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<a href="MapAlignerBase_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: $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Marc Sturm, Clemens Groepl, Hendrik Weisser $</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_MAPALIGNERBASE_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_MAPALIGNERBASE_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="MzMLFile_8h.html">OpenMS/FORMAT/MzMLFile.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="ConsensusXMLFile_8h.html">OpenMS/FORMAT/ConsensusXMLFile.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="FeatureXMLFile_8h.html">OpenMS/FORMAT/FeatureXMLFile.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="IdXMLFile_8h.html">OpenMS/FORMAT/IdXMLFile.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="FileHandler_8h.html">OpenMS/FORMAT/FileHandler.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="FileTypes_8h.html">OpenMS/FORMAT/FileTypes.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="TransformationXMLFile_8h.html">OpenMS/FORMAT/TransformationXMLFile.h</a>></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <<a class="code" href="MapAlignmentAlgorithm_8h.html">OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithm.h</a>></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <<a class="code" href="MapAlignmentTransformer_8h.html">OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentTransformer.h</a>></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <<a class="code" href="TOPPBase_8h.html">OpenMS/APPLICATIONS/TOPPBase.h</a>></span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="keyword">using namespace </span>OpenMS;</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="keyword">using namespace </span>std;</div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="comment">// Doxygen docu</span></div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="comment">// We do not want this class to show up in the docu:</span></div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="comment"></span></div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="keyword">class </span>TOPPMapAlignerBase :</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> {</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  TOPPMapAlignerBase(<a class="code" href="classOpenMS_1_1String.html">String</a> name, <a class="code" href="classOpenMS_1_1String.html">String</a> description, <span class="keywordtype">bool</span> official = <span class="keyword">true</span>) :</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <a class="code" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a>(name, description, official)</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  {</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> </div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="comment">// "public" so it can be used in DefaultParamHandlerDocumenter to get docu</span></div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> getModelDefaults(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & default_model)</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_1Param.html">Param</a> params;</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  params.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"type"</span>, default_model, <span class="stringliteral">"Type of model"</span>);</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="comment">// TODO: avoid referring to each TransformationModel subclass explicitly</span></div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> model_types = <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"linear,b_spline,interpolated"</span>);</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keywordflow">if</span> (!model_types.<a class="code" href="classOpenMS_1_1StringList.html#af4a386323a5a2bdffcbf06bf5a70a0ae">contains</a>(default_model))</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  {</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  model_types.insert(model_types.begin(), default_model);</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>  params.<a class="code" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">setValidStrings</a>(<span class="stringliteral">"type"</span>, model_types);</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> model_params;</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <a class="code" href="classOpenMS_1_1TransformationModelLinear.html#a39100a3d6235b7512df3d2731d016934">TransformationModelLinear::getDefaultParameters</a>(model_params);</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  params.<a class="code" href="classOpenMS_1_1Param.html#ad2dc775a73f96e91dd97c61c39e4e7b8">insert</a>(<span class="stringliteral">"linear:"</span>, model_params);</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  params.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">"linear"</span>, <span class="stringliteral">"Parameters for 'linear' model"</span>);</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <a class="code" href="classOpenMS_1_1TransformationModelBSpline.html#a39100a3d6235b7512df3d2731d016934">TransformationModelBSpline::getDefaultParameters</a>(model_params);</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  params.<a class="code" href="classOpenMS_1_1Param.html#ad2dc775a73f96e91dd97c61c39e4e7b8">insert</a>(<span class="stringliteral">"b_spline:"</span>, model_params);</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  params.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">"b_spline"</span>, <span class="stringliteral">"Parameters for 'b_spline' model"</span>);</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <a class="code" href="classOpenMS_1_1TransformationModelInterpolated.html#a39100a3d6235b7512df3d2731d016934">TransformationModelInterpolated::getDefaultParameters</a>(model_params);</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="comment">// "polynomial" interpolation is not suitable for RT data, so remove it:</span></div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1Param_1_1ParamEntry.html">Param::ParamEntry</a> & entry =</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  model_params.<a class="code" href="classOpenMS_1_1Param.html#a3194828eaca36cc3e3d070fffeea2fbe">getEntry</a>(<span class="stringliteral">"interpolation_type"</span>);</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> interpolation_types = entry.<a class="code" href="structOpenMS_1_1Param_1_1ParamEntry.html#a4b7edb44281637b1b4701b640cfeee70">valid_strings</a>;</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <a class="code" href="classOpenMS_1_1StringList.html#a52cf141ce292251c9c6d7c22f296cbd5">StringList::Iterator</a> pos = find(interpolation_types.begin(),</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  interpolation_types.end(), <span class="stringliteral">"polynomial"</span>);</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  interpolation_types.erase(pos);</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  model_params.<a class="code" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">setValidStrings</a>(<span class="stringliteral">"interpolation_type"</span>, interpolation_types);</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  params.<a class="code" href="classOpenMS_1_1Param.html#ad2dc775a73f96e91dd97c61c39e4e7b8">insert</a>(<span class="stringliteral">"interpolated:"</span>, model_params);</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  params.