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<a href="XTandemInfile_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>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<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>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<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_FORMAT_XTANDEMINFILE_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_FORMAT_XTANDEMINFILE_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="String_8h.html">OpenMS/DATASTRUCTURES/String.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="XTandemInfileXMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XTandemInfileXMLHandler.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="ModificationDefinitionsSet_8h.html">OpenMS/CHEMISTRY/ModificationDefinitionsSet.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="XMLFile_8h.html">OpenMS/FORMAT/XMLFile.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="l00052"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html">   52</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1XTandemInfile.html">XTandemInfile</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_1Internal_1_1XMLFile.html">Internal::XMLFile</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="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a138ca2002a5af71819cd7b721dd0efb4">   58</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a138ca2002a5af71819cd7b721dd0efb4">ErrorUnit</a></div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;    {</div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a138ca2002a5af71819cd7b721dd0efb4a9cbf5dc33257c54d0257036e7d30011b">   60</a></span>&#160;      DALTONS = 0,</div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a138ca2002a5af71819cd7b721dd0efb4ac271a6034e77f707fe192841a95de390">   61</a></span>&#160;      PPM</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;</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#acb24b846f44e558e17a9f47674d2b406">   65</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#acb24b846f44e558e17a9f47674d2b406">MassType</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"><a class="line" href="classOpenMS_1_1XTandemInfile.html#acb24b846f44e558e17a9f47674d2b406aba27416c974c26497ea0f4aa59fcf669">   67</a></span>&#160;      MONOISOTOPIC = 0,</div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#acb24b846f44e558e17a9f47674d2b406ab6f2220659ddcb84a0622d4aa4e0b112">   68</a></span>&#160;      AVERAGE</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;</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    <a class="code" href="classOpenMS_1_1XTandemInfile.html">XTandemInfile</a>();</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1XTandemInfile.html">XTandemInfile</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="comment">//&lt;note type=&quot;input&quot; label=&quot;spectrum, fragment monoisotopic mass error&quot;&gt;0.4&lt;/note&gt;</span></div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;    <span class="comment">//&lt;note type=&quot;input&quot; label=&quot;spectrum, fragment monoisotopic mass error&quot;&gt;0.4&lt;/note&gt;</span></div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    <span class="comment">//&lt;note type=&quot;input&quot; label=&quot;spectrum, parent monoisotopic mass error plus&quot;&gt;100&lt;/note&gt;</span></div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;    <span class="comment">//&lt;note type=&quot;input&quot; label=&quot;spectrum, parent monoisotopic mass error minus&quot;&gt;100&lt;/note&gt;</span></div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    <span class="comment">//&lt;note type=&quot;input&quot; label=&quot;spectrum, parent monoisotopic mass isotope error&quot;&gt;yes&lt;/note&gt;</span></div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="comment">//&lt;note type=&quot;input&quot; label=&quot;spectrum, fragment monoisotopic mass error units&quot;&gt;Daltons&lt;/note&gt;</span></div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;    <span class="comment">//&lt;note&gt;The value for this parameter may be &#39;Daltons&#39; or &#39;ppm&#39;: all other values are ignored&lt;/note&gt;</span></div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;    <span class="comment">//&lt;note type=&quot;input&quot; label=&quot;spectrum, parent monoisotopic mass error units&quot;&gt;ppm&lt;/note&gt;</span></div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;    <span class="comment">//&lt;note&gt;The value for this parameter may be &#39;Daltons&#39; or &#39;ppm&#39;: all other values are ignored&lt;/note&gt;</span></div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;    <span class="comment">//&lt;note type=&quot;input&quot; label=&quot;spectrum, fragment mass type&quot;&gt;monoisotopic&lt;/note&gt;</span></div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;    <span class="comment">//&lt;note&gt;values are monoisotopic|average &lt;/note&gt;</span></div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;    <span class="keywordtype">void</span> setFragmentMassTolerance(<span class="keywordtype">double</span> tolerance);</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;    <span class="keywordtype">double</span> getFragmentMassTolerance() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    <span class="keywordtype">void</span> setPrecursorMassTolerancePlus(<span class="keywordtype">double</span> tol);</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    <span class="keywordtype">double</span> getPrecursorMassTolerancePlus() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;    <span class="keywordtype">void</span> setPrecursorMassToleranceMinus(<span class="keywordtype">double</span> tol);</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;    <span class="keywordtype">double</span> getPrecursorMassToleranceMinus() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;    <span class="keywordtype">void</span> setPrecursorErrorType(MassType mono_isotopic);</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;    MassType getPrecursorErrorType() <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;    <span