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<a href="ModificationsDB_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
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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>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
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<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Stephan Aiche $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Andreas Bertsch $</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_CHEMISTRY_MODIFICATIONSDB_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_CHEMISTRY_MODIFICATIONSDB_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="Map_8h.html">OpenMS/DATASTRUCTURES/Map.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="ResidueModification_8h.html">OpenMS/CHEMISTRY/ResidueModification.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;</div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;set&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;  <span class="comment">// forward declarations</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;  <span class="keyword">class </span>ResidueModification;</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;  <span class="keyword">class </span>Residue;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;</div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModificationsDB.html">   68</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ModificationsDB.html">ModificationsDB</a></div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;  {</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;</div>
<div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModificationsDB.html#a04aaafa9c3d6d2b60e0ba4febd479afa">   72</a></span>&#160;    <span class="keyword">inline</span> <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1ModificationsDB.html">ModificationsDB</a> * <a class="code" href="classOpenMS_1_1ModificationsDB.html#a04aaafa9c3d6d2b60e0ba4febd479afa">getInstance</a>()</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    {</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;      <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1ModificationsDB.html">ModificationsDB</a> * db_ = 0;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;      <span class="keywordflow">if</span> (db_ == 0)</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;        db_ = <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1ModificationsDB.html">ModificationsDB</a>;</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;      <span class="keywordflow">return</span> db_;</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;    }</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getNumberOfModifications() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ResidueModification.html">ResidueModification</a> &amp; getModification(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    <span class="keywordtype">void</span> searchTerminalModifications(std::set&lt;const ResidueModification *&gt; &amp; mods, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name, <a class="code" href="classOpenMS_1_1ResidueModification.html#aa9cd341ac30bebce3b85a3dc64baef65">ResidueModification::Term_Specificity</a> term_spec) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;    <span class="keywordtype">void</span> searchModifications(std::set&lt;const ResidueModification *&gt; &amp; mods, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; orgin, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; mod_name, <a class="code" href="classOpenMS_1_1ResidueModification.html#aa9cd341ac30bebce3b85a3dc64baef65">ResidueModification::Term_Specificity</a> term_spec) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;    <span class="keywordtype">void</span> searchModifications(std::set&lt;const ResidueModification *&gt; &amp; mods, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; mod_name, <a class="code" href="classOpenMS_1_1ResidueModification.html#aa9cd341ac30bebce3b85a3dc64baef65">ResidueModification::Term_Specificity</a> term_spec) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ResidueModification.html">ResidueModification</a> &amp; getTerminalModification(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name, <a class="code" href="classOpenMS_1_1ResidueModification.html#aa9cd341ac30bebce3b85a3dc64baef65">ResidueModification::Term_Specificity</a> term_spec) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ResidueModification.html">ResidueModification</a> &amp; getModification(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; residue_name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; mod_name, <a class="code" href="classOpenMS_1_1ResidueModification.html#aa9cd341ac30bebce3b85a3dc64baef65">ResidueModification::Term_Specificity</a> term_spec) <span class="keyword">const</span>;</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;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ResidueModification.html">ResidueModification</a> &amp; getModification(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; modification) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> findModificationIndex(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; mod_name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;    <span class="keywordtype">void</span> getTerminalModificationsByDiffMonoMass(std::vector&lt;String&gt; &amp; mods, <a class="code" href="classdouble.html">DoubleReal</a> mass, <a class="code" href="classdouble.html">DoubleReal</a> error, <a class="code" href="classOpenMS_1_1ResidueModification.html#aa9cd341ac30bebce3b85a3dc64baef65">ResidueModification::Term_Specificity</a> term_spec);</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;    <span