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">"interpolated"</span>,</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="stringliteral">"Parameters for 'interpolated' model"</span>);</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordflow">return</span> params;</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  }</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordtype">void</span> registerOptionsAndFlags_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & file_formats, <span class="keyword">const</span> <span class="keywordtype">bool</span> add_reference = <span class="keyword">false</span>)</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  {</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  registerInputFileList_(<span class="stringliteral">"in"</span>, <span class="stringliteral">"<files>"</span>, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a>(), <span class="stringliteral">"Input files separated by blanks (all must have the same file type)"</span>, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  setValidFormats_(<span class="stringliteral">"in"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(file_formats));</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  registerOutputFileList_(<span class="stringliteral">"out"</span>, <span class="stringliteral">"<files>"</span>, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a>(), <span class="stringliteral">"Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together."</span>, <span class="keyword">false</span>);</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  setValidFormats_(<span class="stringliteral">"out"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(file_formats));</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  registerOutputFileList_(<span class="stringliteral">"trafo_out"</span>, <span class="stringliteral">"<files>"</span>, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a>(), <span class="stringliteral">"Transformation output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together."</span>, <span class="keyword">false</span>);</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  setValidFormats_(<span class="stringliteral">"trafo_out"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"trafoXML"</span>));</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  addEmptyLine_();</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordflow">if</span> (add_reference)</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  {</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  registerTOPPSubsection_(<span class="stringliteral">"reference"</span>, <span class="stringliteral">"Options to define a reference file (use either 'file' or 'index', not both; if neither is given 'index' is used)."</span>);</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  registerInputFile_(<span class="stringliteral">"reference:file"</span>, <span class="stringliteral">"<file>"</span>, <span class="stringliteral">""</span>, <span class="stringliteral">"File to use as reference (same file format as input files required)"</span>, <span class="keyword">false</span>);</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  setValidFormats_(<span class="stringliteral">"reference:file"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(file_formats));</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  registerIntOption_(<span class="stringliteral">"reference:index"</span>, <span class="stringliteral">"<number>"</span>, 0, <span class="stringliteral">"Use one of the input files as reference ('1' for the first file, etc.).\nIf '0', no explicit reference is set - the algorithm will select a reference."</span>, <span class="keyword">false</span>);</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  setMinInt_(<span class="stringliteral">"reference:index"</span>, 0);</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  }</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  }</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordtype">void</span> handleReference_(<a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a> * alignment)</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  {</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="comment">// note: this function is in the base class to avoid code duplication, but</span></div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="comment">// it only makes sense for some derived classes - don't call the function</span></div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="comment">// in a class that doesn't support a reference!</span></div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="comment">// check reference parameters:</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> reference_index = getIntOption_(<span class="stringliteral">"reference:index"</span>);</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> reference_file = getStringOption_(<span class="stringliteral">"reference:file"</span>);</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordflow">if</span> (reference_index > getStringList_(<span class="stringliteral">"in"</span>).size())</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  {</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1InvalidParameter.html">Exception::InvalidParameter</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"'reference:index' must not be higher than the number of input files"</span>);</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  }</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keywordflow">if</span> (reference_index && !reference_file.empty())</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  {</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1InvalidParameter.html">Exception::InvalidParameter</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"'reference:index' and 'reference:file' cannot be used together"</span>);</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  }</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> </div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="comment">// pass the reference parameters on to the algorithm:</span></div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  alignment-><a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html#aef01d65c73bbdd9f550309195007622b">setReference</a>(reference_index, reference_file);</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  }</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  ExitCodes initialize_(<a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a> * alignment, <span class="keywordtype">bool</span> check_ref = <span class="keyword">false</span>)</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  {</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="comment">// parameter handling</span></div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> ins = getStringList_(<span class="stringliteral">"in"</span>);</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> outs = getStringList_(<span class="stringliteral">"out"</span>);</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> trafos = getStringList_(<span class="stringliteral">"trafo_out"</span>);</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="comment">// check for valid input</span></div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="comment">// check whether some kind of output file is given:</span></div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keywordflow">if</span> (outs.empty() && trafos.empty())</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  {</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  writeLog_(<span class="stringliteral">"Error: Either data output or transformation output files have to be provided!"