa42c762a035786d56a07e2f1ea16">OpenMS::FeatureXMLFile::proteinid_to_accession_</a></div><div class="ttdeci">Map< String, String > proteinid_to_accession_</div><div class="ttdoc">Map from protein id to accession. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:174</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a65fe117944045e89e6add20e3f7ba912"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a65fe117944045e89e6add20e3f7ba912">OpenMS::FeatureXMLFile::identifier_id_</a></div><div class="ttdeci">Map< String, String > identifier_id_</div><div class="ttdoc">Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...</div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:178</div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition< 2 ></a></div></div>
<div class="ttc" id="classOpenMS_1_1PeptideHit_html"><div class="ttname"><a href="classOpenMS_1_1PeptideHit.html">OpenMS::PeptideHit</a></div><div class="ttdoc">Representation of a peptide hit. </div><div class="ttdef"><b>Definition:</b> PeptideHit.h:54</div></div>
<div class="ttc" id="XMLFile_8h_html"><div class="ttname"><a href="XMLFile_8h.html">XMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_aec4ba30d606de78e435df3c5ff9329d0"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#aec4ba30d606de78e435df3c5ff9329d0">OpenMS::FeatureXMLFile::in_description_</a></div><div class="ttdeci">bool in_description_</div><div class="ttdoc">for downward compatibility, all tags in the old description must be ignored </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:157</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_acb2c1043367d1ab128fa399fbf58486f"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#acb2c1043367d1ab128fa399fbf58486f">OpenMS::FeatureXMLFile::model_desc_</a></div><div class="ttdeci">ModelDescription< 2 > model_desc_</div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:147</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFileOptions_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFileOptions.html">OpenMS::FeatureFileOptions</a></div><div class="ttdoc">Options for loading files containing features. </div><div class="ttdef"><b>Definition:</b> FeatureFileOptions.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a3b0075b28e6591f39fafa2720002c5d6"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a3b0075b28e6591f39fafa2720002c5d6">OpenMS::FeatureXMLFile::id_identifier_</a></div><div class="ttdeci">Map< String, String > id_identifier_</div><div class="ttdoc">Map from file xs:id to identification run identifier (for linking peptide identifications to the corr...</div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:180</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_ab59916b51e0840799c0a78ed04d7f859"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#ab59916b51e0840799c0a78ed04d7f859">OpenMS::FeatureXMLFile::pep_id_</a></div><div class="ttdeci">PeptideIdentification pep_id_</div><div class="ttdoc">Temporary peptide ProteinIdentification. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:168</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html"><div class="ttname"><a href="classOpenMS_1_1Feature.html">OpenMS::Feature</a></div><div class="ttdoc">An LC-MS feature. </div><div class="ttdef"><b>Definition:</b> Feature.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a963bc7db375d58bd099601271cc7a011"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a963bc7db375d58bd099601271cc7a011">OpenMS::FeatureXMLFile::pep_hit_</a></div><div class="ttdeci">PeptideHit pep_hit_</div><div class="ttdoc">Temporary peptide hit. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:172</div></div>
<div class="ttc" id="group__Concept_html_ga5162db95dc78bdf2e3a71d73bec703e9"><div class="ttname"><a href="group__Concept.html#ga5162db95dc78bdf2e3a71d73bec703e9">OpenMS::UInt64</a></div><div class="ttdeci">OPENMS_UINT64_TYPE UInt64</div><div class="ttdoc">Unsigned integer type (64bit) </div><div class="ttdef"><b>Definition:</b> Types.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a28c73e623c63a4fe3bfceb1ae8274f39"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a28c73e623c63a4fe3bfceb1ae8274f39">OpenMS::FeatureXMLFile::param_</a></div><div class="ttdeci">Param param_</div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:148</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html">OpenMS::MetaInfoInterface</a></div><div class="ttdoc">Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). </div><div class="ttdef"><b>Definition:</b> MetaInfoInterface.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html"><div class="ttname"><a href="classOpenMS_1_1Param.html">OpenMS::Param</a></div><div class="ttdoc">Management and storage of parameters / INI files. </div><div class="ttdef"><b>Definition:</b> Param.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinHit_html"><div class="ttname"><a href="classOpenMS_1_1ProteinHit.html">OpenMS::ProteinHit</a></div><div class="ttdoc">Representation of a protein hit. </div><div class="ttdef"><b>Definition:</b> ProteinHit.