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<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_695c7fac3e1f44bd8b1eb14243440935.html">APPLICATIONS</a></li> </ul>
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<a href="TOPPBase_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: Stephan Aiche $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Marc Sturm, Clemens Groepl $</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_APPLICATIONS_TOPPBASE_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_APPLICATIONS_TOPPBASE_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="GlobalExceptionHandler_8h.html">OpenMS/CONCEPT/GlobalExceptionHandler.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="LogStream_8h.html">OpenMS/CONCEPT/LogStream.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="VersionInfo_8h.html">OpenMS/CONCEPT/VersionInfo.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="Param_8h.html">OpenMS/DATASTRUCTURES/Param.h</a>></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <<a class="code" href="StringList_8h.html">OpenMS/DATASTRUCTURES/StringList.h</a>></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <<a class="code" href="IntList_8h.html">OpenMS/DATASTRUCTURES/IntList.h</a>></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include <<a class="code" href="DoubleList_8h.html">OpenMS/DATASTRUCTURES/DoubleList.h</a>></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">#include <<a class="code" href="DataProcessing_8h.html">OpenMS/METADATA/DataProcessing.h</a>></span></div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#include <<a class="code" href="DocumentIDTagger_8h.html">OpenMS/METADATA/DocumentIDTagger.h</a>></span></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="preprocessor">#include <<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>></span></div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="preprocessor">#include <<a class="code" href="ParameterInformation_8h.html">OpenMS/APPLICATIONS/ParameterInformation.h</a>></span></div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="preprocessor">#include <<a class="code" href="ToolHandler_8h.html">OpenMS/APPLICATIONS/ToolHandler.h</a>></span></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="preprocessor">#include <iostream></span></div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="preprocessor">#include <fstream></span></div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> <span class="preprocessor">#include <limits></span></div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="keyword">class </span>QStringList;</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> {</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keyword">class </span>ConsensusMap;</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="namespaceOpenMS_1_1Exception.html"> 70</a></span>  <span class="keyword">namespace </span>Exception</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  {</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Exception_1_1UnregisteredParameter.html"> 73</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1Exception_1_1UnregisteredParameter.html">UnregisteredParameter</a> :</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">Exception::BaseException</a></div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  {</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Exception_1_1UnregisteredParameter.html#a4fde43796ef86c84b41d81b4d557d324"> 77</a></span>  <a class="code" href="classOpenMS_1_1Exception_1_1UnregisteredParameter.html#a4fde43796ef86c84b41d81b4d557d324">UnregisteredParameter</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* file, <span class="keywordtype">int</span> line, <span class="keyword">const</span> <span class="keywordtype">char</span>* <span class="keyword">function</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& parameter) :</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">BaseException</a>(file, line, function, <span class="stringliteral">"UnregisteredParameter"</span>, parameter)</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  {</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <a class="code" href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#a0f5c900ab953d53026d2aa977cfc6ace">GlobalExceptionHandler::getInstance</a>().<a class="code" href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#ac351f48d2668c8df16d673b044ff997c">setMessage</a>(what_);</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  }</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  };</div>
<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Exception_1_1WrongParameterType.html"> 85</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1Exception_1_1WrongParameterType.html">WrongParameterType</a> :</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">Exception::BaseException</a></div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  {</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Exception_1_1WrongParameterType.html#a39da6fb0700c89ae5bbcd0ab723fc306"> 89</a></span>  <a class="code" href="classOpenMS_1_1Exception_1_1WrongParameterType.html#a39da6fb0700c89ae5bbcd0ab723fc306">WrongParameterType</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* file, <span class="keywordtype">int</span> line, <span class="keyword">const</span> <span class="keywordtype">char</span>* <span class="keyword">function</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& parameter) :</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">BaseException</a>(file, line, function, <span class="stringliteral">"WrongParameterType"</span>, parameter)</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  {</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <a class="code" href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#a0f5c900ab953d53026d2aa977cfc6ace">GlobalExceptionHandler::getInstance</a>().<a class="code" href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#ac351f48d2668c8df16d673b044ff997c">setMessage</a>(what_);</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  }</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  };</div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Exception_1_1RequiredParameterNotGiven.html"> 97</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1Exception_1_1RequiredParameterNotGiven.html">RequiredParameterNotGiven</a> :</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">Exception::BaseException</a></div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  {</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Exception_1_1RequiredParameterNotGiven.html#a8c76c0508ca070f4abf0f13a7aa34f59"> 101</a></span>  <a class="code" href="classOpenMS_1_1Exception_1_1RequiredParameterNotGiven.html#a8c76c0508ca070f4abf0f13a7aa34f59">RequiredParameterNotGiven</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* file, <span class="keywordtype">int</span> line, <span class="keyword">const</span> <span class="keywordtype">char</span>* <span class="keyword">function</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& parameter) :</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">BaseException</a>(file, line, function, <span class="stringliteral">"RequiredParameterNotGiven"</span>, parameter)</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  {</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <a class="code" href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#a0f5c900ab953d53026d2aa977cfc6ace">GlobalExceptionHandler::getInstance</a>().<a class="code" href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#ac351f48d2668c8df16d673b044ff997c">setMessage</a>(what_);</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  }</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  };</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="l00130"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html"> 130</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  {</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a name="l00135"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537"> 135</a></span>  <span class="keyword">enum</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537">ExitCodes</a></div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  {</div>
<div class="line"><a name="l00137"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a88fa85c1c9370642a3ca9276d6fcff7c"> 137</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a88fa85c1c9370642a3ca9276d6fcff7c">EXECUTION_OK</a>,</div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aa7f4f2e83db4048bd7e4190a53c3fd1a"> 138</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aa7f4f2e83db4048bd7e4190a53c3fd1a">INPUT_FILE_NOT_FOUND</a>,</div>
<div class="line"><a name="l00139"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aaceec1bc6fad40534fb0a9e187ce598e"> 139</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aaceec1bc6fad40534fb0a9e187ce598e">INPUT_FILE_NOT_READABLE</a>,</div>
