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<a href="PeptideAndProteinQuant_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>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<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>&#160;<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>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<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>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Hendrik Weisser $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Hendrik Weisser $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_ANALYSIS_QUANTITATION_PEPTIDEANDPROTEINQUANT_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_QUANTITATION_PEPTIDEANDPROTEINQUANT_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ConsensusMap_8h.html">OpenMS/KERNEL/ConsensusMap.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ProteinIdentification_8h.html">OpenMS/METADATA/ProteinIdentification.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;{</div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideAndProteinQuant.html">   53</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html">PeptideAndProteinQuant</a> :</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;  {</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideAndProteinQuant.html#a5242f4ede25f6f7f0ec9f634244c78d6">   59</a></span>&#160;    <span class="keyword">typedef</span> std::map&lt;UInt64, DoubleReal&gt; <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#a5242f4ede25f6f7f0ec9f634244c78d6">SampleAbundances</a>;</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;</div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html">   62</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html">PeptideData</a></div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    {</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#acfd3381d755aea18f59399348ca86809">   65</a></span>&#160;      std::map&lt;Int, SampleAbundances&gt; <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#acfd3381d755aea18f59399348ca86809">abundances</a>;</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a28c74e05409d9027ed5d90127eb561d7">   68</a></span>&#160;      <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#a5242f4ede25f6f7f0ec9f634244c78d6">SampleAbundances</a> <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a28c74e05409d9027ed5d90127eb561d7">total_abundances</a>;</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a532b76a601a2c4089468ea5c8f4edd22">   71</a></span>&#160;      std::set&lt;String&gt; <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a532b76a601a2c4089468ea5c8f4edd22">accessions</a>;</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a1819575c90213c6e1dca6b8487a906e1">   74</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a1819575c90213c6e1dca6b8487a906e1">id_count</a>;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a5f1667a7032c74db7896886c185e43be">   77</a></span>&#160;      <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a5f1667a7032c74db7896886c185e43be">PeptideData</a>() :</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;        id_count(0) {}</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    };</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;</div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideAndProteinQuant.html#a2750aa75b50972d89e20d01214ff1c01">   82</a></span>&#160;    <span class="keyword">typedef</span> std::map&lt;AASequence, PeptideData&gt; <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#a2750aa75b50972d89e20d01214ff1c01">PeptideQuant</a>;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;</div>
<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html">   85</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html">ProteinData</a></div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;    {</div>
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#a4af368efa85924b7a2b6c7656333a830">   88</a></span>&#160;      std::map&lt;String, SampleAbundances&gt; <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#a4af368efa85924b7a2b6c7656333a830">abundances</a>;</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;</div>
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#a28c74e05409d9027ed5d90127eb561d7">   91</a></span>&#160;      <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#a5242f4ede25f6f7f0ec9f634244c78d6">SampleAbundances</a> <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#a28c74e05409d9027ed5d90127eb561d7">total_abundances</a>;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#a1819575c90213c6e1dca6b8487a906e1">   94</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#a1819575c90213c6e1dca6b8487a906e1">id_count</a>;</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;</div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#ad588e320449512f6befbb9ac4241af56">   97</a></span>&#160;      <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#ad588e320449512f6befbb9ac4241af56">ProteinData</a>() :</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;        id_count(0) {}</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    };</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideAndProteinQuant.html#a38f6c1fb46b4457f1fcde70b207f0cea">  102</a></span>&#160;    <span class="keyword">typedef</span> std::map&lt;String, ProteinData&gt; <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#a38f6c1fb46b4457f1fcde70b207f0cea">ProteinQuant</a>;</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html">  105</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html">Statistics</a></div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;    {</div>
