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<a href="IDFilter_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>
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<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
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<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: Mathias Walzer $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Nico Pfeifer, Mathias Walzer$</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_FILTERING_ID_IDFILTER_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_FILTERING_ID_IDFILTER_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;OpenMS/config.h&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="String_8h.html">OpenMS/DATASTRUCTURES/String.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="ProteinIdentification_8h.html">OpenMS/METADATA/ProteinIdentification.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="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.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="FASTAFile_8h.html">OpenMS/FORMAT/FASTAFile.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="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;climits&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;{</div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDFilter.html">   61</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1IDFilter.html">IDFilter</a></div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;  {</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    <a class="code" href="classOpenMS_1_1IDFilter.html">IDFilter</a>();</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1IDFilter.html">IDFilter</a>();</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> IdentificationType&gt;</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDFilter.html#a42a3948a25feb4e02008d72c65023c3a">   73</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1IDFilter.html#a42a3948a25feb4e02008d72c65023c3a">filterIdentificationsByThreshold</a>(<span class="keyword">const</span> IdentificationType&amp; identification, <a class="code" href="classdouble.html">DoubleReal</a> threshold_fraction, IdentificationType&amp; filtered_identification)</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    {</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;      <span class="keyword">typedef</span> <span class="keyword">typename</span> IdentificationType::HitType HitType;</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;      std::vector&lt;HitType&gt; temp_hits;</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;      std::vector&lt;HitType&gt; filtered_hits;</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;      filtered_identification = identification;</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;      filtered_identification.setHits(std::vector&lt;HitType&gt;());</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> std::vector&lt;HitType&gt;::const_iterator it = identification.getHits().begin();</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;           it != identification.getHits().end();</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;           ++it)</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      {</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;        <span class="keywordflow">if</span> (it-&gt;getScore() &gt;= threshold_fraction * identification.getSignificanceThreshold())</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;        {</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;          filtered_hits.push_back(*it);</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;        }</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;      }</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      <span class="keywordflow">if</span> (!filtered_hits.empty())</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;      {</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;        filtered_identification.setHits(filtered_hits);</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;        filtered_identification.assignRanks();</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;      }</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;    }</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> IdentificationType&gt;</div>
<div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDFilter.html#a2a120b13c7cb47cb07897d54286d78dd">  107</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1IDFilter.html#a2a120b13c7cb47cb07897d54286d78dd">filterIdentificationsByScore</a>(<span class="keyword">const</span> IdentificationType&amp; identification, <a class="code" href="classdouble.html">DoubleReal</a> threshold_score, IdentificationType&amp; filtered_identification)</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;    {</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;      <span class="keyword">typedef</span> <span class="keyword">typename</span> IdentificationType::HitType HitType;</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;      std::vector&lt;HitType&gt; temp_hits;</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;      std::vector&lt;HitType&gt; filtered_hits;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;      filtered_identification = identification;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      filtered_identification.setHits(std::vector&lt;HitType&gt;());</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> std::vector&lt;HitType&gt;::const_iterator