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<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_330fe73d44ce641f33dd6036f80161a5.html">ANALYSIS</a></li><li class="navelem"><a class="el" href="dir_8b5fa5a938a8162745e4cf0197528bc9.html">MAPMATCHING</a></li> </ul>
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<div class="title">BaseSuperimposer.h</div> </div>
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<a href="BaseSuperimposer_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>
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<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
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<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<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>
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<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>
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<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
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<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>
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<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
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<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
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<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Clemens Groepl $</span></div>
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<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Clemens Groepl, Marc Sturm $</span></div>
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<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
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<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> </div>
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<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#ifndef OPENMS_ANALYSIS_MAPMATCHING_BASESUPERIMPOSER_H</span></div>
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<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_MAPMATCHING_BASESUPERIMPOSER_H</span></div>
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<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor"></span></div>
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<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="TransformationDescription_8h.html">OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h</a>></span></div>
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<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
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<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="ConsensusMap_8h.html">OpenMS/KERNEL/ConsensusMap.h</a>></span></div>
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<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
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<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <utility></span></div>
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<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <fstream></span></div>
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<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div>
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<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="keyword">namespace </span>OpenMS</div>
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<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> {</div>
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<div class="line"><a name="l00055"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseSuperimposer.html"> 55</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1BaseSuperimposer.html">BaseSuperimposer</a> :</div>
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<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>,</div>
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<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
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<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  {</div>
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<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> </div>
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<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="keyword">public</span>:</div>
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<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div>
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<div class="line"><a name="l00063"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseSuperimposer.html#a570877055301f3dd8a8f98dfa914dd45"> 63</a></span>  <a class="code" href="classOpenMS_1_1BaseSuperimposer.html#a570877055301f3dd8a8f98dfa914dd45">BaseSuperimposer</a>() :</div>
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<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>(<span class="stringliteral">"BaseSuperimposer"</span>),</div>
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<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a>()</div>
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<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  {</div>
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<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  }</div>
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<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
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<div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseSuperimposer.html#a1dcc5938ef9cf05f3d3d14cc828ffb4f"> 70</a></span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1BaseSuperimposer.html#a1dcc5938ef9cf05f3d3d14cc828ffb4f">~BaseSuperimposer</a>()</div>
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<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  {</div>
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<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  }</div>
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<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div>
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<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> run(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & map_model, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & map_scene, <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> & transformation) = 0;</div>
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<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
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<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keyword">static</span> <span class="keywordtype">void</span> registerChildren();</div>
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<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
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<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="keyword">private</span>:</div>
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<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
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<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <a class="code" href="classOpenMS_1_1BaseSuperimposer.html">BaseSuperimposer</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BaseSuperimposer.html">BaseSuperimposer</a> &);</div>
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<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
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<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <a class="code" href="classOpenMS_1_1BaseSuperimposer.html">BaseSuperimposer</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BaseSuperimposer.html">BaseSuperimposer</a> &);</div>
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<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div>
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<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  };</div>
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<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div>
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<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> } <span class="comment">// namespace OpenMS</span></div>
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<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
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<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> <span class="preprocessor">#endif // OPENMS_ANALYSIS_MAPMATCHING_BASESUPERIMPOSER_H</span></div>
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<div class="ttc" id="ConsensusMap_8h_html"><div class="ttname"><a href="ConsensusMap_8h.html">ConsensusMap.h</a></div></div>
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<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
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<div class="ttc" id="classOpenMS_1_1ConsensusMap_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html">OpenMS::ConsensusMap</a></div><div class="ttdoc">A container for consensus elements. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:60</div></div>
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<div class="ttc" id="classOpenMS_1_1BaseSuperimposer_html"><div class="ttname"><a href="classOpenMS_1_1BaseSuperimposer.html">OpenMS::BaseSuperimposer</a></div><div class="ttdoc">The base class of all superimposer algorithms. </div><div class="ttdef"><b>Definition:</b> BaseSuperimposer.h:55</div></div>
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<div class="ttc" id="classOpenMS_1_1BaseSuperimposer_html_a570877055301f3dd8a8f98dfa914dd45"><div class="ttname"><a href="classOpenMS_1_1BaseSuperimposer.html#a570877055301f3dd8a8f98dfa914dd45">OpenMS::BaseSuperimposer::BaseSuperimposer</a></div><div class="ttdeci">BaseSuperimposer()</div><div class="ttdoc">Constructor. </div><div class="ttdef"><b>Definition:</b> BaseSuperimposer.h:63</div></div>
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<div class="ttc" id="classOpenMS_1_1BaseSuperimposer_html_a1dcc5938ef9cf05f3d3d14cc828ffb4f"><div class="ttname"><a href="classOpenMS_1_1BaseSuperimposer.html#a1dcc5938ef9cf05f3d3d14cc828ffb4f">OpenMS::BaseSuperimposer::~BaseSuperimposer</a></div><div class="ttdeci">virtual ~BaseSuperimposer()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> BaseSuperimposer.h:70</div></div>
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<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>
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<div class="ttc" id="TransformationDescription_8h_html"><div class="ttname"><a href="TransformationDescription_8h.html">TransformationDescription.h</a></div></div>
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<div class="ttc" id="classOpenMS_1_1TransformationDescription_html"><div class="ttname"><a href="classOpenMS_1_1TransformationDescription.html">OpenMS::TransformationDescription</a></div><div class="ttdoc">Generic description of a coordinate transformation. </div><div class="ttdef"><b>Definition:</b> TransformationDescription.h:59</div></div>
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<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:11 using doxygen 1.8.5</font></TD>
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