<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#aa8c25fdd7955d31e7bd4ce34f35b6361">  108</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#aa8c25fdd7955d31e7bd4ce34f35b6361">n_samples</a>;</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;</div>
<div class="line"><a name="l00111"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#ae63f65c79e6263ccc6ab72b483d553cf">  111</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> quant_proteins, <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#ae63f65c79e6263ccc6ab72b483d553cf">too_few_peptides</a>;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;</div>
<div class="line"><a name="l00114"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#a9b3565ea06566c02e0a1982a8c99238f">  114</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> quant_peptides, <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#a9b3565ea06566c02e0a1982a8c99238f">total_peptides</a>;</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;</div>
<div class="line"><a name="l00117"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#a38cfee3fe8e2ee26fd7d6df159f79545">  117</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> quant_features, <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#a38cfee3fe8e2ee26fd7d6df159f79545">total_features</a>, blank_features, ambig_features;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;</div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#abbb2d8b17aeeb5883b910fab07762a14">  120</a></span>&#160;      <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#abbb2d8b17aeeb5883b910fab07762a14">Statistics</a>() :</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;        n_samples(0), quant_proteins(0), too_few_peptides(0),</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;        quant_peptides(0), total_peptides(0), quant_features(0),</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;        total_features(0), blank_features(0), ambig_features(0) {}</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;    };</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;    <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html">PeptideAndProteinQuant</a>();</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;</div>
<div class="line"><a name="l00130"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideAndProteinQuant.html#acc999d51d6f370ed969d0c89a65884b8">  130</a></span>&#160;    <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#acc999d51d6f370ed969d0c89a65884b8">~PeptideAndProteinQuant</a>() {}</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;    <span class="keywordtype">void</span> quantifyPeptides(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a>&amp; features);</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;    <span class="keywordtype">void</span> quantifyPeptides(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a>&amp; consensus);</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;    <span class="keywordtype">void</span> quantifyPeptides(std::vector&lt;ProteinIdentification&gt;&amp; proteins,</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;                          std::vector&lt;PeptideIdentification&gt;&amp; peptides);</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;    <span class="keywordtype">void</span> quantifyProteins(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &amp; proteins =</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;                            <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>());</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;    <span class="keyword">const</span> Statistics &amp; getStatistics();</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;    <span class="keyword">const</span> PeptideQuant &amp; getPeptideResults();</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;    <span class="keyword">const</span> ProteinQuant &amp; getProteinResults();</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideAndProteinQuant.html#adf2156f63e081adc052ffa6fbfe14fb4">  174</a></span>&#160;    <a class="code" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html">Statistics</a> <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#adf2156f63e081adc052ffa6fbfe14fb4">stats_</a>;</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;</div>
<div class="line"><a name="l00177"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideAndProteinQuant.html#a9c294e9f368e113196bb5306dd4ba1f6">  177</a></span>&#160;    <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#a2750aa75b50972d89e20d01214ff1c01">PeptideQuant</a> <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#a9c294e9f368e113196bb5306dd4ba1f6">pep_quant_</a>;</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;</div>