it = identification.getHits().begin();</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;           it != identification.getHits().end();</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;           ++it)</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;      {</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;        <span class="keywordflow">if</span> (identification.isHigherScoreBetter())</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;        {</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;          <span class="keywordflow">if</span> (it-&gt;getScore() &gt;= threshold_score)</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;          {</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;            filtered_hits.push_back(*it);</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;          }</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;        }</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;        {</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;          <span class="keywordflow">if</span> (it-&gt;getScore() &lt;= threshold_score)</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;          {</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;            filtered_hits.push_back(*it);</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;          }</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;        }</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;      }</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;      <span class="keywordflow">if</span> (!filtered_hits.empty())</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;      {</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;        filtered_identification.setHits(filtered_hits);</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;        filtered_identification.assignRanks();</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;      }</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;    }</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> IdentificationType&gt;</div>
<div class="line"><a name="l00150"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDFilter.html#a7908af59fd5a56c76d8dd8bff0bd943a">  150</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1IDFilter.html#a7908af59fd5a56c76d8dd8bff0bd943a">filterIdentificationsByBestNHits</a>(<span class="keyword">const</span> IdentificationType&amp; identification, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n, IdentificationType&amp; filtered_identification)</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;    {</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;      <span class="keyword">typedef</span> <span class="keyword">typename</span> IdentificationType::HitType HitType;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;      std::vector&lt;HitType&gt; temp_hits;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;      std::vector&lt;HitType&gt; filtered_hits;</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> count = 0;</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;      IdentificationType temp_identification = identification;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;      temp_identification.sort(); <span class="comment">// .. by score</span></div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;      filtered_identification = identification;</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;      filtered_identification.setHits(std::vector&lt;HitType&gt;());</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;      <span class="keyword">typename</span> std::vector&lt;HitType&gt;::const_iterator it = temp_identification.getHits().begin();</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;      <span class="keywordflow">while</span> (it != temp_identification.getHits().end()</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;            &amp;&amp; count &lt; n)</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;      {</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;        filtered_hits.push_back(*it);</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;        ++it;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;        ++count;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;      }</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;      <span class="keywordflow">if</span> (!filtered_hits.empty())</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;      {</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;        filtered_identification.setHits(filtered_hits);</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;        filtered_identification.assignRanks();</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;      }</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;    }</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> IdentificationType&gt;</div>