class="keywordtype">void</span> setFragmentMassErrorUnit(ErrorUnit unit);</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;    ErrorUnit getFragmentMassErrorUnit() <span class="keyword">const</span>;</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> setPrecursorMassErrorUnit(ErrorUnit unit);</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;    ErrorUnit getPrecursorMassErrorUnit() <span class="keyword">const</span>;</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> setNumberOfThreads(<a class="code" href="classunsigned_01int.html">UInt</a> threads);</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;    <a class="code" href="classunsigned_01int.html">UInt</a> getNumberOfThreads() <span class="keyword">const</span>;</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> setModifications(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ModificationDefinitionsSet.html">ModificationDefinitionsSet</a>&amp; mods);</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ModificationDefinitionsSet.html">ModificationDefinitionsSet</a>&amp; getModifications() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;    <span class="keywordtype">void</span> setOutputFilename(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; output);</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; getOutputFilename() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;    <span class="keywordtype">void</span> setInputFilename(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; input_file);</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; getInputFilename() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;    <span class="keywordtype">void</span> setTaxonomyFilename(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; filename);</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; getTaxonomyFilename() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;    <span class="keywordtype">void</span> setDefaultParametersFilename(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; filename);</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; getDefaultParametersFilename() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;    <span class="keywordtype">void</span> setTaxon(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; taxon);</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; getTaxon() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;    <span class="keywordtype">void</span> setMaxPrecursorCharge(<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> max_charge);</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;    <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> getMaxPrecursorCharge() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;    <span class="keywordtype">void</span> setNumberOfMissedCleavages(<a class="code" href="classunsigned_01int.html">UInt</a> missed_cleavages);</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> getNumberOfMissedCleavages() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;    <span class="keywordtype">void</span> setMaxValidEValue(<span class="keywordtype">double</span> value);</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;    <span class="keywordtype">double</span> getMaxValidEValue() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;    <span class="keywordtype">bool</span> isRefining() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    <span class="keywordtype">void</span> setSemiCleavage(<span class="keyword">const</span> <span class="keywordtype">bool</span> semi_cleavage);</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;    <span class="keywordtype">void</span> setRefine(<span class="keyword">const</span> <span class="keywordtype">bool</span> refine);</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;    <span class="keywordtype">void</span> write(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; filename);</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;    <span class="keywordtype">void</span> load(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; filename);</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;<span class="keyword">protected</span>:</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;    <a class="code" href="classOpenMS_1_1XTandemInfile.html">XTandemInfile</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html">XTandemInfile</a>&amp; rhs);</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;    <a class="code" href="classOpenMS_1_1XTandemInfile.html">XTandemInfile</a>&amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html">XTandemInfile</a>&amp; rhs);</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;    <span class="keywordtype">void</span> writeTo_(std::ostream&amp; os);</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;    <span class="keywordtype">void</span> writeNote_(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; type, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; label, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; value);</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;    <span class="keywordtype">void</span> writeNote_(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; type, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; label, <span class="keyword">const</span> <span class="keywordtype">char</span>* value);</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;    <span class="keywordtype">void</span> writeNote_(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; type, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; label, <span class="keywordtype">bool</span> value);</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> convertModificationSet_(<span class="keyword">const</span> std::set&lt;ModificationDefinition&gt;&amp; mods) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;</div>
<div class="line"><a name="l00233"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#ace929bc4ac20b10e60ca5e10ce669268">  233</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#ace929bc4ac20b10e60ca5e10ce669268">fragment_mass_tolerance_</a>;</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;</div>