<div class="line"><a name="l00140"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a18661839b1b50ff3c7f13344f1b9dc2b"> 140</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a18661839b1b50ff3c7f13344f1b9dc2b">INPUT_FILE_CORRUPT</a>,</div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a10df6a9738d612d102fe7ef636be66ee"> 141</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a10df6a9738d612d102fe7ef636be66ee">INPUT_FILE_EMPTY</a>,</div>
<div class="line"><a name="l00142"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ac1cb71a829967f44c382c253fdf2d90b"> 142</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ac1cb71a829967f44c382c253fdf2d90b">CANNOT_WRITE_OUTPUT_FILE</a>,</div>
<div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a387a807fbe7719a9e3862b4d72282305"> 143</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a387a807fbe7719a9e3862b4d72282305">ILLEGAL_PARAMETERS</a>,</div>
<div class="line"><a name="l00144"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a3ff91cf9f0ce3066dfb408d97fbe81ff"> 144</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a3ff91cf9f0ce3066dfb408d97fbe81ff">MISSING_PARAMETERS</a>,</div>
<div class="line"><a name="l00145"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a8216aa4b3a817cdf8c15ed32aa946e83"> 145</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a8216aa4b3a817cdf8c15ed32aa946e83">UNKNOWN_ERROR</a>,</div>
<div class="line"><a name="l00146"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a56a605c1df1029022a47df8a5fe57c5a"> 146</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a56a605c1df1029022a47df8a5fe57c5a">EXTERNAL_PROGRAM_ERROR</a>,</div>
<div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ad73f40ad2eef48a6ca24988909c66c3e"> 147</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ad73f40ad2eef48a6ca24988909c66c3e">PARSE_ERROR</a>,</div>
<div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a61cd58829fafa9611e98b767acc3a0a5"> 148</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a61cd58829fafa9611e98b767acc3a0a5">INCOMPATIBLE_INPUT_DATA</a>,</div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aa6160da3d147c897d800efe3a69c941e"> 149</a></span>  <a class="code" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aa6160da3d147c897d800efe3a69c941e">INTERNAL_ERROR</a>,</div>
<div class="line"><a name="l00150"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ae379f86cc4ef6f5ad8eb2b414772bc0a"> 150</a></span>  UNEXPECTED_RESULT</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  };</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <a class="code" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> official = <span class="keyword">true</span>, <span class="keywordtype">bool</span> id_tag_support = <span class="keyword">false</span>, <span class="keywordtype">bool</span> require_args = <span class="keyword">true</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& version = <span class="stringliteral">""</span>);</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span> </div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a>();</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>  ExitCodes <a class="code" href="RNPxl_8C.html#a217dbf8b442f20279ea00b898af96f52">main</a>(<span class="keywordtype">int</span> argc, <span class="keyword">const</span> <span class="keywordtype">char</span>** argv);</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> </div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keyword">static</span> <span class="keywordtype">void</span> setMaxNumberOfThreads(<span class="keywordtype">int</span> num_threads);</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="keyword">private</span>:</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span> </div>
<div class="line"><a name="l00187"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a710b3279a901758436518187692fb0af"> 187</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#a710b3279a901758436518187692fb0af">tool_name_</a>;</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span> </div>
<div class="line"><a name="l00190"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a149061aab047b425371d4079f4a325f4"> 190</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#a149061aab047b425371d4079f4a325f4">tool_description_</a>;</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> </div>
<div class="line"><a name="l00193"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#aca70a0389ab53706a919f2df59c343cf"> 193</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#aca70a0389ab53706a919f2df59c343cf">id_tag_support_</a>;</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span> </div>
<div class="line"><a name="l00196"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a4455a77e7412b4bf41dbd085484196c8"> 196</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#a4455a77e7412b4bf41dbd085484196c8">require_args_</a>;</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> </div>
<div class="line"><a name="l00199"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a9cd430d26f556c2dfcf00d07fe5bc89a"> 199</a></span>  <a class="code" href="classOpenMS_1_1DocumentIDTagger.html">DocumentIDTagger</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#a9cd430d26f556c2dfcf00d07fe5bc89a">id_tagger_</a>;</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span> </div>
<div class="line"><a name="l00202"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a504604d8e42f0ff2cbb9cfac29af2913"> 202</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#a504604d8e42f0ff2cbb9cfac29af2913">instance_number_</a>;</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span> </div>
<div class="line"><a name="l00205"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a0978c0a12989743f76ff4ed8073ffdbc"> 205</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#a0978c0a12989743f76ff4ed8073ffdbc">ini_location_</a>;</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span> </div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <a class="code" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a>();</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span> </div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <a class="code" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a>&);</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> </div>
<div class="line"><a name="l00214"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a28c73e623c63a4fe3bfceb1ae8274f39"> 214</a></span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>;</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
<div class="line"><a name="l00217"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a055bff6c3f219da094965760ab650fb6"> 217</a></span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#a055bff6c3f219da094965760ab650fb6">param_inifile_</a>;</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div>
<div class="line"><a name="l00220"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#aa3c6eb7ecbdfa635c6bfcc16beb44abe"> 220</a></span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#aa3c6eb7ecbdfa635c6bfcc16beb44abe">param_cmdline_</a>;</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a name="l00223"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a4fa1b8a5454d97f09daeaebca7c91f2e"> 223</a></span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#a4fa1b8a5454d97f09daeaebca7c91f2e">param_instance_</a>;</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span> </div>
<div class="line"><a name="l00226"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a8d4d920a1b6f34b180feaa33a4a3b204"> 226</a></span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#a8d4d920a1b6f34b180feaa33a4a3b204">param_common_tool_</a>;</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> </div>
<div class="line"><a name="l00229"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#afa913f3c5495a38dd42c7f329d94753f"> 229</a></span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#afa913f3c5495a38dd42c7f329d94753f">param_common_</a>;</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> </div>
<div class="line"><a name="l00232"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a1fd714af1f19177741eb0b4f6eb43e35"> 232</a></span>  <span class="keyword">mutable</span> std::ofstream <a class="code" href="classOpenMS_1_1TOPPBase.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a>;</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span> </div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keywordtype">void</span> enableLogging_() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span> </div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a3935296a9fde5712d711d2fc1100435f"> 245</a></span>  std::vector<ParameterInformation> <a class="code" href="classOpenMS_1_1TOPPBase.html#a3935296a9fde5712d711d2fc1100435f">parameters_</a>;</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span> </div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> getSubsectionDefaults_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& section) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span> </div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> getSubsectionDefaults_() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span> </div>