<div class="line"><a name="l00180"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideAndProteinQuant.html#af075fa02d32cdcabfb6de54142f9d3ca">  180</a></span>&#160;    <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#a38f6c1fb46b4457f1fcde70b207f0cea">ProteinQuant</a> <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#af075fa02d32cdcabfb6de54142f9d3ca">prot_quant_</a>;</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> getAnnotation_(std::vector&lt;PeptideIdentification&gt; &amp; peptides);</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;    <span class="keywordtype">void</span> quantifyFeature_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureHandle.html">FeatureHandle</a> &amp; feature, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> &amp; hit);</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> T&gt;</div>
<div class="line"><a name="l00204"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideAndProteinQuant.html#a3be41534a677c665572d841c7aa81a7f">  204</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html#a3be41534a677c665572d841c7aa81a7f">orderBest_</a>(<span class="keyword">const</span> std::map&lt;T, SampleAbundances&gt; abundances,</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;                    std::vector&lt;T&gt; &amp; result)</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;    {</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;      <span class="keyword">typedef</span> std::pair&lt;Size, DoubleReal&gt; PairType;</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;      std::multimap&lt;PairType, T, std::greater&lt;PairType&gt; &gt; order;</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> std::map&lt;T, SampleAbundances&gt;::const_iterator ab_it =</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;             abundances.begin(); ab_it != abundances.end(); ++ab_it)</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;      {</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> total = 0.0;</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;        <span class="keywordflow">for</span> (SampleAbundances::const_iterator samp_it = ab_it-&gt;second.begin();</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;             samp_it != ab_it-&gt;second.end(); ++samp_it)</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;        {</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;          total += samp_it-&gt;second;</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;        }</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;        <span class="keywordflow">if</span> (total &lt;= 0.0) <span class="keywordflow">continue</span>;         <span class="comment">// not quantified</span></div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;        PairType key = std::make_pair(ab_it-&gt;second.size(), total);</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;        order.insert(std::make_pair(key, ab_it-&gt;first));</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;      }</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;      result.clear();</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> std::multimap&lt;PairType, T, std::greater&lt;PairType&gt; &gt;::</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;           iterator ord_it = order.begin(); ord_it != order.end(); ++ord_it)</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;      {</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;        result.push_back(ord_it-&gt;second);</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;      }</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;    }</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;    <span class="keywordtype">void</span> quantifyPeptides_();</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;    <span class="keywordtype">void</span> normalizePeptides_();</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> getAccession_(<span class="keyword">const</span> std::set&lt;String&gt; &amp; pep_accessions,</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;                         std::map&lt;String, String&gt; &amp; accession_to_leader);</div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;</div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;    <span class="keywordtype">void</span> countPeptides_(std::vector&lt;PeptideIdentification&gt; &amp; peptides);</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;</div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;    <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;  };   <span class="comment">// class</span></div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;</div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;} <span class="comment">// namespace</span></div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;<span class="preprocessor">#endif // OPENMS_ANALYSIS_QUANTITATION_PEPTIDEANDPROTEINQUANT_H</span></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics_html_ae63f65c79e6263ccc6ab72b483d553cf"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#ae63f65c79e6263ccc6ab72b483d553cf">OpenMS::PeptideAndProteinQuant::Statistics::too_few_peptides</a></div><div class="ttdeci">Size too_few_peptides</div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:111</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="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics_html_abbb2d8b17aeeb5883b910fab07762a14"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#abbb2d8b17aeeb5883b910fab07762a14">OpenMS::PeptideAndProteinQuant::Statistics::Statistics</a></div><div class="ttdeci">Statistics()</div><div class="ttdoc">constructor </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:120</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics_html_a9b3565ea06566c02e0a1982a8c99238f"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#a9b3565ea06566c02e0a1982a8c99238f">OpenMS::PeptideAndProteinQuant::Statistics::total_peptides</a></div><div class="ttdeci">Size total_peptides</div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:114</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="ConsensusMap_8h_html"><div class="ttname"><a href="ConsensusMap_8h.html">ConsensusMap.