<div class="line"><a name="l00235"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#aca7dd9843d0f65c30077f53d5e56c2c3">  235</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#aca7dd9843d0f65c30077f53d5e56c2c3">precursor_mass_tolerance_plus_</a>;</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;</div>
<div class="line"><a name="l00237"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a7b8ddc890668c3e64281c06106e5569d">  237</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a7b8ddc890668c3e64281c06106e5569d">precursor_mass_tolerance_minus_</a>;</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;</div>
<div class="line"><a name="l00239"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#adcdbf79d5d94972659840cea41217b28">  239</a></span>&#160;    <a class="code" href="classOpenMS_1_1XTandemInfile.html#acb24b846f44e558e17a9f47674d2b406">MassType</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#adcdbf79d5d94972659840cea41217b28">precursor_mass_type_</a>;</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;</div>
<div class="line"><a name="l00241"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a3081e522548f77c057fd1fabf0fa8366">  241</a></span>&#160;    <a class="code" href="classOpenMS_1_1XTandemInfile.html#a138ca2002a5af71819cd7b721dd0efb4">ErrorUnit</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a3081e522548f77c057fd1fabf0fa8366">precursor_mass_error_unit_</a>;</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;</div>
<div class="line"><a name="l00243"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#ad70a25c9b136686d2473085ee98603af">  243</a></span>&#160;    <a class="code" href="classOpenMS_1_1XTandemInfile.html#a138ca2002a5af71819cd7b721dd0efb4">ErrorUnit</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#ad70a25c9b136686d2473085ee98603af">fragment_mass_error_unit_</a>;</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;</div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a205f86db2f7913a3351ff8d80102574e">  245</a></span>&#160;    <a class="code" href="classOpenMS_1_1XTandemInfile.html#acb24b846f44e558e17a9f47674d2b406">MassType</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a205f86db2f7913a3351ff8d80102574e">fragment_mass_type_</a>;</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;</div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#ad288c6adb9752b49bc3398e2b283c773">  247</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#ad288c6adb9752b49bc3398e2b283c773">max_precursor_charge_</a>;</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;</div>
<div class="line"><a name="l00249"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#aeff9ec6176c20ae0eae0ec7301d606a4">  249</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#aeff9ec6176c20ae0eae0ec7301d606a4">precursor_lower_mz_</a>;</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;</div>
<div class="line"><a name="l00251"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a56464795f920d3ed7ad1dc7a9f2767ab">  251</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a56464795f920d3ed7ad1dc7a9f2767ab">fragment_lower_mz_</a>;</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;</div>
<div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#ad90ba947694d7060436ed5813ab350cc">  253</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#ad90ba947694d7060436ed5813ab350cc">number_of_threads_</a>;</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;</div>
<div class="line"><a name="l00255"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a48465bc9cd881fbd413b9dd41abe1f09">  255</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a48465bc9cd881fbd413b9dd41abe1f09">batch_size_</a>;</div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;</div>
<div class="line"><a name="l00257"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a721b9410a523f5268cbe52f67741a638">  257</a></span>&#160;    <a class="code" href="classOpenMS_1_1ModificationDefinitionsSet.html">ModificationDefinitionsSet</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a721b9410a523f5268cbe52f67741a638">modifications_</a>;</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;</div>
<div class="line"><a name="l00259"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a0506e0ea13514a1880c1dd7472bc61b0">  259</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a0506e0ea13514a1880c1dd7472bc61b0">input_filename_</a>;</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;</div>
<div class="line"><a name="l00261"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a63ac3f108dba26a50eab0bdd0be62422">  261</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a63ac3f108dba26a50eab0bdd0be62422">output_filename_</a>;</div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;</div>
<div class="line"><a name="l00263"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a9456cad8e17b1ceddd9fd6ca6f7bf9d2">  263</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a9456cad8e17b1ceddd9fd6ca6f7bf9d2">taxonomy_file_</a>;</div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;</div>
<div class="line"><a name="l00265"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a2ebd224514b3401266ded5e29f6530e2">  265</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a2ebd224514b3401266ded5e29f6530e2">taxon_</a>;</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;</div>
<div class="line"><a name="l00267"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a330dd95ca4cdc1c2b17da95489da82ae">  267</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a330dd95ca4cdc1c2b17da95489da82ae">cleavage_site_</a>;</div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;</div>
<div class="line"><a name="l00270"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a8a9945a699a378359b462bab6535842b">  270</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a8a9945a699a378359b462bab6535842b">refine_</a>;</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;</div>
<div class="line"><a name="l00273"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a4c204b2fe1403cca3de086b6d71041f5">  273</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a4c204b2fe1403cca3de086b6d71041f5">semi_cleavage_</a>;</div>
<div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;</div>