<div class="line"><a name="l00188"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDFilter.html#a8a3a8ce850473e14d5e25a9009c26c3d">  188</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1IDFilter.html#a8a3a8ce850473e14d5e25a9009c26c3d">filterIdentificationsByBestNToMHits</a>(<span class="keyword">const</span> IdentificationType&amp; identification, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m, IdentificationType&amp; filtered_identification)</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    {</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;      <span class="keywordflow">if</span> (n &gt; m)</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;      {</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;        std::swap(n, m);</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;      }</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;      <span class="keyword">typedef</span> <span class="keyword">typename</span> IdentificationType::HitType HitType;</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;      std::vector&lt;HitType&gt; filtered_hits;</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;      IdentificationType temp_identification = identification;</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;      temp_identification.sort(); <span class="comment">// .. by score</span></div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;      filtered_identification = identification;</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;      filtered_identification.setHits(std::vector&lt;HitType&gt;());</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;      <span class="keyword">const</span> std::vector&lt;HitType&gt;&amp; hits = temp_identification.getHits();</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = n - 1; n &lt;= m - 1; ++i)</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="keywordflow">if</span> (i &gt;= hits.size())</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;        {</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;          <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;        }</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;        filtered_hits.push_back(hits[i]);</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;      }</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;      <span class="keywordflow">if</span> (!filtered_hits.empty())</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;        filtered_identification.setHits(filtered_hits);</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;        filtered_identification.assignRanks();</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;      }</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;    }</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsByBestHits(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; identification, <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; filtered_identification, <span class="keywordtype">bool</span> strict = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsByProteins(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; identification, <span class="keyword">const</span> std::vector&lt;FASTAFile::FASTAEntry&gt;&amp; proteins, <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; filtered_identification, <span class="keywordtype">bool</span> no_protein_identifiers = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsByProteins(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>&amp; identification, <span class="keyword">const</span> std::vector&lt;FASTAFile::FASTAEntry&gt;&amp; proteins, <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>&amp; filtered_identification);</div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsByExclusionPeptides(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; identification, <span class="keyword">const</span> std::set&lt;String&gt;&amp; peptides, <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; filtered_identification);</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsByLength(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; identification, <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; filtered_identification, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> min_length, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_length = UINT_MAX);</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsByCharge(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; identification, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge, <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; filtered_identification);</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsByVariableModifications(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; identification, <span class="keyword">const</span> std::vector&lt;String&gt;&amp; fixed_modifications, <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; filtered_identification);</div>
<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;</div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;    <span class="keywordtype">void</span> removeUnreferencedProteinHits(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>&amp; identification, <span class="keyword">const</span> std::vector&lt;PeptideIdentification&gt; peptide_identifications, <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>&amp; filtered_identification);</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsUnique(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; identification, <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; filtered_identification);</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;</div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsByMzError(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; identification, <a class="code" href="classdouble.html">DoubleReal</a> mass_error, <span