</span>);</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <span class="keywordflow">return</span> ILLEGAL_PARAMETERS;</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  }</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="comment">// check whether number of input files equals number of output files:</span></div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="keywordflow">if</span> (!outs.empty() && (ins.size() != outs.size()))</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  {</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  writeLog_(<span class="stringliteral">"Error: The number of input and output files has to be equal!"</span>);</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keywordflow">return</span> ILLEGAL_PARAMETERS;</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  }</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordflow">if</span> (!trafos.empty() && (ins.size() != trafos.size()))</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  {</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  writeLog_(<span class="stringliteral">"Error: The number of input and transformation output files has to be equal!"</span>);</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keywordflow">return</span> ILLEGAL_PARAMETERS;</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="comment">// check whether all input files have the same type (this type is used to store the output type too):</span></div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> in_type = <a class="code" href="classOpenMS_1_1FileHandler.html#a851b569c3e65a4eeabdd10425f2e6402">FileHandler::getType</a>(ins[0]);</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 1; i < ins.size(); ++i)</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  {</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FileHandler.html#a851b569c3e65a4eeabdd10425f2e6402">FileHandler::getType</a>(ins[i]) != in_type)</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  {</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  writeLog_(<span class="stringliteral">"Error: All input files have to be in the same format!"</span>);</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordflow">return</span> ILLEGAL_PARAMETERS;</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  }</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  }</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span> </div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keywordflow">if</span> (check_ref) <span class="comment">// a valid index OR file should be given</span></div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  {</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> reference_index = getIntOption_(<span class="stringliteral">"reference:index"</span>);</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> reference_file = getStringOption_(<span class="stringliteral">"reference:file"</span>);</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="keywordflow">if</span> (reference_index > getStringList_(<span class="stringliteral">"in"</span>).size())</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  {</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1InvalidParameter.html">Exception::InvalidParameter</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"'reference:index' must not be higher than the number of input files"</span>);</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  }</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <span class="keywordflow">if</span> (reference_index && !reference_file.empty())</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  {</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1InvalidParameter.html">Exception::InvalidParameter</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"'reference:index' and 'reference:file' cannot be used together"</span>);</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  }</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span> </div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="comment">// file should have same type as other input</span></div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  <span class="keywordflow">if</span> (!reference_file.empty())</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  {</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FileHandler.html#a851b569c3e65a4eeabdd10425f2e6402">FileHandler::getType</a>(reference_file) != in_type)</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  {</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  writeLog_(<span class="stringliteral">"Error: Reference file has not the same format as other input files!"</span>);</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <span class="keywordflow">return</span> ILLEGAL_PARAMETERS;</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  }</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  }</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  }</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="comment">// set up alignment algorithm</span></div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> alignment_param = getParam_().<a class="code" href="classOpenMS_1_1Param.html#a25319a96118d2373efc5af9c8679b98b">copy</a>(<span class="stringliteral">"algorithm:"</span>, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span> </div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  writeDebug_(<span class="stringliteral">"Used alignment parameters"</span>, alignment_param, 3);</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  alignment-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(alignment_param);</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  alignment-><a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log_type_);</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> </div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="keywordflow">return</span> EXECUTION_OK;</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  }</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> </div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  ExitCodes commonMain_(<a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a> * alignment)</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  {</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  ExitCodes ret = initialize_(alignment);</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="keywordflow">if</span> (ret != EXECUTION_OK) <span class="keywordflow">return</span> ret;</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span> </div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> progresslogger;</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log_type_);</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span> </div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span> </div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> ins = getStringList_(<span class="stringliteral">"in"</span>);</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> outs = getStringList_(<span class="stringliteral">"out"</span>);</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> trafos = getStringList_(<span class="stringliteral">"trafo_out"</span>);</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> model_params = getParam_().<a class="code" href="classOpenMS_1_1Param.html#a25319a96118d2373efc5af9c8679b98b">copy</a>(<span class="stringliteral">"model:"</span>, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> model_type = model_params.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"type"</span>);</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  model_params = model_params.