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<a href="InspectOutfile_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_INSPECTOUTFILE_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_INSPECTOUTFILE_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="Exception_8h.html">OpenMS/CONCEPT/Exception.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="FileHandler_8h.html">OpenMS/FORMAT/FileHandler.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="FileTypes_8h.html">OpenMS/FORMAT/FileTypes.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> {</div>
<div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InspectOutfile.html"> 57</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1InspectOutfile.html">InspectOutfile</a></div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  {</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <a class="code" href="classOpenMS_1_1InspectOutfile.html">InspectOutfile</a>();</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <a class="code" href="classOpenMS_1_1InspectOutfile.html">InspectOutfile</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1InspectOutfile.html">InspectOutfile</a> & inspect_outfile);</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1InspectOutfile.html">InspectOutfile</a>();</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <a class="code" href="classOpenMS_1_1InspectOutfile.html">InspectOutfile</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1InspectOutfile.html">InspectOutfile</a> & inspect_outfile);</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordtype">bool</span> operator==(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1InspectOutfile.html">InspectOutfile</a> & inspect_outfile) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  std::vector<Size> load(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & result_filename, std::vector<PeptideIdentification> & peptide_identifications, <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> & protein_identification, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> p_value_threshold, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & database_filename = <span class="stringliteral">""</span>);</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  std::vector<Size> getWantedRecords(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & result_filename, <a class="code" href="classdouble.html">DoubleReal</a> p_value_threshold);</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">void</span> compressTrieDB(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & database_filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & index_filename, std::vector<Size> & wanted_records, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & snd_database_filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & snd_index_filename, <span class="keywordtype">bool</span> append = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordtype">void</span> generateTrieDB(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & source_database_filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & database_filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & index_filename, <span class="keywordtype">bool</span> append = <span class="keyword">false</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> species = <span class="stringliteral">""</span>);</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> </div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keywordtype">void</span> getACAndACType(<a class="code" href="classOpenMS_1_1String.html">String</a> line, <a class="code" href="classOpenMS_1_1String.html">String</a> & accession, <a class="code" href="classOpenMS_1_1String.html">String</a> & accession_type);</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordtype">void</span> getPrecursorRTandMZ(<span class="keyword">const</span> std::vector<std::pair<<a class="code" href="classOpenMS_1_1String.html">String</a>, std::vector<std::pair<Size, Size> > > > & files_and_peptide_identification_with_scan_number, std::vector<PeptideIdentification> & ids);</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span> </div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordtype">void</span> getLabels(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & source_database_filename, <a class="code" href="classOpenMS_1_1String.html">String</a> & ac_label, <a class="code" href="classOpenMS_1_1String.html">String</a> & sequence_start_label, <a class="code" href="classOpenMS_1_1String.html">String</a> & sequence_end_label, <a class="code" href="classOpenMS_1_1String.html">String</a> & comment_label, <a class="code" href="classOpenMS_1_1String.html">String</a> & species_label);</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  std::vector<Size> getSequences(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & database_filename, <span class="keyword">const</span> std::map<Size, Size> & wanted_records, std::vector<String> & sequences);</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> PeakT></div>