class="keywordtype">bool</span> unit_ppm, <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; filtered_identification);</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;</div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsByRTPValues(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; identification, <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; filtered_identification, <a class="code" href="classdouble.html">DoubleReal</a> p_value = 0.05);</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;    <span class="keywordtype">void</span> filterIdentificationsByRTFirstDimPValues(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; identification,</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;                                                  <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&amp; filtered_identification,</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;                                                  <a class="code" href="classdouble.html">DoubleReal</a>                                      p_value = 0.05);</div>
<div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> PeakT&gt;</div>
<div class="line"><a name="l00277"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDFilter.html#a5317f48e0a2b44028ade11faa175dc12">  277</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1IDFilter.html#a5317f48e0a2b44028ade11faa175dc12">filterIdentificationsByThresholds</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;PeakT&gt;</a>&amp; experiment, <a class="code" href="classdouble.html">DoubleReal</a> peptide_threshold_fraction, <a class="code" href="classdouble.html">DoubleReal</a> protein_threshold_fraction)</div>
<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;    {</div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;      <span class="comment">//filter protein hits</span></div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> temp_protein_identification;</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;      std::vector&lt;ProteinIdentification&gt; filtered_protein_identifications;</div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;</div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; experiment.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>().size(); j++)</div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;      {</div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;        filterIdentificationsByThreshold(experiment.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>()[j], protein_threshold_fraction, temp_protein_identification);</div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;        <span class="keywordflow">if</span> (!temp_protein_identification.<a class="code" href="classOpenMS_1_1ProteinIdentification.html#a69a3da6373dcd1505ea046971251023b">getHits</a>().empty())</div>
<div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;        {</div>
<div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;          filtered_protein_identifications.push_back(temp_protein_identification);</div>
<div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;        }</div>
<div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;      }</div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;      experiment.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#a6d85ac28bb82da988383fd19b8504988">setProteinIdentifications</a>(filtered_protein_identifications);</div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;</div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;      <span class="comment">//filter peptide hits</span></div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;      <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> temp_identification;</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;      std::vector&lt;PeptideIdentification&gt; filtered_identifications;</div>
<div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); i++)</div>
<div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;      {</div>
<div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; experiment[i].getPeptideIdentifications().<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); j++)</div>
<div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;        {</div>
<div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;          filterIdentificationsByThreshold(experiment[i].getPeptideIdentifications()[j], peptide_threshold_fraction, temp_identification);</div>
<div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;          <span class="keywordflow">if</span> (!temp_identification.<a class="code" href="classOpenMS_1_1PeptideIdentification.html#a564d2725cd06914a922d6fbda8be8a13">getHits</a>().empty())</div>
<div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;          {</div>
<div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;            filtered_identifications.push_back(temp_identification);</div>
<div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;          }</div>
<div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;        }</div>
<div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;        experiment[i].setPeptideIdentifications(filtered_identifications);</div>
<div class="line"><a name="l00308"></a><span class="lineno">  308</span>&#160;        filtered_identifications.clear();</div>
<div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;      }</div>
<div class="line"><a name="l00310"></a><span class="lineno">  310</span>&#160;    }</div>
<div class="line"><a name="l00311"></a><span class="lineno">  311</span>&#160;</div>