<div class="line"><a name="l00268"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ad06dbbc4e610a7896d24a024789815fd"> 268</a></span>  std::map<String, String> <a class="code" href="classOpenMS_1_1TOPPBase.html#ad06dbbc4e610a7896d24a024789815fd">subsections_</a>;</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span> </div>
<div class="line"><a name="l00271"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a86e4ee1c76d34583514a1a0d20c465a3"> 271</a></span>  std::map<String, String> <a class="code" href="classOpenMS_1_1TOPPBase.html#a86e4ee1c76d34583514a1a0d20c465a3">subsections_TOPP_</a>;</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span> </div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span> </div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> parseCommandLine_(<span class="keyword">const</span> <span class="keywordtype">int</span> argc, <span class="keyword">const</span> <span class="keywordtype">char</span>** argv, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& misc = <span class="stringliteral">"misc"</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& unknown = <span class="stringliteral">"unknown"</span>);</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span> </div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> getParamAsString_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& key, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& default_value = <span class="stringliteral">""</span>) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span> </div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> getParamAsInt_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& key, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> default_value = 0) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span> </div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <a class="code" href="classdouble.html">DoubleReal</a> getParamAsDouble_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& key, <a class="code" href="classdouble.html">DoubleReal</a> default_value = 0) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span> </div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> getParamAsStringList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& key, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1StringList.html">StringList</a>& default_value) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span> </div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  <a class="code" href="classOpenMS_1_1IntList.html">IntList</a> getParamAsIntList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& key, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IntList.html">IntList</a>& default_value) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span> </div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a> getParamAsDoubleList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& key, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a>& default_value) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span> </div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <span class="keywordtype">bool</span> getParamAsBool_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& key) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span> </div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a>& getParam_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& key) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span> </div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> getSubsection_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span> </div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> getDefaultParameters_() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span> </div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> getToolUserDefaults_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& <a class="code" href="TOPPAS_8C.html#a92f8240588f059cb9152498c9d3a3e9d">tool_name</a>) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span> </div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00374"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a4e87a8f69bbc06cd56776556dc1680ed"> 374</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#a4e87a8f69bbc06cd56776556dc1680ed">version_</a>;</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span> </div>
<div class="line"><a name="l00377"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a65de5468e578e72bc9fe6f4e603a29b3"> 377</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#a65de5468e578e72bc9fe6f4e603a29b3">verboseVersion_</a>;</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span> </div>
<div class="line"><a name="l00380"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a980b56a8b0110ffe7e3cda4060b3f289"> 380</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#a980b56a8b0110ffe7e3cda4060b3f289">official_</a>;</div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span> </div>
<div class="line"><a name="l00389"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#ab281176746eb5f3e1ff6441353f0c468"> 389</a></span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& <a class="code" href="classOpenMS_1_1TOPPBase.html#ab281176746eb5f3e1ff6441353f0c468">getIniLocation_</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  <span class="keywordflow">return</span> ini_location_;</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  }</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span> </div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& toolName_() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span> </div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> registerOptionsAndFlags_() = 0;</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span> </div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> getParamArgument_(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1Param_1_1ParamEntry.html">Param::ParamEntry</a>& entry) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span> </div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  std::vector<ParameterInformation> paramToParameterInformation_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a>& param) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span> </div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  <a class="code" href="structOpenMS_1_1ParameterInformation.html">ParameterInformation</a> paramEntryToParameterInformation_(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1Param_1_1ParamEntry.html">Param::ParamEntry</a>& entry, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument = <span class="stringliteral">""</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& full_name = <span class="stringliteral">""</span>) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span> </div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  <span class="keywordtype">void</span> registerParamSubsectionsAsTOPPSubsections_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a>& param);</div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span> </div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  <span class="keywordtype">void</span> registerFullParam_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a>& param);</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span> </div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  <span class="keywordtype">void</span> registerStringOption_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& default_value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> required = <span class="keyword">true</span>, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span> </div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  <span class="keywordtype">void</span> setValidStrings_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> std::vector<String>& strings);</div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span> </div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  <span class="keywordtype">void</span> registerInputFile_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& default_value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> required = <span class="keyword">true</span>, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1StringList.html">StringList</a>& tags = <a class="code" href="classOpenMS_1_1StringList.html">StringList</a>());</div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span> </div>
<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  <span class="keywordtype">void</span> registerOutputFile_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& default_value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> required = <span class="keyword">true</span>, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span> </div>
