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<a href="SequestInfile_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> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <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> <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> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <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> <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> <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> <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> <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> <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> <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> <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> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <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> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <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> <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> <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> <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> <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> <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> <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> <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> <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> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Andreas Bertsch $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Martin Langwisch $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FORMAT_SEQUESTINFILE_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_SEQUESTINFILE_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <map></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> </div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> {</div>
<div class="line"><a name="l00052"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html"> 52</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SequestInfile.html">SequestInfile</a></div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  {</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <a class="code" href="classOpenMS_1_1SequestInfile.html">SequestInfile</a>();</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <a class="code" href="classOpenMS_1_1SequestInfile.html">SequestInfile</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SequestInfile.html">SequestInfile</a> & sequest_infile);</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1SequestInfile.html">SequestInfile</a>();</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <a class="code" href="classOpenMS_1_1SequestInfile.html">SequestInfile</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SequestInfile.html">SequestInfile</a> & sequest_infile);</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordtype">bool</span> operator==(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SequestInfile.html">SequestInfile</a> & sequest_infile) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordtype">void</span> store(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename);</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> getEnzymeInfoAsString() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & getDatabase() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordtype">void</span> setDatabase(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & database);</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & getNeutralLossesForIons() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordtype">void</span> setNeutralLossesForIons(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & neutral_losses_for_ions);</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & getIonSeriesWeights() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordtype">void</span> setIonSeriesWeights(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & ion_series_weights);</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & getPartialSequence() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordtype">void</span> setPartialSequence(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & partial_sequence);</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & getSequenceHeaderFilter() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordtype">void</span> setSequenceHeaderFilter(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & sequence_header_filter);</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> </div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & getProteinMassFilter() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordtype">void</span> setProteinMassFilter(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & protein_mass_filter);</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> getPeakMassTolerance() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordtype">void</span> setPeakMassTolerance(<a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> peak_mass_tolerance);</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> getPrecursorMassTolerance() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keywordtype">void</span> setPrecursorMassTolerance(<a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> precursor_mass_tolerance);</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> getMatchPeakTolerance() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keywordtype">void</span> setMatchPeakTolerance(<a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> match_peak_tolerance);</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> getIonCutoffPercentage() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordtype">void</span> setIonCutoffPercentage(<a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> ion_cutoff_percentage);</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getPeptideMassUnit() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordtype">void</span> setPeptideMassUnit(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peptide_mass_unit);</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span> </div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getOutputLines() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="keywordtype">void</span> setOutputLines(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> output_lines);</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getEnzymeNumber() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> getEnzymeName() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> setEnzyme(<a