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<a href="InclusionExclusionList_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>
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<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Alexandra Zerck $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Alexandra Zerck, Chris Bielow $</span></div>
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<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_ANALYSIS_TARGETED_INCLUSIONEXCLUSIONLIST_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_TARGETED_INCLUSIONEXCLUSIONLIST_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="TargetedExperiment_8h.html">OpenMS/ANALYSIS/TARGETED/TargetedExperiment.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="FASTAFile_8h.html">OpenMS/FORMAT/FASTAFile.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;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;{</div>
<div class="line"><a name="l00050"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InclusionExclusionList.html">   50</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1InclusionExclusionList.html">InclusionExclusionList</a> :</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;  {</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html">   54</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html">IEWindow</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"><a class="line" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#aa72a88c973681f62459e14379365d00e">   56</a></span>&#160;      <a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#aa72a88c973681f62459e14379365d00e">IEWindow</a>(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> RTmin, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> RTmax, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> MZ) :</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;        RTmin_(RTmin),</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;        RTmax_(RTmax),</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;        MZ_(MZ)</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;      {</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;      }</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"><a class="line" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">   63</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">RTmin_</a>;</div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">   64</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">RTmax_</a>;</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#a9d18946e57902db39ff14551e5a4ddbd">   65</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#a9d18946e57902db39ff14551e5a4ddbd">MZ_</a>;</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    };</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;</div>
<div class="line"><a name="l00075"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html">   75</a></span>&#160;    <span class="keyword">class </span><a class="code" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html">WindowDistance_</a></div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;    {</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a649a0bb13bc7d13ae3f9caf058733aa3">   78</a></span>&#160;      <a class="code" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a649a0bb13bc7d13ae3f9caf058733aa3">WindowDistance_</a>(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> rt_bridge, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> mz_max, <span class="keyword">const</span> <span class="keywordtype">bool</span> mz_as_ppm) :</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;        rt_bridge_(rt_bridge),</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;        mz_max_(mz_max),</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;        mz_as_ppm_(mz_as_ppm)</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;      {</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;      }</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      <span class="comment">// measure of SIMILARITY (not distance, i.e. 1-distance)!!</span></div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#aa1640b4bc385bf5b7e1f14cb55e79457">   86</a></span>&#160;      <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#aa1640b4bc385bf5b7e1f14cb55e79457">operator()</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html">IEWindow</a> &amp; first, <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html">IEWindow</a> &amp; second)<span class="keyword"> const</span></div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;<span class="keyword">      </span>{</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;        <span class="comment">// get MZ distance:</span></div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> d_mz = fabs(first.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#a9d18946e57902db39ff14551e5a4ddbd">MZ_</a> - second.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#a9d18946e57902db39ff14551e5a4ddbd">MZ_</a>);</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;        <span class="keywordflow">if</span> (mz_as_ppm_)</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;          d_mz = d_mz / first.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#a9d18946e57902db39ff14551e5a4ddbd">MZ_</a> * 1e6;</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;        <span class="keywordflow">if</span> (d_mz &gt; mz_max_) {<span class="keywordflow">return</span> 0; }</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;        <span class="comment">// mz is close enough ...</span></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;        <span class="comment">// is RT overlapping?</span></div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;        <span class="keywordflow">if</span> (first.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">RTmin_</a> &lt;= second.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">RTmin_</a> &amp;&amp; second.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">RTmin_</a> &lt;= first.