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics_html_aa8c25fdd7955d31e7bd4ce34f35b6361"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#aa8c25fdd7955d31e7bd4ce34f35b6361">OpenMS::PeptideAndProteinQuant::Statistics::n_samples</a></div><div class="ttdeci">Size n_samples</div><div class="ttdoc">number of samples </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:108</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData_html_ad588e320449512f6befbb9ac4241af56"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#ad588e320449512f6befbb9ac4241af56">OpenMS::PeptideAndProteinQuant::ProteinData::ProteinData</a></div><div class="ttdeci">ProteinData()</div><div class="ttdoc">constructor </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:97</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap&lt;&gt;</a></div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics_html_a38cfee3fe8e2ee26fd7d6df159f79545"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#a38cfee3fe8e2ee26fd7d6df159f79545">OpenMS::PeptideAndProteinQuant::Statistics::total_features</a></div><div class="ttdeci">Size total_features</div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html">OpenMS::ConsensusMap</a></div><div class="ttdoc">A container for consensus elements. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:60</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData_html_a532b76a601a2c4089468ea5c8f4edd22"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a532b76a601a2c4089468ea5c8f4edd22">OpenMS::PeptideAndProteinQuant::PeptideData::accessions</a></div><div class="ttdeci">std::set&lt; String &gt; accessions</div><div class="ttdoc">protein accessions for this peptide </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideAndProteinQuant_html_a9c294e9f368e113196bb5306dd4ba1f6"><div class="ttname"><a href="classOpenMS_1_1PeptideAndProteinQuant.html#a9c294e9f368e113196bb5306dd4ba1f6">OpenMS::PeptideAndProteinQuant::pep_quant_</a></div><div class="ttdeci">PeptideQuant pep_quant_</div><div class="ttdoc">Peptide quantification data. </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:177</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideAndProteinQuant_html_acc999d51d6f370ed969d0c89a65884b8"><div class="ttname"><a href="classOpenMS_1_1PeptideAndProteinQuant.html#acc999d51d6f370ed969d0c89a65884b8">OpenMS::PeptideAndProteinQuant::~PeptideAndProteinQuant</a></div><div class="ttdeci">~PeptideAndProteinQuant()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:130</div></div>
<div class="ttc" id="ProteinIdentification_8h_html"><div class="ttname"><a href="ProteinIdentification_8h.html">ProteinIdentification.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PeptideAndProteinQuant_html_a38f6c1fb46b4457f1fcde70b207f0cea"><div class="ttname"><a href="classOpenMS_1_1PeptideAndProteinQuant.html#a38f6c1fb46b4457f1fcde70b207f0cea">OpenMS::PeptideAndProteinQuant::ProteinQuant</a></div><div class="ttdeci">std::map&lt; String, ProteinData &gt; ProteinQuant</div><div class="ttdoc">Mapping: protein accession -&amp;gt; protein data. </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:102</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData_html_acfd3381d755aea18f59399348ca86809"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#acfd3381d755aea18f59399348ca86809">OpenMS::PeptideAndProteinQuant::PeptideData::abundances</a></div><div class="ttdeci">std::map&lt; Int, SampleAbundances &gt; abundances</div><div class="ttdoc">mapping: charge -&amp;gt; sample -&amp;gt; abundance </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideAndProteinQuant_html_a2750aa75b50972d89e20d01214ff1c01"><div class="ttname"><a href="classOpenMS_1_1PeptideAndProteinQuant.html#a2750aa75b50972d89e20d01214ff1c01">OpenMS::PeptideAndProteinQuant::PeptideQuant</a></div><div class="ttdeci">std::map&lt; AASequence, PeptideData &gt; PeptideQuant</div><div class="ttdoc">Mapping: peptide sequence (modified) -&amp;gt; peptide data. </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:82</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData_html_a5f1667a7032c74db7896886c185e43be"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a5f1667a7032c74db7896886c185e43be">OpenMS::PeptideAndProteinQuant::PeptideData::PeptideData</a></div><div class="ttdeci">PeptideData()</div><div class="ttdoc">constructor </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideAndProteinQuant_html"><div class="ttname"><a href="classOpenMS_1_1PeptideAndProteinQuant.html">OpenMS::PeptideAndProteinQuant</a></div><div class="ttdoc">Helper class for peptide and protein quantification based on feature data annotated with IDs...