<div class="line"><a name="l00313"></a><span class="lineno">  313</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> PeakT&gt;</div>
<div class="line"><a name="l00314"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDFilter.html#aeb523c70d4d0f6e8cabd7b8db02cf638">  314</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1IDFilter.html#aeb523c70d4d0f6e8cabd7b8db02cf638">filterIdentificationsByScores</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;PeakT&gt;</a>&amp; experiment, <a class="code" href="classdouble.html">DoubleReal</a> peptide_threshold_score, <a class="code" href="classdouble.html">DoubleReal</a> protein_threshold_score)</div>
<div class="line"><a name="l00315"></a><span class="lineno">  315</span>&#160;    {</div>
<div class="line"><a name="l00316"></a><span class="lineno">  316</span>&#160;      <span class="comment">//filter protein hits</span></div>
<div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> temp_protein_identification;</div>
<div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;      std::vector&lt;ProteinIdentification&gt; filtered_protein_identifications;</div>
<div class="line"><a name="l00319"></a><span class="lineno">  319</span>&#160;</div>
<div class="line"><a name="l00320"></a><span class="lineno">  320</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; experiment.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>().size(); j++)</div>
<div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;      {</div>
<div class="line"><a name="l00322"></a><span class="lineno">  322</span>&#160;        filterIdentificationsByScore(experiment.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>()[j], protein_threshold_score, temp_protein_identification);</div>
<div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;        <span class="keywordflow">if</span> (!temp_protein_identification.<a class="code" href="classOpenMS_1_1ProteinIdentification.html#a69a3da6373dcd1505ea046971251023b">getHits</a>().empty())</div>
<div class="line"><a name="l00324"></a><span class="lineno">  324</span>&#160;        {</div>
<div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;          filtered_protein_identifications.push_back(temp_protein_identification);</div>
<div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;        }</div>
<div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;      }</div>
<div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;      experiment.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#a6d85ac28bb82da988383fd19b8504988">setProteinIdentifications</a>(filtered_protein_identifications);</div>
<div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;</div>
<div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;      <span class="comment">//filter peptide hits</span></div>
<div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;      <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> temp_identification;</div>
<div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;      std::vector&lt;PeptideIdentification&gt; filtered_identifications;</div>
<div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160;</div>
<div class="line"><a name="l00334"></a><span class="lineno">  334</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); i++)</div>
<div class="line"><a name="l00335"></a><span class="lineno">  335</span>&#160;      {</div>
<div class="line"><a name="l00336"></a><span class="lineno">  336</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; experiment[i].getPeptideIdentifications().<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); j++)</div>
<div class="line"><a name="l00337"></a><span class="lineno">  337</span>&#160;        {</div>
<div class="line"><a name="l00338"></a><span class="lineno">  338</span>&#160;          filterIdentificationsByScore(experiment[i].getPeptideIdentifications()[j], peptide_threshold_score, temp_identification);</div>
<div class="line"><a name="l00339"></a><span class="lineno">  339</span>&#160;          <span class="keywordflow">if</span> (!temp_identification.<a class="code" href="classOpenMS_1_1PeptideIdentification.html#a564d2725cd06914a922d6fbda8be8a13">getHits</a>().empty())</div>
<div class="line"><a name="l00340"></a><span class="lineno">  340</span>&#160;          {</div>
<div class="line"><a name="l00341"></a><span class="lineno">  341</span>&#160;            filtered_identifications.push_back(temp_identification);</div>
<div class="line"><a name="l00342"></a><span class="lineno">  342</span>&#160;          }</div>
<div class="line"><a name="l00343"></a><span class="lineno">  343</span>&#160;        }</div>
<div class="line"><a name="l00344"></a><span class="lineno">  344</span>&#160;        experiment[i].setPeptideIdentifications(filtered_identifications);</div>
<div class="line"><a name="l00345"></a><span class="lineno">  345</span>&#160;        filtered_identifications.clear();</div>
<div class="line"><a name="l00346"></a><span class="lineno">  346</span>&#160;      }</div>
<div class="line"><a name="l00347"></a><span class="lineno">  347</span>&#160;    }</div>
<div class="line"><a name="l00348"></a><span class="lineno">  348</span>&#160;</div>
<div class="line"><a name="l00350"></a><span class="lineno">  350</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> PeakT&gt;</div>