class="keywordtype">void</span> getModificationsByDiffMonoMass(std::vector&lt;String&gt; &amp; mods, <a class="code" href="classdouble.html">DoubleReal</a> mass, <a class="code" href="classdouble.html">DoubleReal</a> error = 0.0);</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;    <span class="keywordtype">void</span> getModificationsByDiffMonoMass(std::vector&lt;String&gt; &amp; mods, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; residue, <a class="code" href="classdouble.html">DoubleReal</a> mass, <a class="code" href="classdouble.html">DoubleReal</a> error = 0.0);</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;    <span class="keywordtype">void</span> readFromOBOFile(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename);</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;    <span class="keywordtype">void</span> readFromUnimodXMLFile(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename);</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">  132</span>&#160;    <span class="keywordtype">void</span> getAllSearchModifications(std::vector&lt;String&gt; &amp; modifications);</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="keyword">protected</span>:</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;</div>
<div class="line"><a name="l00137"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModificationsDB.html#aeafe4e138db0cd068ed93c7804d190ec">  137</a></span>&#160;    std::vector&lt;ResidueModification *&gt; <a class="code" href="classOpenMS_1_1ModificationsDB.html#aeafe4e138db0cd068ed93c7804d190ec">mods_</a>;</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;</div>
<div class="line"><a name="l00140"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModificationsDB.html#ae16d02b0300813ccf6eba817104c9476">  140</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, std::set&lt;const ResidueModification *&gt;</a> &gt; <a class="code" href="classOpenMS_1_1ModificationsDB.html#ae16d02b0300813ccf6eba817104c9476">modification_names_</a>;</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="l00143"></a><span class="lineno">  143</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;    <a class="code" href="classOpenMS_1_1ModificationsDB.html">ModificationsDB</a>();</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;    <a class="code" href="classOpenMS_1_1ModificationsDB.html">ModificationsDB</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ModificationsDB.html">ModificationsDB</a> &amp; residue_db);</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1ModificationsDB.html">ModificationsDB</a>();</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;    <a class="code" href="classOpenMS_1_1ModificationsDB.html">ModificationsDB</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ModificationsDB.html">ModificationsDB</a> &amp; aa);</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;  };</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;<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="classOpenMS_1_1ResidueModification_html"><div class="ttname"><a href="classOpenMS_1_1ResidueModification.html">OpenMS::ResidueModification</a></div><div class="ttdoc">Representation of a modification. </div><div class="ttdef"><b>Definition:</b> ResidueModification.h:58</div></div>
<div class="ttc" id="Map_8h_html"><div class="ttname"><a href="Map_8h.html">Map.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ModificationsDB_html_aeafe4e138db0cd068ed93c7804d190ec"><div class="ttname"><a href="classOpenMS_1_1ModificationsDB.html#aeafe4e138db0cd068ed93c7804d190ec">OpenMS::ModificationsDB::mods_</a></div><div class="ttdeci">std::vector&lt; ResidueModification * &gt; mods_</div><div class="ttdoc">stores the modifications </div><div class="ttdef"><b>Definition:</b> ModificationsDB.h:137</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_1ModificationsDB_html_a04aaafa9c3d6d2b60e0ba4febd479afa"><div class="ttname"><a href="classOpenMS_1_1ModificationsDB.html#a04aaafa9c3d6d2b60e0ba4febd479afa">OpenMS::ModificationsDB::getInstance</a></div><div class="ttdeci">static ModificationsDB * getInstance()</div><div class="ttdef"><b>Definition:</b> ModificationsDB.h:72</div></div>
<div class="ttc" id="ResidueModification_8h_html"><div class="ttname"><a href="ResidueModification_8h.html">ResidueModification.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ModificationsDB_html"><div class="ttname"><a href="classOpenMS_1_1ModificationsDB.html">OpenMS::ModificationsDB</a></div><div class="ttdoc">database which holds all residue modifications from UniMod </div><div class="ttdef"><b>Definition:</b> ModificationsDB.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1ResidueModification_html_aa9cd341ac30bebce3b85a3dc64baef65"><div class="ttname"><a href="classOpenMS_1_1ResidueModification.html#aa9cd341ac30bebce3b85a3dc64baef65">OpenMS::ResidueModification::Term_Specificity</a></div><div class="ttdeci">Term_Specificity</div><div class="ttdoc">Position where the modification is allowed to occur. </div><div class="ttdef"><b>Definition:</b> ResidueModification.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="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1ModificationsDB_html_ae16d02b0300813ccf6eba817104c9476"><div class="ttname"><a href="classOpenMS_1_1ModificationsDB.html#ae16d02b0300813ccf6eba817104c9476">OpenMS::ModificationsDB::modification_names_</a></div><div class="ttdeci">Map&lt; String, std::set&lt; const ResidueModification * &gt; &gt; modification_names_</div><div class="ttdoc">stores the mappings of (unique) names to the modifications </div><div class="ttdef"><b>Definition:</b> ModificationsDB.h:140</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 11:19:17 using doxygen 1.8.5</font></TD>
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