<a class="code" href="classOpenMS_1_1Param.html#a25319a96118d2373efc5af9c8679b98b">copy</a>(model_type + <span class="stringliteral">":"</span>, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> in_type = <a class="code" href="classOpenMS_1_1FileHandler.html#a851b569c3e65a4eeabdd10425f2e6402">FileHandler::getType</a>(ins[0]);</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  std::vector<TransformationDescription> transformations;</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span> </div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  <span class="comment">// perform peak alignment</span></div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordflow">if</span> (in_type == <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ab5518cc16bd1f60ebbb47e681a56b75f">FileTypes::MZML</a>)</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  {</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  <span class="comment">// load input</span></div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  std::vector<MSExperiment<> > peak_maps(ins.size());</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <a class="code" href="classOpenMS_1_1MzMLFile.html">MzMLFile</a> f;</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  f.setLogType(log_type_);</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < ins.size(); ++i)</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  {</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  f.load(ins[i], peak_maps[i]);</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  }</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span> </div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="comment">// try to align</span></div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  {</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  alignment-><a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a2038727c06b2e23bf60e1d21d7179815">alignPeakMaps</a>(peak_maps, transformations);</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  }</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1NotImplemented.html">Exception::NotImplemented</a> &)</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  {</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  writeLog_(<span class="stringliteral">"Error: The algorithm '"</span> + alignment-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() + <span class="stringliteral">"' cannot be used for peak data!"</span>);</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="keywordflow">return</span> INTERNAL_ERROR;</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  }</div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  <span class="keywordflow">if</span> (model_type != <span class="stringliteral">"none"</span>)</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  {</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  alignment-><a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html#acc270843ebe2525547c6ac01bf341234">fitModel</a>(model_type, model_params, transformations);</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  }</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  <a class="code" href="classOpenMS_1_1MapAlignmentTransformer.html#a4332bb43125dfc82544302b6a609e055">MapAlignmentTransformer::transformPeakMaps</a>(peak_maps, transformations);</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span> </div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <span class="comment">// write output</span></div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, outs.size(), <span class="stringliteral">"writing output files"</span>);</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < outs.size(); ++i)</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  {</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(i);</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span> </div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="comment">//annotate output with data processing info</span></div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  addDataProcessing_(peak_maps[i], getProcessingInfo_(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a8d86de0851abd047aef8c1cbb3c1603b">DataProcessing::ALIGNMENT</a>));</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span> </div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  f.store(outs[i], peak_maps[i]);</div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  }</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  }</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="comment">// perform feature alignment</span></div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in_type == <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a753b825a63c99787d10e05f7d65a87a6">FileTypes::FEATUREXML</a>)</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  {</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  <span class="comment">// load input</span></div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  std::vector<std::vector<Peak2D> > feat_maps(ins.size());</div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <a class="code" href="classOpenMS_1_1FeatureXMLFile.html">FeatureXMLFile</a> f;</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <span class="comment">// f.setLogType(log_type_); // TODO</span></div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, ins.size(), <span class="stringliteral">"loading input files"</span>);</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < ins.size(); ++i)</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  {</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(i);</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> feature_map;</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  f.load(ins[i], feature_map);</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  feat_maps[i].resize(feature_map.size());</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span> </div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<>::const_iterator</a> it = feature_map.begin();</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  std::vector<Peak2D>::iterator c_it = feat_maps[i].begin();</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="keywordflow">for</span> (; it != feature_map.end(); ++it, ++c_it)</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  {</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  *c_it = <span class="keyword">reinterpret_cast<</span><span class="keyword">const </span><a class="code" href="classOpenMS_1_1Peak2D.html">Peak2D</a> &<span class="keyword">></span>(*it);</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  }</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  }</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span> </div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  <span class="comment">// try to align</span></div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  {</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  alignment-><a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a9e66a73174d03975d49a7e9b3f8854df">alignCompactFeatureMaps</a>(feat_maps, transformations);</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  }</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1NotImplemented.html">Exception::NotImplemented</a> &)</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  {</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  writeLog_(<span class="stringliteral">"Error: The algorithm '"</span> + alignment-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() + <span class="stringliteral">"' cannot be used for feature data!"