<div class="line"><a name="l00351"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDFilter.html#adbddef78d7fcfbd5a87e19762fd1cc7b">  351</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1IDFilter.html#adbddef78d7fcfbd5a87e19762fd1cc7b">filterIdentificationsByBestNHits</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;PeakT&gt;</a>&amp; experiment, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n)</div>
<div class="line"><a name="l00352"></a><span class="lineno">  352</span>&#160;    {</div>
<div class="line"><a name="l00353"></a><span class="lineno">  353</span>&#160;      <span class="comment">//filter protein hits</span></div>
<div class="line"><a name="l00354"></a><span class="lineno">  354</span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> temp_protein_identification;</div>
<div class="line"><a name="l00355"></a><span class="lineno">  355</span>&#160;      std::vector&lt;ProteinIdentification&gt; filtered_protein_identifications;</div>
<div class="line"><a name="l00356"></a><span class="lineno">  356</span>&#160;</div>
<div class="line"><a name="l00357"></a><span class="lineno">  357</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; experiment.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>().size(); j++)</div>
<div class="line"><a name="l00358"></a><span class="lineno">  358</span>&#160;      {</div>
<div class="line"><a name="l00359"></a><span class="lineno">  359</span>&#160;        filterIdentificationsByBestNHits(experiment.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>()[j], n, temp_protein_identification);</div>
<div class="line"><a name="l00360"></a><span class="lineno">  360</span>&#160;        <span class="keywordflow">if</span> (!temp_protein_identification.<a class="code" href="classOpenMS_1_1ProteinIdentification.html#a69a3da6373dcd1505ea046971251023b">getHits</a>().empty())</div>
<div class="line"><a name="l00361"></a><span class="lineno">  361</span>&#160;        {</div>
<div class="line"><a name="l00362"></a><span class="lineno">  362</span>&#160;          filtered_protein_identifications.push_back(temp_protein_identification);</div>
<div class="line"><a name="l00363"></a><span class="lineno">  363</span>&#160;        }</div>
<div class="line"><a name="l00364"></a><span class="lineno">  364</span>&#160;      }</div>
<div class="line"><a name="l00365"></a><span class="lineno">  365</span>&#160;      experiment.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#a6d85ac28bb82da988383fd19b8504988">setProteinIdentifications</a>(filtered_protein_identifications);</div>
<div class="line"><a name="l00366"></a><span class="lineno">  366</span>&#160;</div>
<div class="line"><a name="l00367"></a><span class="lineno">  367</span>&#160;      <span class="comment">//filter peptide hits</span></div>
<div class="line"><a name="l00368"></a><span class="lineno">  368</span>&#160;      <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> temp_identification;</div>
<div class="line"><a name="l00369"></a><span class="lineno">  369</span>&#160;      std::vector&lt;PeptideIdentification&gt; filtered_identifications;</div>
<div class="line"><a name="l00370"></a><span class="lineno">  370</span>&#160;</div>
<div class="line"><a name="l00371"></a><span class="lineno">  371</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); i++)</div>
<div class="line"><a name="l00372"></a><span class="lineno">  372</span>&#160;      {</div>
<div class="line"><a name="l00373"></a><span class="lineno">  373</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; experiment[i].getPeptideIdentifications().<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); j++)</div>
<div class="line"><a name="l00374"></a><span class="lineno">  374</span>&#160;        {</div>
<div class="line"><a name="l00375"></a><span class="lineno">  375</span>&#160;          filterIdentificationsByBestNHits(experiment[i].getPeptideIdentifications()[j], n, temp_identification);</div>
<div class="line"><a name="l00376"></a><span class="lineno">  376</span>&#160;          <span class="keywordflow">if</span> (!temp_identification.<a class="code" href="classOpenMS_1_1PeptideIdentification.html#a564d2725cd06914a922d6fbda8be8a13">getHits</a>().empty())</div>
<div class="line"><a name="l00377"></a><span class="lineno">  377</span>&#160;          {</div>
<div class="line"><a name="l00378"></a><span class="lineno">  378</span>&#160;            filtered_identifications.push_back(temp_identification);</div>
<div class="line"><a name="l00379"></a><span class="lineno">  379</span>&#160;          }</div>
<div class="line"><a name="l00380"></a><span class="lineno">  380</span>&#160;        }</div>
<div class="line"><a name="l00381"></a><span class="lineno">  381</span>&#160;        experiment[i].setPeptideIdentifications(filtered_identifications);</div>
<div class="line"><a name="l00382"></a><span class="lineno">  382</span>&#160;        filtered_identifications.clear();</div>
<div class="line"><a name="l00383"></a><span class="lineno">  383</span>&#160;      }</div>
<div class="line"><a name="l00384"></a><span class="lineno">  384</span>&#160;    }</div>
<div class="line"><a name="l00385"></a><span class="lineno">  385</span>&#160;</div>
<div class="line"><a name="l00387"></a><span class="lineno">  387</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> PeakT&gt;</div>
<div class="line"><a name="l00388"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDFilter.html#a4abee7e9d0f79197ddf80a6af8632d03">  388</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1IDFilter.html#a4abee7e9d0f79197ddf80a6af8632d03">filterIdentificationsByProteins</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;PeakT&gt;</a>&amp; experiment,</div>