class="code" href="classOpenMS_1_1String.html">String</a> enzyme_name);</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> </div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getMaxAAPerModPerPeptide() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keywordtype">void</span> setMaxAAPerModPerPeptide(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_aa_per_mod_per_peptide);</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getMaxModsPerPeptide() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordtype">void</span> setMaxModsPerPeptide(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_mods_per_peptide);</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getNucleotideReadingFrame() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordtype">void</span> setNucleotideReadingFrame(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> nucleotide_reading_frame);</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getMaxInternalCleavageSites() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="keywordtype">void</span> setMaxInternalCleavageSites(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_internal_cleavage_sites);</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> </div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getMatchPeakCount() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="keywordtype">void</span> setMatchPeakCount(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> match_peak_count);</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getMatchPeakAllowedError() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="keywordtype">void</span> setMatchPeakAllowedError(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> match_peak_allowed_error);</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> </div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> </div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordtype">bool</span> getShowFragmentIons() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordtype">void</span> setShowFragmentIons(<span class="keywordtype">bool</span> show_fragments);</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span> </div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <span class="keywordtype">bool</span> getPrintDuplicateReferences() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="keywordtype">void</span> setPrintDuplicateReferences(<span class="keywordtype">bool</span> print_duplicate_references);</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> </div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="keywordtype">bool</span> getRemovePrecursorNearPeaks() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keywordtype">void</span> setRemovePrecursorNearPeaks(<span class="keywordtype">bool</span> remove_precursor_near_peaks);</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span> </div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keywordtype">bool</span> getMassTypeParent() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="keywordtype">void</span> setMassTypeParent(<span class="keywordtype">bool</span> mass_type_parent);</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span> </div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  <span class="keywordtype">bool</span> getMassTypeFragment() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordtype">void</span> setMassTypeFragment(<span class="keywordtype">bool</span> mass_type_fragment);</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> </div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <span class="keywordtype">bool</span> getNormalizeXcorr() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <span class="keywordtype">void</span> setNormalizeXcorr(<span class="keywordtype">bool</span> normalize_xcorr);</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span> </div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="keywordtype">bool</span> getResiduesInUpperCase() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <span class="keywordtype">void</span> setResiduesInUpperCase(<span class="keywordtype">bool</span> residues_in_upper_case);</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span> </div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <span class="keywordtype">void</span> addEnzymeInfo(std::vector<String> & enzyme_info);</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> </div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <span class="keyword">const</span> std::map<String, std::vector<String> > & getModifications() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> </div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keywordtype">void</span> handlePTMs(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & modification_line, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & modifications_filename, <span class="keyword">const</span> <span class="keywordtype">bool</span> monoisotopic);</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span> </div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keyword">const</span> std::map<String, std::vector<String> > & getEnzymeInfo_() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span> </div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="keywordtype">void</span> setStandardEnzymeInfo_();</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span> </div>
<div class="line"><a name="l00251"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a7f4f5e89c5c45c5b37500a5a42882963"> 251</a></span>  std::map<String, std::vector<String> > <a class="code" href="classOpenMS_1_1SequestInfile.html#a7f4f5e89c5c45c5b37500a5a42882963">enzyme_info_</a>; </div>
<div class="line"><a name="l00252"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#ab298dcbfd1a5a670ad50319535a67cc6"> 252</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#ab298dcbfd1a5a670ad50319535a67cc6">database_</a>; </div>
<div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a9a8bc7dd6f5ec1aa4d7b2694bd30ec55"> 253</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a9a8bc7dd6f5ec1aa4d7b2694bd30ec55">snd_database_</a>; </div>
<div class="line"><a name="l00254"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a6e242bfc89d4dc9db1291d54ba623cb7"> 254</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a6e242bfc89d4dc9db1291d54ba623cb7">neutral_losses_for_ions_</a>; </div>