<div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  <span class="keywordtype">void</span> setValidFormats_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> std::vector<String>& formats, <span class="keyword">const</span> <span class="keywordtype">bool</span> force_OpenMS_format = <span class="keyword">true</span>);</div>
<div class="line"><a name="l00504"></a><span class="lineno"> 504</span> </div>
<div class="line"><a name="l00505"></a><span class="lineno"> 505</span> </div>
<div class="line"><a name="l00516"></a><span class="lineno"> 516</span>  <span class="keywordtype">void</span> registerDoubleOption_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument, <span class="keywordtype">double</span> default_value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> required = <span class="keyword">true</span>, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00517"></a><span class="lineno"> 517</span> </div>
<div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  <span class="keywordtype">void</span> setMinInt_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> min);</div>
<div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  <span class="keywordtype">void</span> setMaxInt_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> max);</div>
<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  <span class="keywordtype">void</span> setMinFloat_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <a class="code" href="classdouble.html">DoubleReal</a> min);</div>
<div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  <span class="keywordtype">void</span> setMaxFloat_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <a class="code" href="classdouble.html">DoubleReal</a> max);</div>
<div class="line"><a name="l00542"></a><span class="lineno"> 542</span> </div>
<div class="line"><a name="l00553"></a><span class="lineno"> 553</span>  <span class="keywordtype">void</span> registerIntOption_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument,</div>
<div class="line"><a name="l00554"></a><span class="lineno"> 554</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> default_value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description,</div>
<div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  <span class="keywordtype">bool</span> required = <span class="keyword">true</span>, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00556"></a><span class="lineno"> 556</span> </div>
<div class="line"><a name="l00568"></a><span class="lineno"> 568</span>  <span class="keywordtype">void</span> registerIntList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument, <a class="code" href="classOpenMS_1_1IntList.html">IntList</a> default_value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> required = <span class="keyword">true</span>, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00569"></a><span class="lineno"> 569</span> </div>
<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <span class="keywordtype">void</span> registerDoubleList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument, <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a> default_value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> required = <span class="keyword">true</span>, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00581"></a><span class="lineno"> 581</span> </div>
<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  <span class="keywordtype">void</span> registerStringList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> default_value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> required = <span class="keyword">true</span>, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00593"></a><span class="lineno"> 593</span> </div>
<div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  <span class="keywordtype">void</span> registerInputFileList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> default_value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> required = <span class="keyword">true</span>, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00608"></a><span class="lineno"> 608</span> </div>
<div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  <span class="keywordtype">void</span> registerOutputFileList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& argument, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> default_value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> required = <span class="keyword">true</span>, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00623"></a><span class="lineno"> 623</span> </div>
<div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  <span class="keywordtype">void</span> registerFlag_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description, <span class="keywordtype">bool</span> advanced = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00626"></a><span class="lineno"> 626</span> </div>
<div class="line"><a name="l00634"></a><span class="lineno"> 634</span>  <span class="keywordtype">void</span> registerSubsection_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description);</div>
<div class="line"><a name="l00635"></a><span class="lineno"> 635</span> </div>
<div class="line"><a name="l00645"></a><span class="lineno"> 645</span>  <span class="keywordtype">void</span> registerTOPPSubsection_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& description);</div>
<div class="line"><a name="l00646"></a><span class="lineno"> 646</span> </div>
<div class="line"><a name="l00647"></a><span class="lineno"> 647</span> </div>
<div class="line"><a name="l00649"></a><span class="lineno"> 649</span>  <span class="keywordtype">void</span> addEmptyLine_();</div>
<div class="line"><a name="l00650"></a><span class="lineno"> 650</span> </div>
<div class="line"><a name="l00651"></a><span class="lineno"> 651</span> </div>
<div class="line"><a name="l00660"></a><span class="lineno"> 660</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> getStringOption_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00661"></a><span class="lineno"> 661</span> </div>
<div class="line"><a name="l00670"></a><span class="lineno"> 670</span>  <a class="code" href="classdouble.html">DoubleReal</a> getDoubleOption_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00671"></a><span class="lineno"> 671</span> </div>
<div class="line"><a name="l00680"></a><span class="lineno"> 680</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> getIntOption_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00681"></a><span class="lineno"> 681</span> </div>
<div class="line"><a name="l00690"></a><span class="lineno"> 690</span>  <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> getStringList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00691"></a><span class="lineno"> 691</span> </div>
<div class="line"><a name="l00700"></a><span class="lineno"> 700</span>  <a class="code" href="classOpenMS_1_1IntList.html">IntList</a> getIntList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00701"></a><span class="lineno"> 701</span> </div>
<div class="line"><a name="l00710"></a><span class="lineno"> 710</span>  <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a> getDoubleList_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00711"></a><span class="lineno"> 711</span> </div>
<div class="line"><a name="l00713"></a><span class="lineno"> 713</span>  <span class="keywordtype">bool</span> getFlag_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00714"></a><span class="lineno"> 714</span> </div>
<div class="line"><a name="l00720"></a><span class="lineno"> 720</span>  <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ParameterInformation.html">ParameterInformation</a>& findEntry_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00721"></a><span class="lineno"> 721</span> </div>
<div class="line"><a name="l00727"></a><span class="lineno"> 727</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> <span class="keyword">const</span>& getParam_() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00728"></a><span class="lineno"> 728</span> </div>
<div class="line"><a name="l00742"></a><span class="lineno"> 742</span>  <span class="keywordtype">void</span> checkParam_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a>& param, <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>& location) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00743"></a><span class="lineno"> 743</span> </div>
<div class="line"><a name="l00744"></a><span class="lineno"> 744</span> </div>
<div class="line"><a name="l00752"></a><span class="lineno"> 752</span>  <span class="keywordtype">void</span> checkIfIniParametersAreApplicable_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a>& ini_params);</div>
<div class="line"><a name="l00754"></a><span class="lineno"> 754</span> </div>
<div class="line"><a name="l00756"></a><span class="lineno"> 756</span>  <span class="keywordtype">void</span> printUsage_();</div>
<div class="line"><a name="l00757"></a><span class="lineno"> 757</span> </div>