<div class="line"><a name="l00142"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InspectOutfile.html#a94fe62a5040d77b84878d091f0eb8686"> 142</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1InspectOutfile.html#a94fe62a5040d77b84878d091f0eb8686">getExperiment</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakT></a> & exp, <a class="code" href="classOpenMS_1_1String.html">String</a> & type, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & in_filename)</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  {</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  type.clear();</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ad20897c5c8bd47f5d4005989bead0e55">reset</a>();</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="comment">//input file type</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <a class="code" href="classOpenMS_1_1FileHandler.html">FileHandler</a> fh;</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> in_type = fh.<a class="code" href="classOpenMS_1_1FileHandler.html#a6189bfbef8639c71f3ef2dfa55c4fad7">getTypeByContent</a>(in_filename);</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keywordflow">if</span> (in_type == <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a>)</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  {</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1ParseError.html">Exception::ParseError</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"Could not determine type of the file. Aborting!"</span>, in_filename);</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  }</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  type = <a class="code" href="structOpenMS_1_1FileTypes.html#af5492ebd6be6c42ac2be3f72da408fd2">FileTypes::typeToName</a>(in_type);</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  fh.<a class="code" href="classOpenMS_1_1FileHandler.html#a408091416e0e1f6019abd59bdb6a9269">loadExperiment</a>(in_filename, exp, in_type);</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  }</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="keywordtype">bool</span> getSearchEngineAndVersion(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & cmd_output, <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> & protein_identification);</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordtype">void</span> readOutHeader(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & header_line, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> & spectrum_file_column, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> & scan_column, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> & peptide_column, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> & protein_column, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> & charge_column, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> & MQ_score_column, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> & p_value_column, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> & record_number_column, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> & DB_file_pos_column, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> & spec_file_pos_column, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> & number_of_columns);</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span> </div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00174"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InspectOutfile.html#a30a0740700b25744b612ffaa23863fe3"> 174</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1InspectOutfile.html#a30a0740700b25744b612ffaa23863fe3">db_pos_length_</a>; </div>
<div class="line"><a name="l00175"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InspectOutfile.html#a2d85713d0b31835bf704e73f1a51a282"> 175</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1InspectOutfile.html#a2d85713d0b31835bf704e73f1a51a282">trie_db_pos_length_</a>; </div>
<div class="line"><a name="l00176"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InspectOutfile.html#af766478d455cf1362247ea55af3865ea"> 176</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1InspectOutfile.html#af766478d455cf1362247ea55af3865ea">protein_name_length_</a>; </div>
<div class="line"><a name="l00177"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InspectOutfile.html#a22406b9e4a43d545c303bdf1b8ff593e"> 177</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1InspectOutfile.html#a22406b9e4a43d545c303bdf1b8ff593e">record_length_</a>; </div>
<div class="line"><a name="l00178"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InspectOutfile.html#ad72537c229548eb9b74088eb3ae88ee0"> 178</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> <a class="code" href="classOpenMS_1_1InspectOutfile.html#ad72537c229548eb9b74088eb3ae88ee0">trie_delimiter_</a>; </div>
<div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InspectOutfile.html#a83ffe28bcbf4969b81f1e473bba2a52c"> 179</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1InspectOutfile.html#a83ffe28bcbf4969b81f1e473bba2a52c">score_type_</a>; </div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  };</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> } <span class="comment">//namespace OpenMS</span></div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span> </div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span> <span class="preprocessor">#endif // OPENMS_FORMAT_INSPECTOUTFILE_H</span></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">OpenMS::FileTypes::Type</a></div><div class="ttdeci">Type</div><div class="ttdoc">Actual file types enum. </div><div class="ttdef"><b>Definition:</b> FileTypes.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html">OpenMS::ProteinIdentification</a></div><div class="ttdoc">Representation of a protein identification run. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:61</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_1InspectOutfile_html_a30a0740700b25744b612ffaa23863fe3"><div class="ttname"><a href="classOpenMS_1_1InspectOutfile.html#a30a0740700b25744b612ffaa23863fe3">OpenMS::InspectOutfile::db_pos_length_</a></div><div class="ttdeci">static const Size db_pos_length_</div><div class="ttdoc">length of 1) </div><div class="ttdef"><b>Definition:</b> InspectOutfile.h:174</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ad20897c5c8bd47f5d4005989bead0e55"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ad20897c5c8bd47f5d4005989bead0e55">OpenMS::MSExperiment::reset</a></div><div class="ttdeci">void reset()</div><div class="ttdoc">Resets all internal values. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:635</div></div>
