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<a href="NeutralLossMarker_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>
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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: Andreas Bertsch $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: $</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;<span class="comment">//</span></div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_FILTERING_TRANSFORMERS_NEUTRALLOSSMARKER_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_TRANSFORMERS_NEUTRALLOSSMARKER_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="PeakMarker_8h.html">OpenMS/FILTERING/TRANSFORMERS/PeakMarker.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;map&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;cmath&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;{</div>
<div class="line"><a name="l00052"></a><span class="lineno"><a class="line" href="classOpenMS_1_1NeutralLossMarker.html">   52</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1NeutralLossMarker.html">NeutralLossMarker</a> :</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1PeakMarker.html">PeakMarker</a></div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;  {</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;    <span class="comment">// @name Constructors and Destructors</span></div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;    <span class="comment">// @{</span></div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;<span class="comment"></span>    <a class="code" href="classOpenMS_1_1NeutralLossMarker.html">NeutralLossMarker</a>();</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    <a class="code" href="classOpenMS_1_1NeutralLossMarker.html">NeutralLossMarker</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1NeutralLossMarker.html">NeutralLossMarker</a> &amp; source);</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;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1NeutralLossMarker.html">NeutralLossMarker</a>();</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <span class="comment">// @}</span></div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <span class="comment">// @name Operators</span></div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    <span class="comment">// @{</span></div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;<span class="comment"></span>    <a class="code" href="classOpenMS_1_1NeutralLossMarker.html">NeutralLossMarker</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1NeutralLossMarker.html">NeutralLossMarker</a> &amp; source);</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    <span class="comment">// @}</span></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="comment">// @name Accessors</span></div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;    <span class="comment">// @{</span></div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1NeutralLossMarker.html#a565d0a551885f942a1c7f6644494b93a">   78</a></span>&#160;<span class="comment"></span>    <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1PeakMarker.html">PeakMarker</a> * <a class="code" href="classOpenMS_1_1NeutralLossMarker.html#a565d0a551885f942a1c7f6644494b93a">create</a>() { <span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1NeutralLossMarker.html">NeutralLossMarker</a>(); }</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> SpectrumType&gt;</div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="classOpenMS_1_1NeutralLossMarker.html#a6253a8d1984cc8d5a8eb1ebb66d67e43">   82</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1NeutralLossMarker.html#a6253a8d1984cc8d5a8eb1ebb66d67e43">apply</a>(std::map&lt;double, bool&gt; &amp; marked, SpectrumType &amp; spectrum)</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;      <span class="comment">// how often a peak needs to be marked to be returned</span></div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      <span class="keywordtype">double</span> marks = (<a class="code" href="classdouble.html">double</a>)param_.getValue(<span class="stringliteral">&quot;marks&quot;</span>);</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;      <span class="keywordtype">double</span> tolerance = (<a class="code" href="classdouble.html">double</a>)param_.getValue(<span class="stringliteral">&quot;tolerance&quot;</span>);</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;      std::map&lt;double, SignedSize&gt; ions_w_neutrallosses;</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      spectrum.sortByPosition();</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; spectrum.size(); ++i)</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;        <span class="keywordtype">double</span> mz = spectrum[i].getPosition()[0];</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;        <span class="keywordtype">double</span> intensity = spectrum[i].getIntensity();</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;        <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> j = i - 1;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;        <span class="keywordflow">while</span> (j &gt;= 0)</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;        {</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;          <span class="keywordtype">double</span> curmz = spectrum[j].getPosition()[0];</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;          <span class="keywordtype">double</span> curIntensity = spectrum[j].getIntensity();</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;          <span class="comment">// check for peak thats a a water or ammonia away</span></div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;          <span class="keywordflow">if</span> (std::fabs(mz - curmz - 17) &lt; tolerance || std::fabs(mz - curmz - 18) &lt; tolerance)</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="comment">// neutral loss peak should be smaller</span></div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;            <span class="keywordflow">if</span> (curIntensity &lt; intensity)</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;            {</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;              ions_w_neutrallosses[mz]++;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;              <span class="comment">// neutral loss peak not marked</span></div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;              <span class="comment">//ions_w_neutrallosses[curmz]++;</span></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;          }</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;          <span class="keywordflow">else</span></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="keywordflow">if</span> (mz - curmz &gt; 18.3)</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;            {</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;              <span class="keywordflow">break</span>;</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;          }</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;          --j;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;        }</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;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;      <span class="keywordflow">for</span> (std::map&lt;double, SignedSize&gt;::const_iterator cmit = ions_w_neutrallosses.begin(); cmit != ions_w_neutrallosses.end(); ++cmit)</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;      {</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;        <span class="keywordflow">if</span> (cmit-&gt;second &gt;= marks)</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;        {</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;          marked.insert(std::pair&lt;double, bool&gt;(cmit-&gt;first, <span class="keyword">true</span>));</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;      }</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;      <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;    }</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;</div>
<div class="line"><a name="l00132"></a><span class="lineno"><a class="line" href="classOpenMS_1_1NeutralLossMarker.html#af73fd15708e50e77665070023a09cc87">  132</a></span>&#160;    <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1NeutralLossMarker.html#af73fd15708e50e77665070023a09cc87">getProductName</a>()</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;      <span class="keywordflow">return</span> <span class="stringliteral">&quot;NeutralLossMarker&quot;</span>;</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;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;    <span class="comment">// @}</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="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;<span class="preprocessor">#endif //OPENMS_FILTERING_TRANSFORMERS_NEUTRALLOSSMARKER_H</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="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="group__Concept_html_gae113cb41304c6692c7bf5d0624dc6f0f"><div class="ttname"><a href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">OpenMS::SignedSize</a></div><div class="ttdeci">ptrdiff_t SignedSize</div><div class="ttdoc">Signed Size type e.g. used as pointer difference. </div><div class="ttdef"><b>Definition:</b> Types.h:151</div></div>
<div class="ttc" id="classOpenMS_1_1NeutralLossMarker_html_af73fd15708e50e77665070023a09cc87"><div class="ttname"><a href="classOpenMS_1_1NeutralLossMarker.html#af73fd15708e50e77665070023a09cc87">OpenMS::NeutralLossMarker::getProductName</a></div><div class="ttdeci">static const String getProductName()</div><div class="ttdef"><b>Definition:</b> NeutralLossMarker.h:132</div></div>
<div class="ttc" id="classOpenMS_1_1PeakMarker_html"><div class="ttname"><a href="classOpenMS_1_1PeakMarker.html">OpenMS::PeakMarker</a></div><div class="ttdoc">PeakMarker marks peaks that seem to fulfill some criterion. </div><div class="ttdef"><b>Definition:</b> PeakMarker.h:48</div></div>
<div class="ttc" id="classOpenMS_1_1NeutralLossMarker_html_a6253a8d1984cc8d5a8eb1ebb66d67e43"><div class="ttname"><a href="classOpenMS_1_1NeutralLossMarker.html#a6253a8d1984cc8d5a8eb1ebb66d67e43">OpenMS::NeutralLossMarker::apply</a></div><div class="ttdeci">void apply(std::map&lt; double, bool &gt; &amp;marked, SpectrumType &amp;spectrum)</div><div class="ttdef"><b>Definition:</b> NeutralLossMarker.h:82</div></div>
<div class="ttc" id="classOpenMS_1_1NeutralLossMarker_html_a565d0a551885f942a1c7f6644494b93a"><div class="ttname"><a href="classOpenMS_1_1NeutralLossMarker.html#a565d0a551885f942a1c7f6644494b93a">OpenMS::NeutralLossMarker::create</a></div><div class="ttdeci">static PeakMarker * create()</div><div class="ttdef"><b>Definition:</b> NeutralLossMarker.h:78</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="PeakMarker_8h_html"><div class="ttname"><a href="PeakMarker_8h.html">PeakMarker.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1NeutralLossMarker_html"><div class="ttname"><a href="classOpenMS_1_1NeutralLossMarker.html">OpenMS::NeutralLossMarker</a></div><div class="ttdoc">NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water...</div><div class="ttdef"><b>Definition:</b> NeutralLossMarker.h:52</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 11:19:18 using doxygen 1.8.5</font></TD>
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