<div class="line"><a name="l00759"></a><span class="lineno"> 759</span>  <span class="keyword">virtual</span> ExitCodes main_(<span class="keywordtype">int</span> argc, <span class="keyword">const</span> <span class="keywordtype">char</span>** argv) = 0;</div>
<div class="line"><a name="l00760"></a><span class="lineno"> 760</span> </div>
<div class="line"><a name="l00762"></a><span class="lineno"> 762</span> </div>
<div class="line"><a name="l00763"></a><span class="lineno"> 763</span>  <span class="keywordtype">void</span> writeLog_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& text) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00765"></a><span class="lineno"> 765</span> </div>
<div class="line"><a name="l00767"></a><span class="lineno"> 767</span>  <span class="keywordtype">void</span> writeDebug_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& text, <a class="code" href="classunsigned_01int.html">UInt</a> min_level) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00768"></a><span class="lineno"> 768</span> </div>
<div class="line"><a name="l00770"></a><span class="lineno"> 770</span>  <span class="keywordtype">void</span> writeDebug_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& text, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a>& param, <a class="code" href="classunsigned_01int.html">UInt</a> min_level) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00772"></a><span class="lineno"> 772</span> </div>
<div class="line"><a name="l00773"></a><span class="lineno"> 773</span> </div>
<div class="line"><a name="l00798"></a><span class="lineno"> 798</span>  <span class="keywordtype">void</span> inputFileReadable_(<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>& param_name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00799"></a><span class="lineno"> 799</span> </div>
<div class="line"><a name="l00810"></a><span class="lineno"> 810</span>  <span class="keywordtype">void</span> outputFileWritable_(<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>& param_name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00812"></a><span class="lineno"> 812</span> </div>
<div class="line"><a name="l00814"></a><span class="lineno"> 814</span>  <span class="keywordtype">void</span> parseRange_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& text, <span class="keywordtype">double</span>& low, <span class="keywordtype">double</span>& high) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00815"></a><span class="lineno"> 815</span> </div>
<div class="line"><a name="l00817"></a><span class="lineno"> 817</span>  <span class="keywordtype">void</span> parseRange_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& text, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>& low, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>& high) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00818"></a><span class="lineno"> 818</span> </div>
<div class="line"><a name="l00820"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a5a41e046ecca99c99103faa7214118ee"> 820</a></span>  <a class="code" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">ProgressLogger::LogType</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#a5a41e046ecca99c99103faa7214118ee">log_type_</a>;</div>
<div class="line"><a name="l00821"></a><span class="lineno"> 821</span> </div>
<div class="line"><a name="l00823"></a><span class="lineno"> 823</span> </div>
<div class="line"><a name="l00824"></a><span class="lineno"> 824</span> </div>
<div class="line"><a name="l00826"></a><span class="lineno"> 826</span>  <span class="keywordtype">void</span> addDataProcessing_(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a>& map, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a>& dp) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00827"></a><span class="lineno"> 827</span> </div>
<div class="line"><a name="l00829"></a><span class="lineno"> 829</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> FeatureType></div>
<div class="line"><a name="l00830"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a4ba03f6d26e49c1834ad8acf13a7b0a0"> 830</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#a4ba03f6d26e49c1834ad8acf13a7b0a0">addDataProcessing_</a>(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<FeatureType></a>& map, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a>& dp)<span class="keyword"> const</span></div>
<div class="line"><a name="l00831"></a><span class="lineno"> 831</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00832"></a><span class="lineno"> 832</span>  map.<a class="code" href="classOpenMS_1_1FeatureMap.html#ae131ea2ec923582f86aa9805e72241ad">getDataProcessing</a>().push_back(dp);</div>
<div class="line"><a name="l00833"></a><span class="lineno"> 833</span>  }</div>
<div class="line"><a name="l00834"></a><span class="lineno"> 834</span> </div>
<div class="line"><a name="l00836"></a><span class="lineno"> 836</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> PeakType, <span class="keyword">typename</span> CT></div>
<div class="line"><a name="l00837"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a8e50b81e2c3372c6c9529b10e6f1bf80"> 837</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#a8e50b81e2c3372c6c9529b10e6f1bf80">addDataProcessing_</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType, CT></a>& map, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a>& dp)<span class="keyword"> const</span></div>
<div class="line"><a name="l00838"></a><span class="lineno"> 838</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00839"></a><span class="lineno"> 839</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++i)</div>
<div class="line"><a name="l00840"></a><span class="lineno"> 840</span>  {</div>
<div class="line"><a name="l00841"></a><span class="lineno"> 841</span>  map[i].getDataProcessing().push_back(dp);</div>
<div class="line"><a name="l00842"></a><span class="lineno"> 842</span>  }</div>
<div class="line"><a name="l00843"></a><span class="lineno"> 843</span>  std::vector<MSChromatogram<CT> > chromatograms = map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>();</div>
<div class="line"><a name="l00844"></a><span class="lineno"> 844</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < chromatograms.size(); ++i)</div>
<div class="line"><a name="l00845"></a><span class="lineno"> 845</span>  {</div>
<div class="line"><a name="l00846"></a><span class="lineno"> 846</span>  chromatograms[i].getDataProcessing().push_back(dp);</div>
<div class="line"><a name="l00847"></a><span class="lineno"> 847</span>  }</div>
<div class="line"><a name="l00848"></a><span class="lineno"> 848</span>  map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a4c105ad43f3c61a53997af8ba28720e2">setChromatograms</a>(chromatograms);</div>
<div class="line"><a name="l00849"></a><span class="lineno"> 849</span>  }</div>
<div class="line"><a name="l00850"></a><span class="lineno"> 850</span> </div>
<div class="line"><a name="l00852"></a><span class="lineno"> 852</span>  <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a> getProcessingInfo_(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9">DataProcessing::ProcessingAction</a> action) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00853"></a><span class="lineno"> 853</span> </div>
<div class="line"><a name="l00855"></a><span class="lineno"> 855</span>  <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a> getProcessingInfo_(<span class="keyword">const</span> std::set<DataProcessing::ProcessingAction>& actions) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00856"></a><span class="lineno"> 856</span> </div>
<div class="line"><a name="l00858"></a><span class="lineno"> 858</span> </div>
<div class="line"><a name="l00860"></a><span class="lineno"> 860</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DocumentIDTagger.html">DocumentIDTagger</a>& getDocumentIDTagger_() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00861"></a><span class="lineno"> 861</span> </div>
<div class="line"><a name="l00863"></a><span class="lineno"> 863</span>  <span class="keywordtype">bool</span> writeCTD_();</div>
<div class="line"><a name="l00864"></a><span class="lineno"> 864</span> </div>
<div class="line"><a name="l00866"></a><span class="lineno"> 866</span>  ExitCodes writeWSDL_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename);</div>
<div class="line"><a name="l00867"></a><span class="lineno"> 867</span> </div>
<div class="line"><a name="l00879"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a6e61791b6ff20c4e71142b700b0ad79a"> 879</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TOPPBase.html#a6e61791b6ff20c4e71142b700b0ad79a">test_mode_</a>;</div>
<div class="line"><a name="l00880"></a><span class="lineno"> 880</span> </div>
<div class="line"><a name="l00882"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a3857c6970f5c49182a97916a1aa2d555"> 882</a></span>  <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#a3857c6970f5c49182a97916a1aa2d555">topp_ini_file_</a>;</div>