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">RTmax_</a>) <span class="keywordflow">return</span> 1;  <span class="comment">// intersect #1</span></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;        <span class="keywordflow">if</span> (first.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">RTmin_</a> &lt;= second.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">RTmax_</a> &amp;&amp; second.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">RTmax_</a> &lt;= first.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">RTmax_</a>) <span class="keywordflow">return</span> 1;  <span class="comment">// intersect #2</span></div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;        <span class="keywordflow">if</span> (second.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">RTmin_</a> &lt;= first.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">RTmin_</a> &amp;&amp; first.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">RTmax_</a> &lt;= second.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">RTmax_</a>) <span class="keywordflow">return</span> 1;  <span class="comment">// complete inclusion (only one case; the other is covered above)</span></div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;        <span class="comment">// when windows to not overlap at all:</span></div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;        <span class="comment">// ... are they at least close?</span></div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;        <span class="keywordflow">if</span> ((fabs(first.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">RTmin_</a> - second.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">RTmax_</a>) &lt;= rt_bridge_) ||</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;            (fabs(first.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">RTmax_</a> - second.<a class="code" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">RTmin_</a>) &lt;= rt_bridge_))</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="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;        }</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;        <span class="comment">// not overlapping...</span></div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;        <span class="keywordflow">return</span> 0;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      }</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="keyword">protected</span>:</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;</div>
<div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a0ab668bebd95ca6e5effa344be9c4731">  118</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a0ab668bebd95ca6e5effa344be9c4731">rt_bridge_</a>; </div>
<div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a928fb61988283ac1482ad929f7491ba6">  119</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a928fb61988283ac1482ad929f7491ba6">mz_max_</a>;    </div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a59afce29d8a6df8c16aaeeb44c490452">  120</a></span>&#160;      <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a59afce29d8a6df8c16aaeeb44c490452">mz_as_ppm_</a>;       </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="comment">// end of WindowDistance_</span></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;</div>
<div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">  125</a></span>&#160;    <span class="keyword">typedef</span> std::vector&lt;IEWindow&gt; <a class="code" href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">WindowList</a>;</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;    <span class="keywordtype">void</span> mergeOverlappingWindows_(<a class="code" href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">WindowList</a> &amp; list) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;    <span class="keywordtype">void</span> writeToFile_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; out_path, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">WindowList</a> &amp; windows) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;    <a class="code" href="classOpenMS_1_1InclusionExclusionList.html">InclusionExclusionList</a>();</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;<span class="comment">//     void loadTargets(FeatureMap&lt;&gt;&amp; map, std::vector&lt;IncludeExcludeTarget&gt;&amp; targets,TargetedExperiment&amp; exp);</span></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;<span class="comment">//     void loadTargets(std::vector&lt;FASTAFile::FASTAEntry&gt;&amp; fasta_entries, std::vector&lt;IncludeExcludeTarget&gt;&amp; targets,</span></div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;<span class="comment">//                      TargetedExperiment&amp; exp, Size missed_cleavages = 0);</span></div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;    <span class="keywordtype">void</span> writeTargets(<span class="keyword">const</span> std::vector&lt;FASTAFile::FASTAEntry&gt; &amp; fasta_entries,</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;                      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; out_path,</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;                      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IntList.html">IntList</a> &amp; charges,</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;                      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> rt_model_path);</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;    <span class="keywordtype">void</span> writeTargets(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; map,</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;                      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; out_path);</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;    <span class="keywordtype">void</span> writeTargets(<span class="keyword">const</span> std::vector&lt;PeptideIdentification&gt; &amp; pep_ids,</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;                      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; out_path,</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;                      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IntList.html">IntList</a> &amp; charges);</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;  };</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;</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;}</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;<span class="preprocessor">#endif</span></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="FASTAFile_8h_html"><div class="ttname"><a href="FASTAFile_8h.html">FASTAFile.