<div class="line"><a name="l00255"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a3f8b91fe94ac86875ccc9c40531a6724"> 255</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a3f8b91fe94ac86875ccc9c40531a6724">ion_series_weights_</a>; </div>
<div class="line"><a name="l00256"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a7d1048c4a36aeb4c73fc4c6e45b5f56f"> 256</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a7d1048c4a36aeb4c73fc4c6e45b5f56f">partial_sequence_</a>; </div>
<div class="line"><a name="l00257"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a8d44cab72e0ca3c40e942a1539fb8e6c"> 257</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a8d44cab72e0ca3c40e942a1539fb8e6c">sequence_header_filter_</a>; </div>
<div class="line"><a name="l00258"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a01fdb0b9b4b17a7a7827786d20ff7fe5"> 258</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a01fdb0b9b4b17a7a7827786d20ff7fe5">protein_mass_filter_</a>;</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span> </div>
<div class="line"><a name="l00260"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a17921ca118ae3d8d972b748147f5ef6b"> 260</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a17921ca118ae3d8d972b748147f5ef6b">precursor_mass_tolerance_</a>; </div>
<div class="line"><a name="l00261"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a61cbefb333ea97a322a2d107bc0aa449"> 261</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a61cbefb333ea97a322a2d107bc0aa449">peak_mass_tolerance_</a>; </div>
<div class="line"><a name="l00262"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a0f2b4359a4abaf84e260a41a738c2dc3"> 262</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a0f2b4359a4abaf84e260a41a738c2dc3">match_peak_tolerance_</a>; </div>
<div class="line"><a name="l00263"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a6a803be031c4d84f66532b7b236959d7"> 263</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a6a803be031c4d84f66532b7b236959d7">ion_cutoff_percentage_</a>; </div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span> </div>
<div class="line"><a name="l00265"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a78345ca923a1cd68efc546157505caff"> 265</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a78345ca923a1cd68efc546157505caff">peptide_mass_unit_</a>; </div>
<div class="line"><a name="l00266"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a226c7afb77e0fdce098b480d24fd583c"> 266</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a226c7afb77e0fdce098b480d24fd583c">output_lines_</a>; </div>
<div class="line"><a name="l00267"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#aba446e82e01ec4f3373f67d934992fd7"> 267</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#aba446e82e01ec4f3373f67d934992fd7">enzyme_number_</a>; </div>
<div class="line"><a name="l00268"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#ae526ecf4b83963b4a25ce94ba3ac8f8a"> 268</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#ae526ecf4b83963b4a25ce94ba3ac8f8a">max_AA_per_mod_per_peptide_</a>; </div>
<div class="line"><a name="l00269"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a1308f071bd3f7c7a15755a2a1b9d047f"> 269</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a1308f071bd3f7c7a15755a2a1b9d047f">max_mods_per_peptide_</a>; </div>
<div class="line"><a name="l00270"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a5fe0e0093a45dec5191004f67771d8e1"> 270</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a5fe0e0093a45dec5191004f67771d8e1">nucleotide_reading_frame_</a>; </div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_internal_cleavage_sites_; </div>
<div class="line"><a name="l00282"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a8ebbe40ed77803a5f740c8cde59caef5"> 282</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#a8ebbe40ed77803a5f740c8cde59caef5">match_peak_count_</a>; </div>
<div class="line"><a name="l00283"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#aceb506dea19952637f7168c7c3d83e0f"> 283</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SequestInfile.html#aceb506dea19952637f7168c7c3d83e0f">match_peak_allowed_error_</a>; </div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span> </div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span> </div>
<div class="line"><a name="l00286"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a7d8ce1e93c26117380dcac2b5361786b"> 286</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SequestInfile.html#a7d8ce1e93c26117380dcac2b5361786b">show_fragment_ions_</a>; </div>
<div class="line"><a name="l00287"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#abda497ef7a71f331ddc72063975a877e"> 287</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SequestInfile.html#abda497ef7a71f331ddc72063975a877e">print_duplicate_references_</a>; </div>
<div class="line"><a name="l00288"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a7abc7a6d8eeb5c868685d40e53575b9b"> 288</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SequestInfile.html#a7abc7a6d8eeb5c868685d40e53575b9b">remove_precursor_near_peaks_</a>; </div>
<div class="line"><a name="l00289"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#aae111b8c5e800e289cf3696589f27a7b"> 289</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SequestInfile.html#aae111b8c5e800e289cf3696589f27a7b">mass_type_parent_</a>; </div>
<div class="line"><a name="l00290"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#acb808bdba3c3f0ba6c8a92e7563a1610"> 290</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SequestInfile.html#acb808bdba3c3f0ba6c8a92e7563a1610">mass_type_fragment_</a>; </div>
<div class="line"><a name="l00291"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#ae14edfadc520b6f624c52141835b4a94"> 291</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SequestInfile.html#ae14edfadc520b6f624c52141835b4a94">normalize_xcorr_</a>; </div>
<div class="line"><a name="l00292"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#a57c2fba9aa61eaba9e713013544d45f7"> 292</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SequestInfile.html#a57c2fba9aa61eaba9e713013544d45f7">residues_in_upper_case_</a>; </div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span> </div>