<div class="line"><a name="l00883"></a><span class="lineno"> 883</span> </div>
<div class="line"><a name="l00885"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TOPPBase.html#a92afa13732182773146571769799a6e3"> 885</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1TOPPBase.html#a92afa13732182773146571769799a6e3">debug_level_</a>;</div>
<div class="line"><a name="l00886"></a><span class="lineno"> 886</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00887"></a><span class="lineno"> 887</span> </div>
<div class="line"><a name="l00893"></a><span class="lineno"> 893</span>  <span class="keywordtype">void</span> addText_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& text);</div>
<div class="line"><a name="l00894"></a><span class="lineno"> 894</span> </div>
<div class="line"><a name="l00902"></a><span class="lineno"> 902</span>  <a class="code" href="structOpenMS_1_1ParameterInformation.html">ParameterInformation</a>& getParameterByName_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& name);</div>
<div class="line"><a name="l00903"></a><span class="lineno"> 903</span> </div>
<div class="line"><a name="l00904"></a><span class="lineno"> 904</span>  };</div>
<div class="line"><a name="l00905"></a><span class="lineno"> 905</span> </div>
<div class="line"><a name="l00906"></a><span class="lineno"> 906</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00907"></a><span class="lineno"> 907</span> </div>
<div class="line"><a name="l00908"></a><span class="lineno"> 908</span> <span class="preprocessor">#endif //OPENMS_APPLICATIONS_TOPPBASE_H</span></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a65de5468e578e72bc9fe6f4e603a29b3"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a65de5468e578e72bc9fe6f4e603a29b3">OpenMS::TOPPBase::verboseVersion_</a></div><div class="ttdeci">String verboseVersion_</div><div class="ttdoc">Version string including additional revision/date time information. Note: This differs from version_ ...</div><div class="ttdef"><b>Definition:</b> TOPPBase.h:377</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537a3ff91cf9f0ce3066dfb408d97fbe81ff"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a3ff91cf9f0ce3066dfb408d97fbe81ff">OpenMS::TOPPBase::MISSING_PARAMETERS</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:144</div></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_1DataProcessing_html"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html">OpenMS::DataProcessing</a></div><div class="ttdoc">Descripton of the applied preprocessing steps. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a86e4ee1c76d34583514a1a0d20c465a3"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a86e4ee1c76d34583514a1a0d20c465a3">OpenMS::TOPPBase::subsections_TOPP_</a></div><div class="ttdeci">std::map< String, String > subsections_TOPP_</div><div class="ttdoc">Storage location and description for allowed subsections from TOPP tool&#39;s command-line parameters...</div><div class="ttdef"><b>Definition:</b> TOPPBase.h:271</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1UnregisteredParameter_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1UnregisteredParameter.html">OpenMS::Exception::UnregisteredParameter</a></div><div class="ttdoc">An unregistered parameter was accessed. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537a88fa85c1c9370642a3ca9276d6fcff7c"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a88fa85c1c9370642a3ca9276d6fcff7c">OpenMS::TOPPBase::EXECUTION_OK</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:137</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537a18661839b1b50ff3c7f13344f1b9dc2b"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a18661839b1b50ff3c7f13344f1b9dc2b">OpenMS::TOPPBase::INPUT_FILE_CORRUPT</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:140</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="TOPPAS_8C_html_a92f8240588f059cb9152498c9d3a3e9d"><div class="ttname"><a href="TOPPAS_8C.html#a92f8240588f059cb9152498c9d3a3e9d">tool_name</a></div><div class="ttdeci">const char * tool_name</div><div class="ttdef"><b>Definition:</b> TOPPAS.C:91</div></div>
<div class="ttc" id="StringList_8h_html"><div class="ttname"><a href="StringList_8h.html">StringList.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_af67907baa897e9fb84df0cb89795b87c"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">OpenMS::ProgressLogger::LogType</a></div><div class="ttdeci">LogType</div><div class="ttdoc">Possible log types. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1UnregisteredParameter_html_a4fde43796ef86c84b41d81b4d557d324"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1UnregisteredParameter.html#a4fde43796ef86c84b41d81b4d557d324">OpenMS::Exception::UnregisteredParameter::UnregisteredParameter</a></div><div class="ttdeci">UnregisteredParameter(const char *file, int line, const char *function, const String &parameter)</div><div class="ttdef"><b>Definition:</b> TOPPBase.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1RequiredParameterNotGiven_html_a8c76c0508ca070f4abf0f13a7aa34f59"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1RequiredParameterNotGiven.html#a8c76c0508ca070f4abf0f13a7aa34f59">OpenMS::Exception::RequiredParameterNotGiven::RequiredParameterNotGiven</a></div><div class="ttdeci">RequiredParameterNotGiven(const char *file, int line, const char *function, const String &parameter)</div><div class="ttdef"><b>Definition:</b> TOPPBase.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a1fd714af1f19177741eb0b4f6eb43e35"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a1fd714af1f19177741eb0b4f6eb43e35">OpenMS::TOPPBase::log_</a></div><div class="ttdeci">std::ofstream log_</div><div class="ttdoc">Log file stream. Use the writeLog_() and writeDebug_() methods to access it. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:232</div></div>
<div class="ttc" id="ToolHandler_8h_html"><div class="ttname"><a href="ToolHandler_8h.html">ToolHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap</a></div><div class="ttdoc">A container for features. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:111</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a980b56a8b0110ffe7e3cda4060b3f289"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a980b56a8b0110ffe7e3cda4060b3f289">OpenMS::TOPPBase::official_</a></div><div class="ttdeci">bool official_</div><div class="ttdoc">Flag indicating if this an official TOPP tool. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:380</div></div>
<div class="ttc" id="structOpenMS_1_1Param_1_1ParamEntry_html"><div class="ttname"><a href="structOpenMS_1_1Param_1_1ParamEntry.html">OpenMS::Param::ParamEntry</a></div><div class="ttdoc">Parameter entry used to store the actual information inside of a Param entry. </div><div class="ttdef"><b>Definition:</b> Param.h:74</div></div>
<div class="ttc" id="structOpenMS_1_1ParameterInformation_html"><div class="ttname"><a href="structOpenMS_1_1ParameterInformation.html">OpenMS::ParameterInformation</a></div><div class="ttdoc">Struct that captures all information of a command line parameter. </div><div class="ttdef"><b>Definition:</b> ParameterInformation.h:48</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html">OpenMS::ConsensusMap</a></div><div class="ttdoc">A container for consensus elements. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:60</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_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537a8216aa4b3a817cdf8c15ed32aa946e83"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a8216aa4b3a817cdf8c15ed32aa946e83">OpenMS::TOPPBase::UNKNOWN_ERROR</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:145</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537a10df6a9738d612d102fe7ef636be66ee"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a10df6a9738d612d102fe7ef636be66ee">OpenMS::TOPPBase::INPUT_FILE_EMPTY</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:141</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ad06dbbc4e610a7896d24a024789815fd"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ad06dbbc4e610a7896d24a024789815fd">OpenMS::TOPPBase::subsections_</a></div><div class="ttdeci">std::map< String, String > subsections_</div><div class="ttdoc">Storage location and description for allowed subsections. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:268</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ab281176746eb5f3e1ff6441353f0c468"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ab281176746eb5f3e1ff6441353f0c468">OpenMS::TOPPBase::getIniLocation_</a></div><div class="ttdeci">const String & getIniLocation_() const </div><div class="ttdoc">Returns the location of the ini file where parameters are taken from. E.g. if the command line was TO...</div><div class="ttdef"><b>Definition:</b> TOPPBase.h:389</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537ad73f40ad2eef48a6ca24988909c66c3e"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ad73f40ad2eef48a6ca24988909c66c3e">OpenMS::TOPPBase::PARSE_ERROR</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:147</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a6e61791b6ff20c4e71142b700b0ad79a"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a6e61791b6ff20c4e71142b700b0ad79a">OpenMS::TOPPBase::test_mode_</a></div><div class="ttdeci">bool test_mode_</div><div class="ttdoc">Test mode. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:879</div></div>