<div class="ttc" id="classOpenMS_1_1InspectOutfile_html_a83ffe28bcbf4969b81f1e473bba2a52c"><div class="ttname"><a href="classOpenMS_1_1InspectOutfile.html#a83ffe28bcbf4969b81f1e473bba2a52c">OpenMS::InspectOutfile::score_type_</a></div><div class="ttdeci">static const String score_type_</div><div class="ttdoc">type of score </div><div class="ttdef"><b>Definition:</b> InspectOutfile.h:179</div></div>
<div class="ttc" id="FileHandler_8h_html"><div class="ttname"><a href="FileHandler_8h.html">FileHandler.h</a></div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1InspectOutfile_html_af766478d455cf1362247ea55af3865ea"><div class="ttname"><a href="classOpenMS_1_1InspectOutfile.html#af766478d455cf1362247ea55af3865ea">OpenMS::InspectOutfile::protein_name_length_</a></div><div class="ttdeci">static const Size protein_name_length_</div><div class="ttdoc">length of 3) </div><div class="ttdef"><b>Definition:</b> InspectOutfile.h:176</div></div>
<div class="ttc" id="classOpenMS_1_1FileHandler_html_a6189bfbef8639c71f3ef2dfa55c4fad7"><div class="ttname"><a href="classOpenMS_1_1FileHandler.html#a6189bfbef8639c71f3ef2dfa55c4fad7">OpenMS::FileHandler::getTypeByContent</a></div><div class="ttdeci">static FileTypes::Type getTypeByContent(const String &filename)</div><div class="ttdoc">Determines the file type of a file by parsing the first few lines. </div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1InspectOutfile_html_a22406b9e4a43d545c303bdf1b8ff593e"><div class="ttname"><a href="classOpenMS_1_1InspectOutfile.html#a22406b9e4a43d545c303bdf1b8ff593e">OpenMS::InspectOutfile::record_length_</a></div><div class="ttdeci">static const Size record_length_</div><div class="ttdoc">length of the whole record </div><div class="ttdef"><b>Definition:</b> InspectOutfile.h:177</div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">OpenMS::FileTypes::UNKNOWN</a></div><div class="ttdoc">Unknown file extension. </div><div class="ttdef"><b>Definition:</b> FileTypes.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1InspectOutfile_html_a2d85713d0b31835bf704e73f1a51a282"><div class="ttname"><a href="classOpenMS_1_1InspectOutfile.html#a2d85713d0b31835bf704e73f1a51a282">OpenMS::InspectOutfile::trie_db_pos_length_</a></div><div class="ttdeci">static const Size trie_db_pos_length_</div><div class="ttdoc">length of 2) </div><div class="ttdef"><b>Definition:</b> InspectOutfile.h:175</div></div>
<div class="ttc" id="classOpenMS_1_1InspectOutfile_html_ad72537c229548eb9b74088eb3ae88ee0"><div class="ttname"><a href="classOpenMS_1_1InspectOutfile.html#ad72537c229548eb9b74088eb3ae88ee0">OpenMS::InspectOutfile::trie_delimiter_</a></div><div class="ttdeci">static const char trie_delimiter_</div><div class="ttdoc">the sequences in the trie database are delimited by this character </div><div class="ttdef"><b>Definition:</b> InspectOutfile.h:178</div></div>
<div class="ttc" id="classOpenMS_1_1InspectOutfile_html"><div class="ttname"><a href="classOpenMS_1_1InspectOutfile.html">OpenMS::InspectOutfile</a></div><div class="ttdoc">Representation of an Inspect outfile. </div><div class="ttdef"><b>Definition:</b> InspectOutfile.h:57</div></div>
<div class="ttc" id="PeptideIdentification_8h_html"><div class="ttname"><a href="PeptideIdentification_8h.html">PeptideIdentification.h</a></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_1FileHandler_html_a408091416e0e1f6019abd59bdb6a9269"><div class="ttname"><a href="classOpenMS_1_1FileHandler.html#a408091416e0e1f6019abd59bdb6a9269">OpenMS::FileHandler::loadExperiment</a></div><div class="ttdeci">bool loadExperiment(const String &filename, MSExperiment< PeakType > &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool compute_hash=true)</div><div class="ttdoc">Loads a file into an MSExperiment. </div><div class="ttdef"><b>Definition:</b> FileHandler.h:121</div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_af5492ebd6be6c42ac2be3f72da408fd2"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#af5492ebd6be6c42ac2be3f72da408fd2">OpenMS::FileTypes::typeToName</a></div><div class="ttdeci">static String typeToName(Type type)</div><div class="ttdoc">Returns the name/extension of the type. </div></div>
<div class="ttc" id="classOpenMS_1_1InspectOutfile_html_a94fe62a5040d77b84878d091f0eb8686"><div class="ttname"><a href="classOpenMS_1_1InspectOutfile.html#a94fe62a5040d77b84878d091f0eb8686">OpenMS::InspectOutfile::getExperiment</a></div><div class="ttdeci">void getExperiment(MSExperiment< PeakT > &exp, String &type, const String &in_filename)</div><div class="ttdef"><b>Definition:</b> InspectOutfile.h:142</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="Exception_8h_html"><div class="ttname"><a href="Exception_8h.html">Exception.h</a></div></div>
<div class="ttc" id="FileTypes_8h_html"><div class="ttname"><a href="FileTypes_8h.html">FileTypes.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FileHandler_html"><div class="ttname"><a href="classOpenMS_1_1FileHandler.html">OpenMS::FileHandler</a></div><div class="ttdoc">Facilitates file handling by file type recognition. </div><div class="ttdef"><b>Definition:</b> FileHandler.h:73</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_1Exception_1_1ParseError_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1ParseError.html">OpenMS::Exception::ParseError</a></div><div class="ttdoc">Parse Error exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:608</div></div>
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