<div class="line"><a name="l00275"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a48b3fbd29cb3c6c27c34beb3c167611e">  275</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a48b3fbd29cb3c6c27c34beb3c167611e">refine_max_valid_evalue_</a>;</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;    <span class="comment">// scoring</span></div>
<div class="line"><a name="l00278"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a461ba78cb1427cd58895580623301fe4">  278</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#a461ba78cb1427cd58895580623301fe4">number_of_missed_cleavages_</a>;</div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;</div>
<div class="line"><a name="l00280"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#ae7de871158c00c6eabfc71a8a3dc20c7">  280</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1XTandemInfile.html#ae7de871158c00c6eabfc71a8a3dc20c7">default_parameters_file_</a>;</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;</div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;    <span class="comment">// output parameters</span></div>
<div class="line"><a name="l00283"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#af7e21bd68b1d4041d01cda9e964bd2d1">  283</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1XTandemInfile.html#af7e21bd68b1d4041d01cda9e964bd2d1">max_valid_evalue_</a>;</div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;</div>
<div class="line"><a name="l00289"></a><span class="lineno"><a class="line" href="classOpenMS_1_1XTandemInfile.html#a7f68b780ba2f5aa60277272425275676">  289</a></span>&#160;    std::vector&lt;Internal::XTandemInfileNote&gt; <a class="code" href="classOpenMS_1_1XTandemInfile.html#a7f68b780ba2f5aa60277272425275676">notes_</a>;</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;</div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;<span class="preprocessor">#endif // OPENMS_FORMAT_XTANDEMINFILE_H</span></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a205f86db2f7913a3351ff8d80102574e"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a205f86db2f7913a3351ff8d80102574e">OpenMS::XTandemInfile::fragment_mass_type_</a></div><div class="ttdeci">MassType fragment_mass_type_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:245</div></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_1XTandemInfile_html_ad288c6adb9752b49bc3398e2b283c773"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#ad288c6adb9752b49bc3398e2b283c773">OpenMS::XTandemInfile::max_precursor_charge_</a></div><div class="ttdeci">UInt max_precursor_charge_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:247</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html">OpenMS::XTandemInfile</a></div><div class="ttdoc">XTandem input file. </div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a138ca2002a5af71819cd7b721dd0efb4"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a138ca2002a5af71819cd7b721dd0efb4">OpenMS::XTandemInfile::ErrorUnit</a></div><div class="ttdeci">ErrorUnit</div><div class="ttdoc">error unit, either Da or ppm </div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a48465bc9cd881fbd413b9dd41abe1f09"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a48465bc9cd881fbd413b9dd41abe1f09">OpenMS::XTandemInfile::batch_size_</a></div><div class="ttdeci">UInt batch_size_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:255</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a3081e522548f77c057fd1fabf0fa8366"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a3081e522548f77c057fd1fabf0fa8366">OpenMS::XTandemInfile::precursor_mass_error_unit_</a></div><div class="ttdeci">ErrorUnit precursor_mass_error_unit_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:241</div></div>
<div class="ttc" id="ModificationDefinitionsSet_8h_html"><div class="ttname"><a href="ModificationDefinitionsSet_8h.html">ModificationDefinitionsSet.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_ae7de871158c00c6eabfc71a8a3dc20c7"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#ae7de871158c00c6eabfc71a8a3dc20c7">OpenMS::XTandemInfile::default_parameters_file_</a></div><div class="ttdeci">String default_parameters_file_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:280</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_ad90ba947694d7060436ed5813ab350cc"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#ad90ba947694d7060436ed5813ab350cc">OpenMS::XTandemInfile::number_of_threads_</a></div><div class="ttdeci">UInt number_of_threads_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:253</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_ad70a25c9b136686d2473085ee98603af"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#ad70a25c9b136686d2473085ee98603af">OpenMS::XTandemInfile::fragment_mass_error_unit_</a></div><div class="ttdeci">ErrorUnit fragment_mass_error_unit_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:243</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_acb24b846f44e558e17a9f47674d2b406"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#acb24b846f44e558e17a9f47674d2b406">OpenMS::XTandemInfile::MassType</a></div><div class="ttdeci">MassType</div><div class="ttdoc">Mass type of the precursor, either monoisotopic or average. </div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:65</div></div>
<div class="ttc" id="XTandemInfileXMLHandler_8h_html"><div class="ttname"><a href="XTandemInfileXMLHandler_8h.html">XTandemInfileXMLHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a0506e0ea13514a1880c1dd7472bc61b0"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a0506e0ea13514a1880c1dd7472bc61b0">OpenMS::XTandemInfile::input_filename_</a></div><div class="ttdeci">String input_filename_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:259</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_adcdbf79d5d94972659840cea41217b28"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#adcdbf79d5d94972659840cea41217b28">OpenMS::XTandemInfile::precursor_mass_type_</a></div><div class="ttdeci">MassType precursor_mass_type_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:239</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a9456cad8e17b1ceddd9fd6ca6f7bf9d2"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a9456cad8e17b1ceddd9fd6ca6f7bf9d2">OpenMS::XTandemInfile::taxonomy_file_</a></div><div class="ttdeci">String taxonomy_file_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:263</div></div>