<div class="ttc" id="DataProcessing_8h_html"><div class="ttname"><a href="DataProcessing_8h.html">DataProcessing.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537a56a605c1df1029022a47df8a5fe57c5a"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a56a605c1df1029022a47df8a5fe57c5a">OpenMS::TOPPBase::EXTERNAL_PROGRAM_ERROR</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:146</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html">OpenMS::TOPPBase</a></div><div class="ttdoc">Base class for TOPP applications. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:130</div></div>
<div class="ttc" id="Param_8h_html"><div class="ttname"><a href="Param_8h.html">Param.h</a></div></div>
<div class="ttc" id="DocumentIDTagger_8h_html"><div class="ttname"><a href="DocumentIDTagger_8h.html">DocumentIDTagger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1GlobalExceptionHandler_html_a0f5c900ab953d53026d2aa977cfc6ace"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#a0f5c900ab953d53026d2aa977cfc6ace">OpenMS::Exception::GlobalExceptionHandler::getInstance</a></div><div class="ttdeci">static GlobalExceptionHandler & getInstance()</div><div class="ttdoc">The accessor for the singleton. It also serves as a replacement for the constructor. </div><div class="ttdef"><b>Definition:</b> GlobalExceptionHandler.h:89</div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html"><div class="ttname"><a href="classOpenMS_1_1DataValue.html">OpenMS::DataValue</a></div><div class="ttdoc">Class to hold strings, numeric values, lists of strings and lists of numeric values. </div><div class="ttdef"><b>Definition:</b> DataValue.h:57</div></div>
<div class="ttc" id="IntList_8h_html"><div class="ttname"><a href="IntList_8h.html">IntList.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537a387a807fbe7719a9e3862b4d72282305"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a387a807fbe7719a9e3862b4d72282305">OpenMS::TOPPBase::ILLEGAL_PARAMETERS</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:143</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_ae131ea2ec923582f86aa9805e72241ad"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#ae131ea2ec923582f86aa9805e72241ad">OpenMS::FeatureMap::getDataProcessing</a></div><div class="ttdeci">const std::vector< DataProcessing > & getDataProcessing() const </div><div class="ttdoc">returns a const reference to the description of the applied data processing </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:446</div></div>
<div class="ttc" id="GlobalExceptionHandler_8h_html"><div class="ttname"><a href="GlobalExceptionHandler_8h.html">GlobalExceptionHandler.h</a></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_1Exception_1_1WrongParameterType_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1WrongParameterType.html">OpenMS::Exception::WrongParameterType</a></div><div class="ttdoc">A parameter was accessed with the wrong type. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:85</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537ac1cb71a829967f44c382c253fdf2d90b"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ac1cb71a829967f44c382c253fdf2d90b">OpenMS::TOPPBase::CANNOT_WRITE_OUTPUT_FILE</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:142</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_aa3c6eb7ecbdfa635c6bfcc16beb44abe"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#aa3c6eb7ecbdfa635c6bfcc16beb44abe">OpenMS::TOPPBase::param_cmdline_</a></div><div class="ttdeci">Param param_cmdline_</div><div class="ttdoc">Parameters from command line. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:220</div></div>
<div class="ttc" id="ParameterInformation_8h_html"><div class="ttname"><a href="ParameterInformation_8h.html">ParameterInformation.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DocumentIDTagger_html"><div class="ttname"><a href="classOpenMS_1_1DocumentIDTagger.html">OpenMS::DocumentIDTagger</a></div><div class="ttdoc">Tags OpenMS file containers with a DocumentID. </div><div class="ttdef"><b>Definition:</b> DocumentIDTagger.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a8d4d920a1b6f34b180feaa33a4a3b204"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a8d4d920a1b6f34b180feaa33a4a3b204">OpenMS::TOPPBase::param_common_tool_</a></div><div class="ttdeci">Param param_common_tool_</div><div class="ttdoc">Parameters from common section with tool name. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:226</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9">OpenMS::DataProcessing::ProcessingAction</a></div><div class="ttdeci">ProcessingAction</div><div class="ttdef"><b>Definition:</b> DataProcessing.h:58</div></div>
<div class="ttc" id="RNPxl_8C_html_a217dbf8b442f20279ea00b898af96f52"><div class="ttname"><a href="RNPxl_8C.html#a217dbf8b442f20279ea00b898af96f52">main</a></div><div class="ttdeci">int main(int argc, const char **argv)</div><div class="ttdef"><b>Definition:</b> RNPxl.C:1354</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_aca70a0389ab53706a919f2df59c343cf"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#aca70a0389ab53706a919f2df59c343cf">OpenMS::TOPPBase::id_tag_support_</a></div><div class="ttdeci">bool id_tag_support_</div><div class="ttdoc">Tool indicates it supports assignment of unique DocumentID from IDPool. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:193</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537a61cd58829fafa9611e98b767acc3a0a5"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a61cd58829fafa9611e98b767acc3a0a5">OpenMS::TOPPBase::INCOMPATIBLE_INPUT_DATA</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:148</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537aa6160da3d147c897d800efe3a69c941e"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aa6160da3d147c897d800efe3a69c941e">OpenMS::TOPPBase::INTERNAL_ERROR</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:149</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a4455a77e7412b4bf41dbd085484196c8"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a4455a77e7412b4bf41dbd085484196c8">OpenMS::TOPPBase::require_args_</a></div><div class="ttdeci">bool require_args_</div><div class="ttdoc">Require at least one command line argument, exit immediately otherwise. GUI tools should disable this...</div><div class="ttdef"><b>Definition:</b> TOPPBase.h:196</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1BaseException_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1BaseException.html">OpenMS::Exception::BaseException</a></div><div class="ttdoc">Exception base class. </div><div class="ttdef"><b>Definition:</b> Exception.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_afa913f3c5495a38dd42c7f329d94753f"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#afa913f3c5495a38dd42c7f329d94753f">OpenMS::TOPPBase::param_common_</a></div><div class="ttdeci">Param param_common_</div><div class="ttdoc">Parameters from common section without tool name. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:229</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a4e87a8f69bbc06cd56776556dc1680ed"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a4e87a8f69bbc06cd56776556dc1680ed">OpenMS::TOPPBase::version_</a></div><div class="ttdeci">String version_</div><div class="ttdoc">Version string (if empty, the OpenMS/TOPP version is printed) </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:374</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a9cd430d26f556c2dfcf00d07fe5bc89a"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a9cd430d26f556c2dfcf00d07fe5bc89a">OpenMS::TOPPBase::id_tagger_</a></div><div class="ttdeci">DocumentIDTagger id_tagger_</div><div class="ttdoc">Instance of DocumentIDTagger, which can be accessed using getDocumentIDTagger_() </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:199</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html"><div class="ttname"><a href="classOpenMS_1_1Param.html">OpenMS::Param</a></div><div class="ttdoc">Management and storage of parameters / INI files. </div><div class="ttdef"><b>Definition:</b> Param.h:69</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_1Exception_1_1WrongParameterType_html_a39da6fb0700c89ae5bbcd0ab723fc306"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1WrongParameterType.html#a39da6fb0700c89ae5bbcd0ab723fc306">OpenMS::Exception::WrongParameterType::WrongParameterType</a></div><div class="ttdeci">WrongParameterType(const char *file, int line, const char *function, const String &parameter)</div><div class="ttdef"><b>Definition:</b> TOPPBase.h:89</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a4c105ad43f3c61a53997af8ba28720e2"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a4c105ad43f3c61a53997af8ba28720e2">OpenMS::MSExperiment::setChromatograms</a></div><div class="ttdeci">void setChromatograms(const std::vector< MSChromatogram< ChromatogramPeakType > > &chromatograms)</div><div class="ttdoc">sets the chromatogram list </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:756</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537aaceec1bc6fad40534fb0a9e187ce598e"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aaceec1bc6fad40534fb0a9e187ce598e">OpenMS::TOPPBase::INPUT_FILE_NOT_READABLE</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:139</div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html"><div class="ttname"><a href="classOpenMS_1_1StringList.html">OpenMS::StringList</a></div><div class="ttdoc">String list. </div><div class="ttdef"><b>Definition:</b> StringList.h:56</div></div>