</span>);</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  <span class="keywordflow">return</span> INTERNAL_ERROR;</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  }</div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="keywordflow">if</span> (model_type != <span class="stringliteral">"none"</span>)</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  {</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  alignment-><a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html#acc270843ebe2525547c6ac01bf341234">fitModel</a>(model_type, model_params, transformations);</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  }</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  <span class="comment">// alignment->transformFeatureMaps(feat_maps, transformations);</span></div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span> </div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="comment">// write output</span></div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, outs.size(), <span class="stringliteral">"writing output files"</span>);</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < outs.size(); ++i)</div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  {</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(i);</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span> </div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> feature_map;</div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  f.load(ins[i], feature_map);</div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span> </div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <a class="code" href="classOpenMS_1_1MapAlignmentTransformer.html#aa4969c372aacb889028c6d60d432bf2b">MapAlignmentTransformer::transformSingleFeatureMap</a>(feature_map, transformations[i]);</div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span> </div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="comment">//annotate output with data processing info</span></div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  addDataProcessing_(feature_map, getProcessingInfo_(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a8d86de0851abd047aef8c1cbb3c1603b">DataProcessing::ALIGNMENT</a>));</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span> </div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  f.store(outs[i], feature_map);</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  }</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  }</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <span class="comment">// perform consensus alignment</span></div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in_type == <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a7419287729941a7a7717defda1f6b354">FileTypes::CONSENSUSXML</a>)</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  {</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  <span class="comment">// load input</span></div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  std::vector<ConsensusMap> cons_maps(ins.size());</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html">ConsensusXMLFile</a> f;</div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  <span class="comment">// f.setLogType(log_type_); // TODO</span></div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, ins.size(), <span class="stringliteral">"loading input files"</span>);</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < ins.size(); ++i)</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  {</div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(i);</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  f.load(ins[i], cons_maps[i]);</div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  }</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span> </div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="comment">// try to align</span></div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  {</div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  alignment-><a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a7385e8b646ae9d282c3c06abf1620083">alignConsensusMaps</a>(cons_maps, transformations);</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  }</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1NotImplemented.html">Exception::NotImplemented</a> &)</div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  {</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  writeLog_(<span class="stringliteral">"Error: The algorithm '"</span> + alignment-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() + <span class="stringliteral">"' cannot be used for consensus feature data!"</span>);</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <span class="keywordflow">return</span> INTERNAL_ERROR;</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  }</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="keywordflow">if</span> (model_type != <span class="stringliteral">"none"</span>)</div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  {</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  alignment-><a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html#acc270843ebe2525547c6ac01bf341234">fitModel</a>(model_type, model_params, transformations);</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  }</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  <a class="code" href="classOpenMS_1_1MapAlignmentTransformer.html#a5401d49c941d6c9b98b241959a3e0f47">MapAlignmentTransformer::transformConsensusMaps</a>(cons_maps, transformations);</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span> </div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  <span class="comment">// write output</span></div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, outs.size(), <span class="stringliteral">"writing output files"</span>);</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < outs.size(); ++i)</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  {</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(i);</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span> </div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  <span class="comment">//annotate output with data processing info</span></div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  addDataProcessing_(cons_maps[i], getProcessingInfo_(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a8d86de0851abd047aef8c1cbb3c1603b">DataProcessing::ALIGNMENT</a>));</div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span> </div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  f.store(outs[i], cons_maps[i]);</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  }</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  }</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  <span class="comment">// perform peptide alignment</span></div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  <span class="comment">//-------------------------------------------------------------</span></div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in_type == <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ab11f34894c9d7062f12a006a68c52859">FileTypes::IDXML</a>)</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  {</div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  <span class="comment">// load input</span></div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  std::vector<std::vector<ProteinIdentification> > protein_ids_vec(ins.size());</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  std::vector<std::vector<PeptideIdentification> > peptide_ids_vec(ins.size());</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span> </div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  <a class="code" href="classOpenMS_1_1IdXMLFile.html">IdXMLFile</a> f;</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  <span class="comment">// f.setLogType_(log_type_);</span></div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span> </div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, ins.size(), <span