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1InclusionExclusionList_1_1IEWindow_html_aa72a88c973681f62459e14379365d00e"><div class="ttname"><a href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#aa72a88c973681f62459e14379365d00e">OpenMS::InclusionExclusionList::IEWindow::IEWindow</a></div><div class="ttdeci">IEWindow(const DoubleReal RTmin, const DoubleReal RTmax, const DoubleReal MZ)</div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:56</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="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1InclusionExclusionList_html"><div class="ttname"><a href="classOpenMS_1_1InclusionExclusionList.html">OpenMS::InclusionExclusionList</a></div><div class="ttdoc">Provides functionalty for writing inclusion or exclusion lists. </div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:50</div></div>
<div class="ttc" id="structOpenMS_1_1InclusionExclusionList_1_1IEWindow_html_ae6203af4dfe6b3dc034e1133da89756f"><div class="ttname"><a href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#ae6203af4dfe6b3dc034e1133da89756f">OpenMS::InclusionExclusionList::IEWindow::RTmax_</a></div><div class="ttdeci">DoubleReal RTmax_</div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance___html_a0ab668bebd95ca6e5effa344be9c4731"><div class="ttname"><a href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a0ab668bebd95ca6e5effa344be9c4731">OpenMS::InclusionExclusionList::WindowDistance_::rt_bridge_</a></div><div class="ttdeci">DoubleReal rt_bridge_</div><div class="ttdoc">max rt distance between two windows in order to be considered overlapping </div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:118</div></div>
<div class="ttc" id="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance___html_a928fb61988283ac1482ad929f7491ba6"><div class="ttname"><a href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a928fb61988283ac1482ad929f7491ba6">OpenMS::InclusionExclusionList::WindowDistance_::mz_max_</a></div><div class="ttdeci">DoubleReal mz_max_</div><div class="ttdoc">max m/z distance between two ... </div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:119</div></div>
<div class="ttc" id="structOpenMS_1_1InclusionExclusionList_1_1IEWindow_html_afd5b56017f716c165df35480f7042bd8"><div class="ttname"><a href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#afd5b56017f716c165df35480f7042bd8">OpenMS::InclusionExclusionList::IEWindow::RTmin_</a></div><div class="ttdeci">DoubleReal RTmin_</div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance___html_aa1640b4bc385bf5b7e1f14cb55e79457"><div class="ttname"><a href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#aa1640b4bc385bf5b7e1f14cb55e79457">OpenMS::InclusionExclusionList::WindowDistance_::operator()</a></div><div class="ttdeci">double operator()(const IEWindow &amp;first, const IEWindow &amp;second) const </div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1InclusionExclusionList_html_a37ce296761514de1523091ecdc8e138e"><div class="ttname"><a href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">OpenMS::InclusionExclusionList::WindowList</a></div><div class="ttdeci">std::vector&lt; IEWindow &gt; WindowList</div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:125</div></div>
<div class="ttc" id="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance___html"><div class="ttname"><a href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html">OpenMS::InclusionExclusionList::WindowDistance_</a></div><div class="ttdoc">Determine distance between two spectra. </div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance___html_a59afce29d8a6df8c16aaeeb44c490452"><div class="ttname"><a href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a59afce29d8a6df8c16aaeeb44c490452">OpenMS::InclusionExclusionList::WindowDistance_::mz_as_ppm_</a></div><div class="ttdeci">bool mz_as_ppm_</div><div class="ttdoc">m/z distance unit </div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:120</div></div>
<div class="ttc" id="TargetedExperiment_8h_html"><div class="ttname"><a href="TargetedExperiment_8h.html">TargetedExperiment.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1InclusionExclusionList_1_1IEWindow_html_a9d18946e57902db39ff14551e5a4ddbd"><div class="ttname"><a href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html#a9d18946e57902db39ff14551e5a4ddbd">OpenMS::InclusionExclusionList::IEWindow::MZ_</a></div><div class="ttdeci">DoubleReal MZ_</div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance___html_a649a0bb13bc7d13ae3f9caf058733aa3"><div class="ttname"><a href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html#a649a0bb13bc7d13ae3f9caf058733aa3">OpenMS::InclusionExclusionList::WindowDistance_::WindowDistance_</a></div><div class="ttdeci">WindowDistance_(const DoubleReal rt_bridge, const DoubleReal mz_max, const bool mz_as_ppm)</div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:78</div></div>
<div class="ttc" id="structOpenMS_1_1InclusionExclusionList_1_1IEWindow_html"><div class="ttname"><a href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html">OpenMS::InclusionExclusionList::IEWindow</a></div><div class="ttdef"><b>Definition:</b> InclusionExclusionList.h:54</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="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1IntList_html"><div class="ttname"><a href="classOpenMS_1_1IntList.html">OpenMS::IntList</a></div><div class="ttdoc">Int list. </div><div class="ttdef"><b>Definition:</b> IntList.h:56</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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