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Merge pull request #44 from hgb-bin-proteomics/develop
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add documentation
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michabirklbauer authored Aug 5, 2024
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4 changes: 4 additions & 0 deletions docs/html/_candidate_search_8cs.js
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<a href="_candidate_search_8cs.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="keyword">using </span><a class="code hl_namespace" href="namespace_candidate_search_1_1util.html">CandidateSearch.util</a>;</div>
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span> </div>
<div class="foldopen" id="foldopen00003" data-start="{" data-end="}">
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"><a class="line" href="namespace_candidate_search.html"> 3</a></span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespace_candidate_search.html">CandidateSearch</a></div>
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span>{</div>
<div class="foldopen" id="foldopen00010" data-start="{" data-end="};">
<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"><a class="line" href="class_candidate_search_1_1_candidate_search.html"> 10</a></span> <span class="keyword">public</span> <span class="keyword">class </span><a class="code hl_namespace" href="namespace_candidate_search.html">CandidateSearch</a></div>
<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span> {</div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"><a class="line" href="class_candidate_search_1_1_candidate_search.html#abdc2e237c89f801ca9f47ba447710281"> 15</a></span> <span class="keyword">public</span> <span class="keyword">const</span> <span class="keywordtype">string</span> version = <span class="stringliteral">&quot;1.1.2&quot;</span>;</div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> </div>
<div class="foldopen" id="foldopen00021" data-start="{" data-end="}">
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"><a class="line" href="class_candidate_search_1_1_candidate_search.html#a0958147526f9d44e92d4f23315d95d74"> 21</a></span> <span class="keyword">public</span> <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code hl_function" href="class_candidate_search_1_1_candidate_search.html#a0958147526f9d44e92d4f23315d95d74">Main</a>(<span class="keywordtype">string</span>[] args)</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> {</div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> <span class="keywordflow">if</span> (args.Length == 3) {</div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> var spectraFile = args[0];</div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> var databaseFile = args[1];</div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> var settingsFile = args[2];</div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> </div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> Console.WriteLine($<span class="stringliteral">&quot;Starting Candidate Search v{version} ...&quot;</span>);</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> </div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> var settings = SettingsReader.readSettings(settingsFile);</div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> Console.WriteLine($<span class="stringliteral">&quot;Read settings file &#39;{settingsFile}&#39; with the following settings:&quot;</span>);</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> Console.WriteLine(settings.ToString());</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> </div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> <span class="keywordflow">if</span> (settings.MODE.Split(<span class="stringliteral">&quot;_&quot;</span>).First().Trim() == <span class="stringliteral">&quot;GPU&quot;</span>)</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> {</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> CandidateSearchGPU.Search(spectraFile, databaseFile, settings);</div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> }</div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> <span class="keywordflow">else</span></div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> {</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> CandidateSearchCPU.Search(spectraFile, databaseFile, settings);</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> }</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> </div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> <span class="keywordflow">return</span>;</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> }</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> Console.WriteLine(<span class="stringliteral">&quot;Incorrect number of arguments! CandidateSearch needs exactly 3 arguments: spectra.mgf database.fasta settings.txt&quot;</span>);</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">return</span>;</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> }</div>
</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> }</div>
</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span>}</div>
</div>
<div class="ttc" id="aclass_candidate_search_1_1_candidate_search_html_a0958147526f9d44e92d4f23315d95d74"><div class="ttname"><a href="class_candidate_search_1_1_candidate_search.html#a0958147526f9d44e92d4f23315d95d74">CandidateSearch.CandidateSearch.Main</a></div><div class="ttdeci">static void Main(string[] args)</div><div class="ttdoc">Main function that is executed when CandidateSearch is run.</div><div class="ttdef"><b>Definition</b> <a href="_candidate_search_8cs_source.html#l00021">CandidateSearch.cs:21</a></div></div>
<div class="ttc" id="anamespace_candidate_search_1_1util_html"><div class="ttname"><a href="namespace_candidate_search_1_1util.html">CandidateSearch.util</a></div><div class="ttdef"><b>Definition</b> <a href="_database_8cs_source.html#l00003">Database.cs:4</a></div></div>
<div class="ttc" id="anamespace_candidate_search_html"><div class="ttname"><a href="namespace_candidate_search.html">CandidateSearch</a></div><div class="ttdef"><b>Definition</b> <a href="_candidate_search_8cs_source.html#l00003">CandidateSearch.cs:4</a></div></div>
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