<div class="ttc" id="LogStream_8h_html"><div class="ttname"><a href="LogStream_8h.html">LogStream.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1GlobalExceptionHandler_html_ac351f48d2668c8df16d673b044ff997c"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#ac351f48d2668c8df16d673b044ff997c">OpenMS::Exception::GlobalExceptionHandler::setMessage</a></div><div class="ttdeci">static void setMessage(const std::string &message)</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_1TOPPBase_html_a710b3279a901758436518187692fb0af"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a710b3279a901758436518187692fb0af">OpenMS::TOPPBase::tool_name_</a></div><div class="ttdeci">String const tool_name_</div><div class="ttdoc">Tool name. This is assigned once and for all in the constructor. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:187</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a28c73e623c63a4fe3bfceb1ae8274f39"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a28c73e623c63a4fe3bfceb1ae8274f39">OpenMS::TOPPBase::param_</a></div><div class="ttdeci">Param param_</div><div class="ttdoc">All parameters relevant to this invocation of the program. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:214</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a4ba03f6d26e49c1834ad8acf13a7b0a0"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a4ba03f6d26e49c1834ad8acf13a7b0a0">OpenMS::TOPPBase::addDataProcessing_</a></div><div class="ttdeci">void addDataProcessing_(FeatureMap< FeatureType > &map, const DataProcessing &dp) const </div><div class="ttdoc">Data processing setter for feature maps. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:830</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537aa7f4f2e83db4048bd7e4190a53c3fd1a"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aa7f4f2e83db4048bd7e4190a53c3fd1a">OpenMS::TOPPBase::INPUT_FILE_NOT_FOUND</a></div><div class="ttdef"><b>Definition:</b> TOPPBase.h:138</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a3935296a9fde5712d711d2fc1100435f"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a3935296a9fde5712d711d2fc1100435f">OpenMS::TOPPBase::parameters_</a></div><div class="ttdeci">std::vector< ParameterInformation > parameters_</div><div class="ttdoc">Storage location for parameter information. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:245</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_ac74ddc700cf9fcf91d688b6d31ff9537"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537">OpenMS::TOPPBase::ExitCodes</a></div><div class="ttdeci">ExitCodes</div><div class="ttdoc">Exit codes. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:135</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a0978c0a12989743f76ff4ed8073ffdbc"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a0978c0a12989743f76ff4ed8073ffdbc">OpenMS::TOPPBase::ini_location_</a></div><div class="ttdeci">String const ini_location_</div><div class="ttdoc">Location in the ini file where to look for parameters. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:205</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a149061aab047b425371d4079f4a325f4"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a149061aab047b425371d4079f4a325f4">OpenMS::TOPPBase::tool_description_</a></div><div class="ttdeci">String const tool_description_</div><div class="ttdoc">Tool description. This is assigned once and for all in the constructor. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:190</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a055bff6c3f219da094965760ab650fb6"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a055bff6c3f219da094965760ab650fb6">OpenMS::TOPPBase::param_inifile_</a></div><div class="ttdeci">Param param_inifile_</div><div class="ttdoc">All parameters specified in the ini file. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:217</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="VersionInfo_8h_html"><div class="ttname"><a href="VersionInfo_8h.html">VersionInfo.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a4fa1b8a5454d97f09daeaebca7c91f2e"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a4fa1b8a5454d97f09daeaebca7c91f2e">OpenMS::TOPPBase::param_instance_</a></div><div class="ttdeci">Param param_instance_</div><div class="ttdoc">Parameters from instance section. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:223</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a8e50b81e2c3372c6c9529b10e6f1bf80"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a8e50b81e2c3372c6c9529b10e6f1bf80">OpenMS::TOPPBase::addDataProcessing_</a></div><div class="ttdeci">void addDataProcessing_(MSExperiment< PeakType, CT > &map, const DataProcessing &dp) const </div><div class="ttdoc">Data processing setter for peak maps. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:837</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a92afa13732182773146571769799a6e3"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a92afa13732182773146571769799a6e3">OpenMS::TOPPBase::debug_level_</a></div><div class="ttdeci">Int debug_level_</div><div class="ttdoc">Debug level set by -debug. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:885</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="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DoubleList_html"><div class="ttname"><a href="classOpenMS_1_1DoubleList.html">OpenMS::DoubleList</a></div><div class="ttdoc">DoubleReal list. </div><div class="ttdef"><b>Definition:</b> DoubleList.h:56</div></div>
<div class="ttc" id="DoubleList_8h_html"><div class="ttname"><a href="DoubleList_8h.html">DoubleList.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a5a41e046ecca99c99103faa7214118ee"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a5a41e046ecca99c99103faa7214118ee">OpenMS::TOPPBase::log_type_</a></div><div class="ttdeci">ProgressLogger::LogType log_type_</div><div class="ttdoc">Type of progress logging. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:820</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a02fccfed86a20f8bd0f6b98c23fadb2e"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">OpenMS::MSExperiment::getChromatograms</a></div><div class="ttdeci">const std::vector< MSChromatogram< ChromatogramPeakType > > & getChromatograms() const </div><div class="ttdoc">returns the chromatogram list </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:768</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a504604d8e42f0ff2cbb9cfac29af2913"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a504604d8e42f0ff2cbb9cfac29af2913">OpenMS::TOPPBase::instance_number_</a></div><div class="ttdeci">Int const instance_number_</div><div class="ttdoc">Instance number. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:202</div></div>
<div class="ttc" id="classOpenMS_1_1TOPPBase_html_a3857c6970f5c49182a97916a1aa2d555"><div class="ttname"><a href="classOpenMS_1_1TOPPBase.html#a3857c6970f5c49182a97916a1aa2d555">OpenMS::TOPPBase::topp_ini_file_</a></div><div class="ttdeci">static String topp_ini_file_</div><div class="ttdoc">.TOPP.ini file for storing system default parameters </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:882</div></div>
<div class="ttc" id="classOpenMS_1_1IntList_html"><div class="ttname"><a href="classOpenMS_1_1IntList.html">OpenMS::IntList</a></div><div class="ttdoc">Int list. </div><div class="ttdef"><b>Definition:</b> IntList.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1RequiredParameterNotGiven_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1RequiredParameterNotGiven.html">OpenMS::Exception::RequiredParameterNotGiven</a></div><div class="ttdoc">A required parameter was not given. </div><div class="ttdef"><b>Definition:</b> TOPPBase.h:97</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 11:19:22 using doxygen 1.8.5</font></TD>
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