<div class="line"><a name="l00389"></a><span class="lineno">  389</span>&#160;                                         <span class="keyword">const</span> std::vector&lt;FASTAFile::FASTAEntry&gt;&amp; proteins)</div>
<div class="line"><a name="l00390"></a><span class="lineno">  390</span>&#160;    {</div>
<div class="line"><a name="l00391"></a><span class="lineno">  391</span>&#160;      std::vector&lt;PeptideIdentification&gt; temp_identifications;</div>
<div class="line"><a name="l00392"></a><span class="lineno">  392</span>&#160;      std::vector&lt;PeptideIdentification&gt; filtered_identifications;</div>
<div class="line"><a name="l00393"></a><span class="lineno">  393</span>&#160;      <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> temp_identification;</div>
<div class="line"><a name="l00394"></a><span class="lineno">  394</span>&#160;</div>
<div class="line"><a name="l00395"></a><span class="lineno">  395</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); i++)</div>
<div class="line"><a name="l00396"></a><span class="lineno">  396</span>&#160;      {</div>
<div class="line"><a name="l00397"></a><span class="lineno">  397</span>&#160;        <span class="keywordflow">if</span> (experiment[i].getMSLevel() == 2)</div>
<div class="line"><a name="l00398"></a><span class="lineno">  398</span>&#160;        {</div>
<div class="line"><a name="l00399"></a><span class="lineno">  399</span>&#160;          temp_identifications = experiment[i].getPeptideIdentifications();</div>
<div class="line"><a name="l00400"></a><span class="lineno">  400</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; temp_identifications.size(); j++)</div>
<div class="line"><a name="l00401"></a><span class="lineno">  401</span>&#160;          {</div>
<div class="line"><a name="l00402"></a><span class="lineno">  402</span>&#160;            filterIdentificationsByProteins(temp_identifications[j], proteins, temp_identification);</div>
<div class="line"><a name="l00403"></a><span class="lineno">  403</span>&#160;            <span class="keywordflow">if</span> (!temp_identification.<a class="code" href="classOpenMS_1_1PeptideIdentification.html#a564d2725cd06914a922d6fbda8be8a13">getHits</a>().empty())</div>
<div class="line"><a name="l00404"></a><span class="lineno">  404</span>&#160;            {</div>
<div class="line"><a name="l00405"></a><span class="lineno">  405</span>&#160;              filtered_identifications.push_back(temp_identification);</div>
<div class="line"><a name="l00406"></a><span class="lineno">  406</span>&#160;            }</div>
<div class="line"><a name="l00407"></a><span class="lineno">  407</span>&#160;          }</div>
<div class="line"><a name="l00408"></a><span class="lineno">  408</span>&#160;          experiment[i].setPeptideIdentifications(filtered_identifications);</div>
<div class="line"><a name="l00409"></a><span class="lineno">  409</span>&#160;          filtered_identifications.clear();</div>
<div class="line"><a name="l00410"></a><span class="lineno">  410</span>&#160;        }</div>
<div class="line"><a name="l00411"></a><span class="lineno">  411</span>&#160;      }</div>
<div class="line"><a name="l00412"></a><span class="lineno">  412</span>&#160;    }</div>
<div class="line"><a name="l00413"></a><span class="lineno">  413</span>&#160;</div>
<div class="line"><a name="l00414"></a><span class="lineno">  414</span>&#160;  };</div>
<div class="line"><a name="l00415"></a><span class="lineno">  415</span>&#160;</div>
<div class="line"><a name="l00416"></a><span class="lineno">  416</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00417"></a><span class="lineno">  417</span>&#160;</div>
<div class="line"><a name="l00418"></a><span class="lineno">  418</span>&#160;<span class="preprocessor">#endif // OPENMS_FILTERING_ID_IDFILTER_H</span></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="classOpenMS_1_1ExperimentalSettings_html_a6d85ac28bb82da988383fd19b8504988"><div class="ttname"><a href="classOpenMS_1_1ExperimentalSettings.html#a6d85ac28bb82da988383fd19b8504988">OpenMS::ExperimentalSettings::setProteinIdentifications</a></div><div class="ttdeci">void setProteinIdentifications(const std::vector&lt; ProteinIdentification &gt; &amp;protein_identifications)</div><div class="ttdoc">sets the protein ProteinIdentification vector </div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1ExperimentalSettings_html_acef58bf2531b77d0191c4780739281c6"><div class="ttname"><a href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">OpenMS::ExperimentalSettings::getProteinIdentifications</a></div><div class="ttdeci">const std::vector&lt; ProteinIdentification &gt; &amp; getProteinIdentifications() const </div><div class="ttdoc">returns a const reference to the protein ProteinIdentification vector </div></div>
<div class="ttc" id="classOpenMS_1_1IDFilter_html_a42a3948a25feb4e02008d72c65023c3a"><div class="ttname"><a href="classOpenMS_1_1IDFilter.html#a42a3948a25feb4e02008d72c65023c3a">OpenMS::IDFilter::filterIdentificationsByThreshold</a></div><div class="ttdeci">void filterIdentificationsByThreshold(const IdentificationType &amp;identification, DoubleReal threshold_fraction, IdentificationType &amp;filtered_identification)</div><div class="ttdoc">filters a ProteinIdentification or PeptideIdentification by only allowing peptides/proteins which rea...</div><div class="ttdef"><b>Definition:</b> IDFilter.h:73</div></div>