</div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:53</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="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData_html_a1819575c90213c6e1dca6b8487a906e1"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a1819575c90213c6e1dca6b8487a906e1">OpenMS::PeptideAndProteinQuant::PeptideData::id_count</a></div><div class="ttdeci">Size id_count</div><div class="ttdoc">number of identifications </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:74</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData_html"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html">OpenMS::PeptideAndProteinQuant::PeptideData</a></div><div class="ttdoc">Quantitative and associated data for a peptide. </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideAndProteinQuant_html_adf2156f63e081adc052ffa6fbfe14fb4"><div class="ttname"><a href="classOpenMS_1_1PeptideAndProteinQuant.html#adf2156f63e081adc052ffa6fbfe14fb4">OpenMS::PeptideAndProteinQuant::stats_</a></div><div class="ttdeci">Statistics stats_</div><div class="ttdoc">Processing statistics for output in the end. </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:174</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData_html_a28c74e05409d9027ed5d90127eb561d7"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#a28c74e05409d9027ed5d90127eb561d7">OpenMS::PeptideAndProteinQuant::PeptideData::total_abundances</a></div><div class="ttdeci">SampleAbundances total_abundances</div><div class="ttdoc">mapping: sample -&amp;gt; total abundance </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:68</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData_html_a28c74e05409d9027ed5d90127eb561d7"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#a28c74e05409d9027ed5d90127eb561d7">OpenMS::PeptideAndProteinQuant::ProteinData::total_abundances</a></div><div class="ttdeci">SampleAbundances total_abundances</div><div class="ttdoc">mapping: sample -&amp;gt; total abundance </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:91</div></div>
<div class="ttc" id="PeptideIdentification_8h_html"><div class="ttname"><a href="PeptideIdentification_8h.html">PeptideIdentification.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PeptideAndProteinQuant_html_a5242f4ede25f6f7f0ec9f634244c78d6"><div class="ttname"><a href="classOpenMS_1_1PeptideAndProteinQuant.html#a5242f4ede25f6f7f0ec9f634244c78d6">OpenMS::PeptideAndProteinQuant::SampleAbundances</a></div><div class="ttdeci">std::map&lt; UInt64, DoubleReal &gt; SampleAbundances</div><div class="ttdoc">Mapping: sample ID -&amp;gt; abundance. </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:59</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_1PeptideAndProteinQuant_html_a3be41534a677c665572d841c7aa81a7f"><div class="ttname"><a href="classOpenMS_1_1PeptideAndProteinQuant.html#a3be41534a677c665572d841c7aa81a7f">OpenMS::PeptideAndProteinQuant::orderBest_</a></div><div class="ttdeci">void orderBest_(const std::map&lt; T, SampleAbundances &gt; abundances, std::vector&lt; T &gt; &amp;result)</div><div class="ttdoc">Order keys (charges/peptides for peptide/protein quantification) according to how many samples they a...</div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:204</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureHandle_html"><div class="ttname"><a href="classOpenMS_1_1FeatureHandle.html">OpenMS::FeatureHandle</a></div><div class="ttdoc">Representation of a Peak2D, RichPeak2D or Feature . </div><div class="ttdef"><b>Definition:</b> FeatureHandle.h:54</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics_html"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html">OpenMS::PeptideAndProteinQuant::Statistics</a></div><div class="ttdoc">Statistics for processing summary. </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData_html_a4af368efa85924b7a2b6c7656333a830"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#a4af368efa85924b7a2b6c7656333a830">OpenMS::PeptideAndProteinQuant::ProteinData::abundances</a></div><div class="ttdeci">std::map&lt; String, SampleAbundances &gt; abundances</div><div class="ttdoc">mapping: peptide (unmodified) -&amp;gt; sample -&amp;gt; abundance </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:88</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData_html"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html">OpenMS::PeptideAndProteinQuant::ProteinData</a></div><div class="ttdoc">Quantitative and associated data for a protein. </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:85</div></div>
<div class="ttc" id="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData_html_a1819575c90213c6e1dca6b8487a906e1"><div class="ttname"><a href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#a1819575c90213c6e1dca6b8487a906e1">OpenMS::PeptideAndProteinQuant::ProteinData::id_count</a></div><div class="ttdeci">Size id_count</div><div class="ttdoc">total number of identifications (of peptides mapping to this protein) </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideAndProteinQuant_html_af075fa02d32cdcabfb6de54142f9d3ca"><div class="ttname"><a href="classOpenMS_1_1PeptideAndProteinQuant.html#af075fa02d32cdcabfb6de54142f9d3ca">OpenMS::PeptideAndProteinQuant::prot_quant_</a></div><div class="ttdeci">ProteinQuant prot_quant_</div><div class="ttdoc">Protein quantification data. </div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:180</div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
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