<div class="line"><a name="l00294"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SequestInfile.html#ac919b7736871856656aba57c85cd0a6a"> 294</a></span>  std::map<String, std::vector<String> > <a class="code" href="classOpenMS_1_1SequestInfile.html#ac919b7736871856656aba57c85cd0a6a">PTMname_residues_mass_type_</a>; </div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  };</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span> </div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span> </div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span> <span class="preprocessor">#endif // OPENMS_FORMAT_SEQUESTINFILE_H</span></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_ae14edfadc520b6f624c52141835b4a94"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#ae14edfadc520b6f624c52141835b4a94">OpenMS::SequestInfile::normalize_xcorr_</a></div><div class="ttdeci">bool normalize_xcorr_</div><div class="ttdoc">whether to display normalized xcorr values </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:291</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_ab298dcbfd1a5a670ad50319535a67cc6"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#ab298dcbfd1a5a670ad50319535a67cc6">OpenMS::SequestInfile::database_</a></div><div class="ttdeci">String database_</div><div class="ttdoc">database used </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:252</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a57c2fba9aa61eaba9e713013544d45f7"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a57c2fba9aa61eaba9e713013544d45f7">OpenMS::SequestInfile::residues_in_upper_case_</a></div><div class="ttdeci">bool residues_in_upper_case_</div><div class="ttdoc">whether residues are in upper case </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:292</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a17921ca118ae3d8d972b748147f5ef6b"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a17921ca118ae3d8d972b748147f5ef6b">OpenMS::SequestInfile::precursor_mass_tolerance_</a></div><div class="ttdeci">Real precursor_mass_tolerance_</div><div class="ttdoc">tolerance for matching a theoretical to an experimental peptide </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:260</div></div>
<div class="ttc" id="group__Concept_html_gab685845059e8a2c92743427d9a698c70"><div class="ttname"><a href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">OpenMS::Real</a></div><div class="ttdeci">float Real</div><div class="ttdoc">Real type. </div><div class="ttdef"><b>Definition:</b> Types.h:109</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_1SequestInfile_html_aba446e82e01ec4f3373f67d934992fd7"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#aba446e82e01ec4f3373f67d934992fd7">OpenMS::SequestInfile::enzyme_number_</a></div><div class="ttdeci">Size enzyme_number_</div><div class="ttdoc">number of the enzyme used for cleavage </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:267</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a3f8b91fe94ac86875ccc9c40531a6724"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a3f8b91fe94ac86875ccc9c40531a6724">OpenMS::SequestInfile::ion_series_weights_</a></div><div class="ttdeci">String ion_series_weights_</div><div class="ttdoc">weights for the a-; b-; c-; d-; v-; w-; x-; y- and z-ion series; space delimited </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:255</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a6e242bfc89d4dc9db1291d54ba623cb7"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a6e242bfc89d4dc9db1291d54ba623cb7">OpenMS::SequestInfile::neutral_losses_for_ions_</a></div><div class="ttdeci">String neutral_losses_for_ions_</div><div class="ttdoc">whether neutral losses are considered for the a-; b- and y-ions (e.g. 011 for b- and y-ions) ...</div><div class="ttdef"><b>Definition:</b> SequestInfile.h:254</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_ac919b7736871856656aba57c85cd0a6a"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#ac919b7736871856656aba57c85cd0a6a">OpenMS::SequestInfile::PTMname_residues_mass_type_</a></div><div class="ttdeci">std::map< String, std::vector< String > > PTMname_residues_mass_type_</div><div class="ttdoc">the modification names map to the affected residues, the mass change and the type ...</div><div class="ttdef"><b>Definition:</b> SequestInfile.h:294</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a7d1048c4a36aeb4c73fc4c6e45b5f56f"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a7d1048c4a36aeb4c73fc4c6e45b5f56f">OpenMS::SequestInfile::partial_sequence_</a></div><div class="ttdeci">String partial_sequence_</div><div class="ttdoc">space-delimited list of sequence parts that have to occur in the theortical spectra ...</div><div class="ttdef"><b>Definition:</b> SequestInfile.h:256</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_aae111b8c5e800e289cf3696589f27a7b"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#aae111b8c5e800e289cf3696589f27a7b">OpenMS::SequestInfile::mass_type_parent_</a></div><div class="ttdeci">bool mass_type_parent_</div><div class="ttdoc">mass type of the parent peak (0 - monoisotopic; 1 - average) </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:289</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a5fe0e0093a45dec5191004f67771d8e1"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a5fe0e0093a45dec5191004f67771d8e1">OpenMS::SequestInfile::nucleotide_reading_frame_</a></div><div class="ttdeci">Size nucleotide_reading_frame_</div><div class="ttdef"><b>Definition:</b> SequestInfile.h:270</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a0f2b4359a4abaf84e260a41a738c2dc3"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a0f2b4359a4abaf84e260a41a738c2dc3">OpenMS::SequestInfile::match_peak_tolerance_</a></div><div class="ttdeci">Real match_peak_tolerance_</div><div class="ttdoc">minimum distance between two experimental peaks </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:262</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a61cbefb333ea97a322a2d107bc0aa449"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a61cbefb333ea97a322a2d107bc0aa449">OpenMS::SequestInfile::peak_mass_tolerance_</a></div><div class="ttdeci">Real peak_mass_tolerance_</div><div class="ttdoc">tolerance for matching a theoretical to an experimental peak </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:261</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a6a803be031c4d84f66532b7b236959d7"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a6a803be031c4d84f66532b7b236959d7">OpenMS::SequestInfile::ion_cutoff_percentage_</a></div><div class="ttdeci">Real