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<a href="ModifierRep_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
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<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
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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">// $Maintainer: Clemens Groepl,Andreas Bertsch$</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;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;</div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor">#ifndef OPENMS_CHEMISTRY_MODIFIERREP_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_CHEMISTRY_MODIFIERREP_H</span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;map&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;vector&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="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>&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="l00045"></a><span class="lineno">   45</span>&#160;</div>
<div class="line"><a name="l00050"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModifierRep.html">   50</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ModifierRep.html">ModifierRep</a></div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;  {</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">public</span>:</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;    <a class="code" href="classOpenMS_1_1ModifierRep.html">ModifierRep</a>();</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    <a class="code" href="classOpenMS_1_1ModifierRep.html">ModifierRep</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ModifierRep.html">ModifierRep</a> &amp; source);</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1ModifierRep.html">ModifierRep</a>();</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;    <span class="keywordtype">void</span> setNumberOfModifications(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i);</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getNumberOfModifications() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;    <span class="keyword">const</span> std::vector&lt;std::vector&lt;double&gt; &gt; &amp; getModificationTable();</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;    <span class="keywordtype">void</span> refreshModificationList(std::map&lt;double, SignedSize&gt; &amp; mod_map, <span class="keyword">const</span> <span class="keywordtype">char</span> &amp; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>);</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getMaxModificationMasses();</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;    std::vector&lt;String&gt; getModificationsForMass(<span class="keywordtype">double</span> &amp; m);</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;    std::vector&lt;String&gt; getModificationsForMass(<span class="keywordtype">double</span> &amp; m, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; seq);</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;<span class="keyword">protected</span>:</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"><a class="line" href="classOpenMS_1_1ModifierRep.html#a32b1bbbf4ab7468d7baeae2f2afdb364">  119</a></span>&#160;    std::vector&lt;std::vector&lt;double&gt; &gt; <a class="code" href="classOpenMS_1_1ModifierRep.html#a32b1bbbf4ab7468d7baeae2f2afdb364">modification_table_</a>; </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"><a class="line" href="classOpenMS_1_1ModifierRep.html#a5609ab550eb96c106ca2be458a149fcc">  121</a></span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1ModifierRep.html#a5609ab550eb96c106ca2be458a149fcc">number_of_modifications_</a>; </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"><a class="line" href="classOpenMS_1_1ModifierRep.html#a6dfda100b47c61a93075d5a42ecbb1c5">  123</a></span>&#160;    std::map&lt;String, std::vector&lt;String&gt; &gt; <a class="code" href="classOpenMS_1_1ModifierRep.html#a6dfda100b47c61a93075d5a42ecbb1c5">mass_mapping_</a>; </div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;  };</div>
<div class="line"><a name="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;</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;<span class="preprocessor">#endif //OPENMS_CHEMISTRY_MODIFIERREP_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="classOpenMS_1_1ModifierRep_html_a32b1bbbf4ab7468d7baeae2f2afdb364"><div class="ttname"><a href="classOpenMS_1_1ModifierRep.html#a32b1bbbf4ab7468d7baeae2f2afdb364">OpenMS::ModifierRep::modification_table_</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; double &gt; &gt; modification_table_</div><div class="ttdoc">all possible modifications </div><div class="ttdef"><b>Definition:</b> ModifierRep.h:119</div></div>
<div class="ttc" id="classOpenMS_1_1ModifierRep_html"><div class="ttname"><a href="classOpenMS_1_1ModifierRep.html">OpenMS::ModifierRep</a></div><div class="ttdoc">Implements modification for suffix arrays. </div><div class="ttdef"><b>Definition:</b> ModifierRep.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1ModifierRep_html_a6dfda100b47c61a93075d5a42ecbb1c5"><div class="ttname"><a href="classOpenMS_1_1ModifierRep.html#a6dfda100b47c61a93075d5a42ecbb1c5">OpenMS::ModifierRep::mass_mapping_</a></div><div class="ttdeci">std::map&lt; String, std::vector&lt; String &gt; &gt; mass_mapping_</div><div class="ttdoc">maps a mass to the combination of modifications </div><div class="ttdef"><b>Definition:</b> ModifierRep.h:123</div></div>
<div class="ttc" id="classOpenMS_1_1ModifierRep_html_a5609ab550eb96c106ca2be458a149fcc"><div class="ttname"><a href="classOpenMS_1_1ModifierRep.html#a5609ab550eb96c106ca2be458a149fcc">OpenMS::ModifierRep::number_of_modifications_</a></div><div class="ttdeci">Size number_of_modifications_</div><div class="ttdoc">number of maximal modifications </div><div class="ttdef"><b>Definition:</b> ModifierRep.h:121</div></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a8fc6defe4e499b1b9b9c275689e44352"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">OpenMS::Constants::c</a></div><div class="ttdeci">const double c</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="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
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