class="stringliteral">"loading input files"</span>);</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < ins.size(); ++i)</div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  {</div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(i);</div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  f.load(ins[i], protein_ids_vec[i], peptide_ids_vec[i]);</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  }</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span> </div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  <span class="comment">// try to align</span></div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  {</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  alignment-><a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a4f223602464cbafef563871036b5dfc1">alignPeptideIdentifications</a>(peptide_ids_vec, transformations);</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  }</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1NotImplemented.html">Exception::NotImplemented</a> &)</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  {</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  writeLog_(<span class="stringliteral">"Error: The algorithm '"</span> + alignment-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() + <span class="stringliteral">"' cannot be used for peptide data!"</span>);</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  <span class="keywordflow">return</span> INTERNAL_ERROR;</div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  }</div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  <span class="keywordflow">if</span> (model_type != <span class="stringliteral">"none"</span>)</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  {</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  alignment-><a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html#acc270843ebe2525547c6ac01bf341234">fitModel</a>(model_type, model_params, transformations);</div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  }</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  <a class="code" href="classOpenMS_1_1MapAlignmentTransformer.html#a91a65fd4dafd6f9925b1d28b3461a699">MapAlignmentTransformer::transformPeptideIdentifications</a>(peptide_ids_vec,</div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  transformations);</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="comment">// write output</span></div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, outs.size(), <span class="stringliteral">"writing output files"</span>);</div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < outs.size(); ++i)</div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  {</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(i);</div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  f.store(outs[i], protein_ids_vec[i], peptide_ids_vec[i]);</div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  }</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  progresslogger.<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  }</div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  {</div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  <span class="comment">// TODO can this really happen? I think it is tested above. Otherwise</span></div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  <span class="comment">// throw an appropriate exception?</span></div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  <span class="keywordflow">return</span> ILLEGAL_PARAMETERS;</div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  }</div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span> </div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  <span class="keywordflow">if</span> (!trafos.empty())</div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  {</div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < transformations.size(); ++i)</div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  {</div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  <a class="code" href="classOpenMS_1_1TransformationXMLFile.html">TransformationXMLFile</a>().<a class="code" href="classOpenMS_1_1TransformationXMLFile.html#abdddea80e737ce717013609e58e755f0">store</a>(trafos[i], transformations[i]);</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  }</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  }</div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span> </div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  <span class="keywordflow">return</span> EXECUTION_OK;</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  }</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span> </div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span> };</div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span> </div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span> </div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span> <span class="preprocessor">#endif // OPENMS_APPLICATIONS_MAPALIGNERBASE_H</span></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">OpenMS::FileTypes::Type</a></div><div class="ttdeci">Type</div><div class="ttdoc">Actual file types enum. </div><div class="ttdef"><b>Definition:</b> FileTypes.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentTransformer_html_aa4969c372aacb889028c6d60d432bf2b"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentTransformer.html#aa4969c372aacb889028c6d60d432bf2b">OpenMS::MapAlignmentTransformer::transformSingleFeatureMap</a></div><div class="ttdeci">static void transformSingleFeatureMap(FeatureMap<> &fmap, const TransformationDescription &trafo)</div><div class="ttdoc">Applies the given transformations to a single feature map. </div></div>
<div class="ttc" id="FeatureXMLFile_8h_html"><div class="ttname"><a href="FeatureXMLFile_8h.html">FeatureXMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FileHandler_html_a851b569c3e65a4eeabdd10425f2e6402"><div class="ttname"><a href="classOpenMS_1_1FileHandler.html#a851b569c3e65a4eeabdd10425f2e6402">OpenMS::FileHandler::getType</a></div><div class="ttdeci">static FileTypes::Type getType(const String &filename)</div><div class="ttdoc">Tries to determine the file type (by name or content) </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a3194828eaca36cc3e3d070fffeea2fbe"><div class="ttname"><a href="classOpenMS_1_1Param.html#a3194828eaca36cc3e3d070fffeea2fbe">OpenMS::Param::getEntry</a></div><div class="ttdeci">const ParamEntry & getEntry(const String &key) const </div><div class="ttdoc">Returns the whole parameter entry. </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a432099944e11263aa20aaf8ea1389790"><div class="ttname"><a href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">OpenMS::Param::setValue</a></div><div class="ttdeci">void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())</div><div class="ttdoc">Sets a value. </div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_ad2dc775a73f96e91dd97c61c39e4e7b8"><div class="ttname"><a href="classOpenMS_1_1Param.html#ad2dc775a73f96e91dd97c61c39e4e7b8">OpenMS::Param::insert</a></div><div class="ttdeci">void insert(const String &prefix, const Param &param)</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html">OpenMS::Peak2D</a></div><div class="ttdoc">A 2-dimensional raw data point or peak. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html_af4a386323a5a2bdffcbf06bf5a70a0ae"><div class="ttname"><a href="classOpenMS_1_1StringList.html#af4a386323a5a2bdffcbf06bf5a70a0ae">OpenMS::StringList::contains</a></div><div class="ttdeci">bool contains(const String &s) const </div><div class="ttdoc">Returns if a string is contained in the list. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap<></a></div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7ab11f34894c9d7062f12a006a68c52859"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ab11f34894c9d7062f12a006a68c52859">OpenMS::FileTypes::IDXML</a></div><div class="ttdoc">OpenMS identification format (.idXML) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentTransformer_html_a5401d49c941d6c9b98b241959a3e0f47"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentTransformer.html#a5401d49c941d6c9b98b241959a3e0f47">OpenMS::MapAlignmentTransformer::transformConsensusMaps</a></div><div class="ttdeci">static void transformConsensusMaps(std::vector< ConsensusMap > &maps, const std::vector< TransformationDescription > &given_trafos)</div><div class="ttdoc">Applies the given transformations to consensus maps. </div></div>