ion_cutoff_percentage_</div><div class="ttdoc">cutoff of the ratio matching theoretical peaks/theoretical peaks </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:263</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a7abc7a6d8eeb5c868685d40e53575b9b"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a7abc7a6d8eeb5c868685d40e53575b9b">OpenMS::SequestInfile::remove_precursor_near_peaks_</a></div><div class="ttdeci">bool remove_precursor_near_peaks_</div><div class="ttdoc">whether peaks near (15 amu) the precursor peak are removed </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:288</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a9a8bc7dd6f5ec1aa4d7b2694bd30ec55"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a9a8bc7dd6f5ec1aa4d7b2694bd30ec55">OpenMS::SequestInfile::snd_database_</a></div><div class="ttdeci">String snd_database_</div><div class="ttdoc">second database used </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:253</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_aceb506dea19952637f7168c7c3d83e0f"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#aceb506dea19952637f7168c7c3d83e0f">OpenMS::SequestInfile::match_peak_allowed_error_</a></div><div class="ttdeci">Size match_peak_allowed_error_</div><div class="ttdoc">number of peaks that may lack this test </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:283</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_ae526ecf4b83963b4a25ce94ba3ac8f8a"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#ae526ecf4b83963b4a25ce94ba3ac8f8a">OpenMS::SequestInfile::max_AA_per_mod_per_peptide_</a></div><div class="ttdeci">Size max_AA_per_mod_per_peptide_</div><div class="ttdoc">maximum number of amino acids containing the same modification in a peptide </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:268</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a1308f071bd3f7c7a15755a2a1b9d047f"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a1308f071bd3f7c7a15755a2a1b9d047f">OpenMS::SequestInfile::max_mods_per_peptide_</a></div><div class="ttdeci">Size max_mods_per_peptide_</div><div class="ttdoc">maximum number of modifications per peptide </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:269</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a226c7afb77e0fdce098b480d24fd583c"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a226c7afb77e0fdce098b480d24fd583c">OpenMS::SequestInfile::output_lines_</a></div><div class="ttdeci">Size output_lines_</div><div class="ttdoc">number of peptides to be displayed </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:266</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a7d8ce1e93c26117380dcac2b5361786b"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a7d8ce1e93c26117380dcac2b5361786b">OpenMS::SequestInfile::show_fragment_ions_</a></div><div class="ttdeci">bool show_fragment_ions_</div><div class="ttdoc">whether to display fragment ions </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:286</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a8ebbe40ed77803a5f740c8cde59caef5"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a8ebbe40ed77803a5f740c8cde59caef5">OpenMS::SequestInfile::match_peak_count_</a></div><div class="ttdeci">Size match_peak_count_</div><div class="ttdoc">number of the top abundant peaks to match with theoretical one </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:282</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a7f4f5e89c5c45c5b37500a5a42882963"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a7f4f5e89c5c45c5b37500a5a42882963">OpenMS::SequestInfile::enzyme_info_</a></div><div class="ttdeci">std::map< String, std::vector< String > > enzyme_info_</div><div class="ttdoc">an endline-delimited list of enzymes; each with cutting direction 0 (N to C) /1; cuts after (list of ...</div><div class="ttdef"><b>Definition:</b> SequestInfile.h:251</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_abda497ef7a71f331ddc72063975a877e"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#abda497ef7a71f331ddc72063975a877e">OpenMS::SequestInfile::print_duplicate_references_</a></div><div class="ttdeci">bool print_duplicate_references_</div><div class="ttdoc">whether all proteins containing a found peptide should be displayed </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:287</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a01fdb0b9b4b17a7a7827786d20ff7fe5"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a01fdb0b9b4b17a7a7827786d20ff7fe5">OpenMS::SequestInfile::protein_mass_filter_</a></div><div class="ttdeci">String protein_mass_filter_</div><div class="ttdef"><b>Definition:</b> SequestInfile.h:258</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_1SequestInfile_html"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html">OpenMS::SequestInfile</a></div><div class="ttdoc">Sequest input file adapter. </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a8d44cab72e0ca3c40e942a1539fb8e6c"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a8d44cab72e0ca3c40e942a1539fb8e6c">OpenMS::SequestInfile::sequence_header_filter_</a></div><div class="ttdeci">String sequence_header_filter_</div><div class="ttdoc">space-delimited list of sequences that have to occur or be absend (preceeded by a tilde) in a protein...</div><div class="ttdef"><b>Definition:</b> SequestInfile.h:257</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_a78345ca923a1cd68efc546157505caff"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#a78345ca923a1cd68efc546157505caff">OpenMS::SequestInfile::peptide_mass_unit_</a></div><div class="ttdeci">Size peptide_mass_unit_</div><div class="ttdoc">peptide mass unit (0 = amu; 1 = mmu; 2 = ppm) </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:265</div></div>
<div class="ttc" id="classOpenMS_1_1SequestInfile_html_acb808bdba3c3f0ba6c8a92e7563a1610"><div class="ttname"><a href="classOpenMS_1_1SequestInfile.html#acb808bdba3c3f0ba6c8a92e7563a1610">OpenMS::SequestInfile::mass_type_fragment_</a></div><div class="ttdeci">bool mass_type_fragment_</div><div class="ttdoc">mass type of fragment peaks (0 - monoisotopic; 1 - average) </div><div class="ttdef"><b>Definition:</b> SequestInfile.h:290</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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<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 11:19:20 using doxygen 1.8.5</font></TD>
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