<div class="ttc" id="FASTAFile_8h_html"><div class="ttname"><a href="FASTAFile_8h.html">FASTAFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1IDFilter_html_adbddef78d7fcfbd5a87e19762fd1cc7b"><div class="ttname"><a href="classOpenMS_1_1IDFilter.html#adbddef78d7fcfbd5a87e19762fd1cc7b">OpenMS::IDFilter::filterIdentificationsByBestNHits</a></div><div class="ttdeci">void filterIdentificationsByBestNHits(MSExperiment&lt; PeakT &gt; &amp;experiment, Size n)</div><div class="ttdoc">filters an MS/MS experiment corresponding to the best n hits for every spectrum </div><div class="ttdef"><b>Definition:</b> IDFilter.h:351</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1IDFilter_html_aeb523c70d4d0f6e8cabd7b8db02cf638"><div class="ttname"><a href="classOpenMS_1_1IDFilter.html#aeb523c70d4d0f6e8cabd7b8db02cf638">OpenMS::IDFilter::filterIdentificationsByScores</a></div><div class="ttdeci">void filterIdentificationsByScores(MSExperiment&lt; PeakT &gt; &amp;experiment, DoubleReal peptide_threshold_score, DoubleReal protein_threshold_score)</div><div class="ttdoc">filters an MS/MS experiment corresponding to the threshold_fractions </div><div class="ttdef"><b>Definition:</b> IDFilter.h:314</div></div>
<div class="ttc" id="classOpenMS_1_1IDFilter_html_a7908af59fd5a56c76d8dd8bff0bd943a"><div class="ttname"><a href="classOpenMS_1_1IDFilter.html#a7908af59fd5a56c76d8dd8bff0bd943a">OpenMS::IDFilter::filterIdentificationsByBestNHits</a></div><div class="ttdeci">void filterIdentificationsByBestNHits(const IdentificationType &amp;identification, Size n, IdentificationType &amp;filtered_identification)</div><div class="ttdoc">filters a ProteinIdentification or PeptideIdentification corresponding to the score. </div><div class="ttdef"><b>Definition:</b> IDFilter.h:150</div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></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_1IDFilter_html_a2a120b13c7cb47cb07897d54286d78dd"><div class="ttname"><a href="classOpenMS_1_1IDFilter.html#a2a120b13c7cb47cb07897d54286d78dd">OpenMS::IDFilter::filterIdentificationsByScore</a></div><div class="ttdeci">void filterIdentificationsByScore(const IdentificationType &amp;identification, DoubleReal threshold_score, IdentificationType &amp;filtered_identification)</div><div class="ttdoc">filters a ProteinIdentification or PeptideIdentification corresponding to the threshold_score ...</div><div class="ttdef"><b>Definition:</b> IDFilter.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html_a564d2725cd06914a922d6fbda8be8a13"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html#a564d2725cd06914a922d6fbda8be8a13">OpenMS::PeptideIdentification::getHits</a></div><div class="ttdeci">const std::vector&lt; PeptideHit &gt; &amp; getHits() const </div><div class="ttdoc">returns the peptide hits </div></div>
<div class="ttc" id="classOpenMS_1_1IDFilter_html_a8a3a8ce850473e14d5e25a9009c26c3d"><div class="ttname"><a href="classOpenMS_1_1IDFilter.html#a8a3a8ce850473e14d5e25a9009c26c3d">OpenMS::IDFilter::filterIdentificationsByBestNToMHits</a></div><div class="ttdeci">void filterIdentificationsByBestNToMHits(const IdentificationType &amp;identification, Size n, Size m, IdentificationType &amp;filtered_identification)</div><div class="ttdoc">filters a ProteinIdentification or PeptideIdentification corresponding to the score. </div><div class="ttdef"><b>Definition:</b> IDFilter.h:188</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</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_1IDFilter_html_a5317f48e0a2b44028ade11faa175dc12"><div class="ttname"><a href="classOpenMS_1_1IDFilter.html#a5317f48e0a2b44028ade11faa175dc12">OpenMS::IDFilter::filterIdentificationsByThresholds</a></div><div class="ttdeci">void filterIdentificationsByThresholds(MSExperiment&lt; PeakT &gt; &amp;experiment, DoubleReal peptide_threshold_fraction, DoubleReal protein_threshold_fraction)</div><div class="ttdoc">filters an MS/MS experiment corresponding to the threshold_fractions </div><div class="ttdef"><b>Definition:</b> IDFilter.h:277</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a69a3da6373dcd1505ea046971251023b"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a69a3da6373dcd1505ea046971251023b">OpenMS::ProteinIdentification::getHits</a></div><div class="ttdeci">const std::vector&lt; ProteinHit &gt; &amp; getHits() const </div><div class="ttdoc">Returns the protein hits. </div></div>
<div class="ttc" id="classOpenMS_1_1IDFilter_html"><div class="ttname"><a href="classOpenMS_1_1IDFilter.html">OpenMS::IDFilter</a></div><div class="ttdoc">used to filter identifications by different criteria </div><div class="ttdef"><b>Definition:</b> IDFilter.h:61</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="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1IDFilter_html_a4abee7e9d0f79197ddf80a6af8632d03"><div class="ttname"><a href="classOpenMS_1_1IDFilter.html#a4abee7e9d0f79197ddf80a6af8632d03">OpenMS::IDFilter::filterIdentificationsByProteins</a></div><div class="ttdeci">void filterIdentificationsByProteins(MSExperiment&lt; PeakT &gt; &amp;experiment, const std::vector&lt; FASTAFile::FASTAEntry &gt; &amp;proteins)</div><div class="ttdoc">filters an MS/MS experiment corresponding to the given proteins </div><div class="ttdef"><b>Definition:</b> IDFilter.h:388</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 11:19:15 using doxygen 1.8.5</font></TD>
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