<div class="ttc" id="FileHandler_8h_html"><div class="ttname"><a href="FileHandler_8h.html">FileHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithm_html"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithm.html">OpenMS::MapAlignmentAlgorithm</a></div><div class="ttdoc">Base class for all map-alignment algorithms. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithm.h:58</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="classOpenMS_1_1Param_html_a7dae78ea20f5b33125f50c6ee27b1a60"><div class="ttname"><a href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">OpenMS::Param::setSectionDescription</a></div><div class="ttdeci">void setSectionDescription(const String &key, const String &description)</div><div class="ttdoc">Sets a description for an existing section. </div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentTransformer_html_a4332bb43125dfc82544302b6a609e055"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentTransformer.html#a4332bb43125dfc82544302b6a609e055">OpenMS::MapAlignmentTransformer::transformPeakMaps</a></div><div class="ttdeci">static void transformPeakMaps(std::vector< MSExperiment<> > &maps, const std::vector< TransformationDescription > &given_trafos)</div><div class="ttdoc">Applies the given transformations to peak maps. </div></div>
<div class="ttc" id="IdXMLFile_8h_html"><div class="ttname"><a href="IdXMLFile_8h.html">IdXMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TransformationXMLFile_html_abdddea80e737ce717013609e58e755f0"><div class="ttname"><a href="classOpenMS_1_1TransformationXMLFile.html#abdddea80e737ce717013609e58e755f0">OpenMS::TransformationXMLFile::store</a></div><div class="ttdeci">void store(String filename, const TransformationDescription &transformation)</div><div class="ttdoc">Stores the data in an TransformationXML file. </div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_abc8067511cfc949ae942ea2b08588f81"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">OpenMS::DefaultParamHandler::setParameters</a></div><div class="ttdeci">void setParameters(const Param &param)</div><div class="ttdoc">Sets the parameters. </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="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a7419287729941a7a7717defda1f6b354"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a7419287729941a7a7717defda1f6b354">OpenMS::FileTypes::CONSENSUSXML</a></div><div class="ttdoc">OpenMS consensus map format (.consensusXML) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a25319a96118d2373efc5af9c8679b98b"><div class="ttname"><a href="classOpenMS_1_1Param.html#a25319a96118d2373efc5af9c8679b98b">OpenMS::Param::copy</a></div><div class="ttdeci">Param copy(const String &prefix, bool remove_prefix=false) const </div><div class="ttdoc">Returns a new Param object containing all entries that start with prefix. </div></div>
<div class="ttc" id="classOpenMS_1_1MzMLFile_html"><div class="ttname"><a href="classOpenMS_1_1MzMLFile.html">OpenMS::MzMLFile</a></div><div class="ttdoc">File adapter for MzML files. </div><div class="ttdef"><b>Definition:</b> MzMLFile.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1TransformationXMLFile.html">OpenMS::TransformationXMLFile</a></div><div class="ttdoc">Used to load and store TransformationXML files. </div><div class="ttdef"><b>Definition:</b> TransformationXMLFile.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_a1cc1012b0cdaea97f58d571af1ff45de"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">OpenMS::ProgressLogger::endProgress</a></div><div class="ttdeci">void endProgress() const </div><div class="ttdoc">Ends the progress display. </div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithm_html_a7385e8b646ae9d282c3c06abf1620083"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithm.html#a7385e8b646ae9d282c3c06abf1620083">OpenMS::MapAlignmentAlgorithm::alignConsensusMaps</a></div><div class="ttdeci">virtual void alignConsensusMaps(std::vector< ConsensusMap > &, std::vector< TransformationDescription > &)</div><div class="ttdoc">Aligns consensus maps. </div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithm_html_a2038727c06b2e23bf60e1d21d7179815"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithm.html#a2038727c06b2e23bf60e1d21d7179815">OpenMS::MapAlignmentAlgorithm::alignPeakMaps</a></div><div class="ttdeci">virtual void alignPeakMaps(std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &)</div><div class="ttdoc">Aligns peak maps. </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_abd0f5571675ec99e1aa647b39e2a8711"><div class="ttname"><a href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">OpenMS::Param::getValue</a></div><div class="ttdeci">const DataValue & getValue(const String &key) const </div><div class="ttdoc">Returns a value of a parameter. </div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_aaee0f2845288173de9f6ad47e6ad31d5"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">OpenMS::DefaultParamHandler::getName</a></div><div class="ttdeci">const String & getName() const </div><div class="ttdoc">Non-mutable access to the name. </div></div>
<div class="ttc" id="MapAlignmentTransformer_8h_html"><div class="ttname"><a href="MapAlignmentTransformer_8h.html">MapAlignmentTransformer.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html">OpenMS::ConsensusXMLFile</a></div><div class="ttdoc">This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...</div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelInterpolated_html_a39100a3d6235b7512df3d2731d016934"><div class="ttname"><a href="classOpenMS_1_1TransformationModelInterpolated.html#a39100a3d6235b7512df3d2731d016934">OpenMS::TransformationModelInterpolated::getDefaultParameters</a></div><div class="ttdeci">static void getDefaultParameters(Param &params)</div><div class="ttdoc">Gets the default parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html_a52cf141ce292251c9c6d7c22f296cbd5"><div class="ttname"><a href="classOpenMS_1_1StringList.html#a52cf141ce292251c9c6d7c22f296cbd5">OpenMS::StringList::Iterator</a></div><div class="ttdeci">iterator Iterator</div><div class="ttdoc">Mutable iterator. </div><div class="ttdef"><b>Definition:</b> StringList.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentTransformer_html_a91a65fd4dafd6f9925b1d28b3461a699"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentTransformer.html#a91a65fd4dafd6f9925b1d28b3461a699">OpenMS::MapAlignmentTransformer::transformPeptideIdentifications</a></div><div class="ttdeci">static void transformPeptideIdentifications(std::vector< std::vector< PeptideIdentification > > &maps, const std::vector< TransformationDescription > &given_trafos)</div><div class="ttdoc">Applies the given transformations to peptide identifications. </div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html_a5f86b59b547048311dd50df5fb6d3bb5"><div class="ttname"><a href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">OpenMS::StringList::create</a></div><div class="ttdeci">static StringList create(const String &list, const char splitter= ',')</div><div class="ttdoc">Returns a list that is created by splitting the given (comma-separated) string (String are not trimme...