<div class="ttc" id="classOpenMS_1_1ModificationDefinitionsSet_html"><div class="ttname"><a href="classOpenMS_1_1ModificationDefinitionsSet.html">OpenMS::ModificationDefinitionsSet</a></div><div class="ttdoc">Representation of a set of modification definitions. </div><div class="ttdef"><b>Definition:</b> ModificationDefinitionsSet.h:57</div></div>
<div class="ttc" id="XMLFile_8h_html"><div class="ttname"><a href="XMLFile_8h.html">XMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a461ba78cb1427cd58895580623301fe4"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a461ba78cb1427cd58895580623301fe4">OpenMS::XTandemInfile::number_of_missed_cleavages_</a></div><div class="ttdeci">UInt number_of_missed_cleavages_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:278</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a63ac3f108dba26a50eab0bdd0be62422"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a63ac3f108dba26a50eab0bdd0be62422">OpenMS::XTandemInfile::output_filename_</a></div><div class="ttdeci">String output_filename_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:261</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a48b3fbd29cb3c6c27c34beb3c167611e"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a48b3fbd29cb3c6c27c34beb3c167611e">OpenMS::XTandemInfile::refine_max_valid_evalue_</a></div><div class="ttdeci">double refine_max_valid_evalue_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:275</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_aca7dd9843d0f65c30077f53d5e56c2c3"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#aca7dd9843d0f65c30077f53d5e56c2c3">OpenMS::XTandemInfile::precursor_mass_tolerance_plus_</a></div><div class="ttdeci">double precursor_mass_tolerance_plus_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:235</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_ace929bc4ac20b10e60ca5e10ce669268"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#ace929bc4ac20b10e60ca5e10ce669268">OpenMS::XTandemInfile::fragment_mass_tolerance_</a></div><div class="ttdeci">double fragment_mass_tolerance_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:233</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_aeff9ec6176c20ae0eae0ec7301d606a4"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#aeff9ec6176c20ae0eae0ec7301d606a4">OpenMS::XTandemInfile::precursor_lower_mz_</a></div><div class="ttdeci">double precursor_lower_mz_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:249</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a330dd95ca4cdc1c2b17da95489da82ae"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a330dd95ca4cdc1c2b17da95489da82ae">OpenMS::XTandemInfile::cleavage_site_</a></div><div class="ttdeci">String cleavage_site_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:267</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLFile_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLFile.html">OpenMS::Internal::XMLFile</a></div><div class="ttdoc">Base class for loading/storing XML files that have a handler derived from XMLHandler. </div><div class="ttdef"><b>Definition:</b> XMLFile.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a4c204b2fe1403cca3de086b6d71041f5"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a4c204b2fe1403cca3de086b6d71041f5">OpenMS::XTandemInfile::semi_cleavage_</a></div><div class="ttdeci">bool semi_cleavage_</div><div class="ttdoc">semi cleavage </div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:273</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a2ebd224514b3401266ded5e29f6530e2"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a2ebd224514b3401266ded5e29f6530e2">OpenMS::XTandemInfile::taxon_</a></div><div class="ttdeci">String taxon_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:265</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_af7e21bd68b1d4041d01cda9e964bd2d1"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#af7e21bd68b1d4041d01cda9e964bd2d1">OpenMS::XTandemInfile::max_valid_evalue_</a></div><div class="ttdeci">double max_valid_evalue_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:283</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="classOpenMS_1_1XTandemInfile_html_a721b9410a523f5268cbe52f67741a638"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a721b9410a523f5268cbe52f67741a638">OpenMS::XTandemInfile::modifications_</a></div><div class="ttdeci">ModificationDefinitionsSet modifications_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:257</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a7f68b780ba2f5aa60277272425275676"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a7f68b780ba2f5aa60277272425275676">OpenMS::XTandemInfile::notes_</a></div><div class="ttdeci">std::vector&lt; Internal::XTandemInfileNote &gt; notes_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:289</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a7b8ddc890668c3e64281c06106e5569d"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a7b8ddc890668c3e64281c06106e5569d">OpenMS::XTandemInfile::precursor_mass_tolerance_minus_</a></div><div class="ttdeci">double precursor_mass_tolerance_minus_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:237</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_1XTandemInfile_html_a56464795f920d3ed7ad1dc7a9f2767ab"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a56464795f920d3ed7ad1dc7a9f2767ab">OpenMS::XTandemInfile::fragment_lower_mz_</a></div><div class="ttdeci">double fragment_lower_mz_</div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:251</div></div>
<div class="ttc" id="classOpenMS_1_1XTandemInfile_html_a8a9945a699a378359b462bab6535842b"><div class="ttname"><a href="classOpenMS_1_1XTandemInfile.html#a8a9945a699a378359b462bab6535842b">OpenMS::XTandemInfile::refine_</a></div><div class="ttdeci">bool refine_</div><div class="ttdoc">Enable/disable xtandem refinement. </div><div class="ttdef"><b>Definition:</b> XTandemInfile.h:270</div></div>
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