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a23a7355f9a0e61f3990a763f0fa7c528"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a23a7355f9a0e61f3990a763f0fa7c528">OpenMS::FeatureXMLFile::last_meta_</a></div><div class="ttdeci">MetaInfoInterface * last_meta_</div><div class="ttdoc">Pointer to last read object as a MetaInfoInterface, or null. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:163</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a3e0c76f05a12825817a8437397efebfe"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a3e0c76f05a12825817a8437397efebfe">OpenMS::FeatureXMLFile::map_</a></div><div class="ttdeci">FeatureMap< Feature > * map_</div><div class="ttdoc">Feature map pointer for reading. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:137</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_ab5aad57e2888d802c723198751fb316c"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#ab5aad57e2888d802c723198751fb316c">OpenMS::FeatureXMLFile::dim_</a></div><div class="ttdeci">UInt dim_</div><div class="ttdoc">current dimension of the feature position, quality, or convex hull point </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:154</div></div>
<div class="ttc" id="classOpenMS_1_1ModelDescription_html"><div class="ttname"><a href="classOpenMS_1_1ModelDescription.html">OpenMS::ModelDescription< 2 ></a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html">OpenMS::FeatureXMLFile</a></div><div class="ttdoc">This class provides Input/Output functionality for feature maps. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a8601bf4da7f6183ac9dc6251893dd9d6"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a8601bf4da7f6183ac9dc6251893dd9d6">OpenMS::FeatureXMLFile::subordinate_feature_level_</a></div><div class="ttdeci">Int subordinate_feature_level_</div><div class="ttdoc">level in Feature stack during parsing </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:160</div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a855d1cd159f5a8295c3d6be4327a1542"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a855d1cd159f5a8295c3d6be4327a1542">OpenMS::FeatureXMLFile::prot_hit_</a></div><div class="ttdeci">ProteinHit prot_hit_</div><div class="ttdoc">Temporary protein hit. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:170</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLFile_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLFile.html">OpenMS::Internal::XMLFile</a></div><div class="ttdoc">Base class for loading/storing XML files that have a handler derived from XMLHandler. </div><div class="ttdef"><b>Definition:</b> XMLFile.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a15e5e3bc144b437972738bf1d168b741"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a15e5e3bc144b437972738bf1d168b741">OpenMS::FeatureXMLFile::accession_to_id_</a></div><div class="ttdeci">Map< String, Size > accession_to_id_</div><div class="ttdoc">Map from search identifier concatenated with protein accession to id. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:176</div></div>
<div class="ttc" id="FeatureFileOptions_8h_html"><div class="ttname"><a href="FeatureFileOptions_8h.html">FeatureFileOptions.h</a></div></div>
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_afd35ebe459662ff4470a8ed425008114"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#afd35ebe459662ff4470a8ed425008114">OpenMS::FeatureXMLFile::expected_size_</a></div><div class="ttdeci">Size expected_size_</div><div class="ttdoc">holds the putative size given in count </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:143</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a5e548fc9726de1f64e315fa215f4de19"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a5e548fc9726de1f64e315fa215f4de19">OpenMS::FeatureXMLFile::prot_id_</a></div><div class="ttdeci">ProteinIdentification prot_id_</div><div class="ttdoc">Temporary protein ProteinIdentification. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:166</div></div>
<div class="ttc" id="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_aa737b20acdbdace31394d0d052e595c4"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#aa737b20acdbdace31394d0d052e595c4">OpenMS::FeatureXMLFile::options_</a></div><div class="ttdeci">FeatureFileOptions options_</div><div class="ttdoc">Options that can be set. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:139</div></div>
<div class="ttc" id="XMLHandler_8h_html"><div class="ttname"><a href="XMLHandler_8h.html">XMLHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_abcf2390e346a8cf1a3ba92ed7a18c0a5"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#abcf2390e346a8cf1a3ba92ed7a18c0a5">OpenMS::FeatureXMLFile::current_chull_</a></div><div class="ttdeci">ConvexHull2D::PointArrayType current_chull_</div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:149</div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html">OpenMS::PeptideIdentification</a></div><div class="ttdoc">Represents the peptide hits for a spectrum. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:63</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:14 using doxygen 1.8.5</font></TD>
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