</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1InvalidParameter_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1InvalidParameter.html">OpenMS::Exception::InvalidParameter</a></div><div class="ttdoc">Exception indicating that an invalid parameter was handed over to an algorithm. </div><div class="ttdef"><b>Definition:</b> Exception.h:348</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithm_html_a9e66a73174d03975d49a7e9b3f8854df"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithm.html#a9e66a73174d03975d49a7e9b3f8854df">OpenMS::MapAlignmentAlgorithm::alignCompactFeatureMaps</a></div><div class="ttdeci">virtual void alignCompactFeatureMaps(std::vector< std::vector< Peak2D > > &, std::vector< TransformationDescription > &)</div><div class="ttdoc">Aligns vectors of 2D peaks (memory efficient version of FeatureMap) </div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9a8d86de0851abd047aef8c1cbb3c1603b"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a8d86de0851abd047aef8c1cbb3c1603b">OpenMS::DataProcessing::ALIGNMENT</a></div><div class="ttdoc">Retention time alignment of different maps. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelLinear_html_a39100a3d6235b7512df3d2731d016934"><div class="ttname"><a href="classOpenMS_1_1TransformationModelLinear.html#a39100a3d6235b7512df3d2731d016934">OpenMS::TransformationModelLinear::getDefaultParameters</a></div><div class="ttdeci">static void getDefaultParameters(Param &params)</div><div class="ttdoc">Gets the default parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a10933782584a46cded91c40574027ee2"><div class="ttname"><a href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">OpenMS::Param::setValidStrings</a></div><div class="ttdeci">void setValidStrings(const String &key, const std::vector< String > &strings)</div><div class="ttdoc">Sets the valid strings for the parameter key. </div></div>
<div class="ttc" id="ConsensusXMLFile_8h_html"><div class="ttname"><a href="ConsensusXMLFile_8h.html">ConsensusXMLFile.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a753b825a63c99787d10e05f7d65a87a6"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a753b825a63c99787d10e05f7d65a87a6">OpenMS::FileTypes::FEATUREXML</a></div><div class="ttdoc">OpenMS feature file (.featureXML) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:66</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_1FeatureXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html">OpenMS::FeatureXMLFile</a></div><div class="ttdoc">This class provides Input/Output functionality for feature maps. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:59</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="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_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_af1c45ecd71b5041b70319249e8e73591"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">OpenMS::ProgressLogger::startProgress</a></div><div class="ttdeci">void startProgress(SignedSize begin, SignedSize end, const String &label) const </div><div class="ttdoc">Initializes the progress display. </div></div>
<div class="ttc" id="structOpenMS_1_1Param_1_1ParamEntry_html_a4b7edb44281637b1b4701b640cfeee70"><div class="ttname"><a href="structOpenMS_1_1Param_1_1ParamEntry.html#a4b7edb44281637b1b4701b640cfeee70">OpenMS::Param::ParamEntry::valid_strings</a></div><div class="ttdeci">std::vector< String > valid_strings</div><div class="ttdoc">Default: empty. </div><div class="ttdef"><b>Definition:</b> Param.h:104</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_a8852277abd03220cc7b80d6c1bed6fed"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">OpenMS::ProgressLogger::setProgress</a></div><div class="ttdeci">void setProgress(SignedSize value) const </div><div class="ttdoc">Sets the current progress. </div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithm_html_acc270843ebe2525547c6ac01bf341234"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithm.html#acc270843ebe2525547c6ac01bf341234">OpenMS::MapAlignmentAlgorithm::fitModel</a></div><div class="ttdeci">static void fitModel(const String &model_type, const Param &params, std::vector< TransformationDescription > &trafos)</div><div class="ttdoc">Fits a model with given parameters to the transformations. </div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithm_html_aef01d65c73bbdd9f550309195007622b"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithm.html#aef01d65c73bbdd9f550309195007622b">OpenMS::MapAlignmentAlgorithm::setReference</a></div><div class="ttdeci">virtual void setReference(Size reference_index=0, const String &reference_file="")</div><div class="ttdoc">Defines a reference for the alignment. </div></div>
<div class="ttc" id="MapAlignmentAlgorithm_8h_html"><div class="ttname"><a href="MapAlignmentAlgorithm_8h.html">MapAlignmentAlgorithm.h</a></div></div>
<div class="ttc" id="TOPPBase_8h_html"><div class="ttname"><a href="TOPPBase_8h.html">TOPPBase.h</a></div></div>
<div class="ttc" id="TransformationXMLFile_8h_html"><div class="ttname"><a href="TransformationXMLFile_8h.html">TransformationXMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithm_html_a4f223602464cbafef563871036b5dfc1"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithm.html#a4f223602464cbafef563871036b5dfc1">OpenMS::MapAlignmentAlgorithm::alignPeptideIdentifications</a></div><div class="ttdeci">virtual void alignPeptideIdentifications(std::vector< std::vector< PeptideIdentification > > &, std::vector< TransformationDescription > &)</div><div class="ttdoc">Aligns peptide identifications. </div></div>
<div class="ttc" id="FileTypes_8h_html"><div class="ttname"><a href="FileTypes_8h.html">FileTypes.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1NotImplemented_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1NotImplemented.html">OpenMS::Exception::NotImplemented</a></div><div class="ttdoc">Not implemented exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:437</div></div>
<div class="ttc" id="MzMLFile_8h_html"><div class="ttname"><a href="MzMLFile_8h.html">MzMLFile.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7ab5518cc16bd1f60ebbb47e681a56b75f"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ab5518cc16bd1f60ebbb47e681a56b75f">OpenMS::FileTypes::MZML</a></div><div class="ttdoc">MzML file (.mzML) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_acc3538c5284777d8702ccaefeb61e74c"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">OpenMS::ProgressLogger::setLogType</a></div><div class="ttdeci">void setLogType(LogType type) const </div><div class="ttdoc">Sets the progress log that should be used. The default type is NONE! </div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelBSpline_html_a39100a3d6235b7512df3d2731d016934"><div class="ttname"><a href="classOpenMS_1_1TransformationModelBSpline.html#a39100a3d6235b7512df3d2731d016934">OpenMS::TransformationModelBSpline::getDefaultParameters</a></div><div class="ttdeci">static void getDefaultParameters(Param &params)</div><div class="ttdoc">Gets the default parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1IdXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1IdXMLFile.html">OpenMS::IdXMLFile</a></div><div class="ttdoc">Used to load and store idXML files. </div><div class="ttdef"><b>Definition:</b> IdXMLFile.h:63</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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