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<a href="LocalLinearMap_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: Alexandra Scherbart $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: $</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_ANALYSIS_PIP_LOCALLINEARMAP_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_PIP_LOCALLINEARMAP_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="Matrix_8h.html">OpenMS/DATASTRUCTURES/Matrix.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> {</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
<div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LocalLinearMap.html"> 57</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1LocalLinearMap.html">LocalLinearMap</a></div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  {</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> </div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div>
<div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html"> 69</a></span>  <span class="keyword">struct </span>OPENMS_DLLAPI <a class="code" href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html">LLMParam</a></div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  {</div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html#afa4f6397251e67572658bb492485fd71"> 71</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html#afa4f6397251e67572658bb492485fd71">xdim</a>; </div>
<div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html#ab8c6a65d159dbdaf9cbcdeb65b9eae21"> 72</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html#ab8c6a65d159dbdaf9cbcdeb65b9eae21">ydim</a>; </div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html#a5ba495b5ed499e9340ba75999ec131b4"> 73</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html#a5ba495b5ed499e9340ba75999ec131b4">radius</a>; </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="l00077"></a><span class="lineno"> 77</span>  <a class="code" href="classOpenMS_1_1LocalLinearMap.html">LocalLinearMap</a>();</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1LocalLinearMap.html">LocalLinearMap</a>();</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html">LLMParam</a> & getLLMParam() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<DoubleReal></a> & getCodebooks() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<DoubleReal></a> & getMatrixA() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keyword">const</span> std::vector<DoubleReal> & getVectorWout() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<UInt></a> & getCord() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordtype">void</span> normalizeVector(std::vector<DoubleReal> & aaIndexVariables);</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  std::vector<DoubleReal> neigh(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<UInt></a> & cord, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> win, <a class="code" href="classdouble.html">DoubleReal</a> radius);</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LocalLinearMap.html#a114b8fab16086dbe2d9b8a607ae62008"> 98</a></span>  <a class="code" href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html">LLMParam</a> <a class="code" href="classOpenMS_1_1LocalLinearMap.html#a114b8fab16086dbe2d9b8a607ae62008">param_</a>; </div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LocalLinearMap.html#ab2ba14abb2eab29b72bf78c5ff795b89"> 99</a></span>  <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<DoubleReal></a> <a class="code" href="classOpenMS_1_1LocalLinearMap.html#ab2ba14abb2eab29b72bf78c5ff795b89">code_</a>; </div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LocalLinearMap.html#a18092568340f5be7e5023be1ca2890d5"> 100</a></span>  <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<DoubleReal></a> <a class="code" href="classOpenMS_1_1LocalLinearMap.html#a18092568340f5be7e5023be1ca2890d5">A_</a>; </div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LocalLinearMap.html#aea0fcf699ccc353515587f409dd2acdf"> 101</a></span>  std::vector<DoubleReal> <a class="code" href="classOpenMS_1_1LocalLinearMap.html#aea0fcf699ccc353515587f409dd2acdf">wout_</a>; </div>
<div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LocalLinearMap.html#ab4122e68439e16e56dabee1971f3d4eb"> 102</a></span>  <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<UInt></a> <a class="code" href="classOpenMS_1_1LocalLinearMap.html#ab4122e68439e16e56dabee1971f3d4eb">cord_</a>; </div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> </div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<UInt></a> genCord_(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> xdim, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> ydim);</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <a class="code" href="classdouble.html">DoubleReal</a> dist_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<UInt></a> & u, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<UInt></a> & v, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> a, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> b);</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <a class="code" href="classOpenMS_1_1LocalLinearMap.html">LocalLinearMap</a>(<a class="code" href="classOpenMS_1_1LocalLinearMap.html">LocalLinearMap</a> & rhs);</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <a class="code" href="classOpenMS_1_1LocalLinearMap.html">LocalLinearMap</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LocalLinearMap.html">LocalLinearMap</a> & llm);</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</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> </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> }</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> <span class="preprocessor">#endif</span></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1LocalLinearMap_html_ab2ba14abb2eab29b72bf78c5ff795b89"><div class="ttname"><a href="classOpenMS_1_1LocalLinearMap.html#ab2ba14abb2eab29b72bf78c5ff795b89">OpenMS::LocalLinearMap::code_</a></div><div class="ttdeci">Matrix< DoubleReal > code_</div><div class="ttdoc">codebook vectors </div><div class="ttdef"><b>Definition:</b> LocalLinearMap.h:99</div></div>
<div class="ttc" id="structOpenMS_1_1LocalLinearMap_1_1LLMParam_html"><div class="ttname"><a href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html">OpenMS::LocalLinearMap::LLMParam</a></div><div class="ttdoc">Define parameters needed by the Local Linear Map (LLM) model. </div><div class="ttdef"><b>Definition:</b> LocalLinearMap.h:69</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="structOpenMS_1_1LocalLinearMap_1_1LLMParam_html_afa4f6397251e67572658bb492485fd71"><div class="ttname"><a href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html#afa4f6397251e67572658bb492485fd71">OpenMS::LocalLinearMap::LLMParam::xdim</a></div><div class="ttdeci">UInt xdim</div><div class="ttdef"><b>Definition:</b> LocalLinearMap.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1LocalLinearMap_html_ab4122e68439e16e56dabee1971f3d4eb"><div class="ttname"><a href="classOpenMS_1_1LocalLinearMap.html#ab4122e68439e16e56dabee1971f3d4eb">OpenMS::LocalLinearMap::cord_</a></div><div class="ttdeci">Matrix< UInt > cord_</div><div class="ttdoc">coordinates of codebooks on grid </div><div class="ttdef"><b>Definition:</b> LocalLinearMap.h:102</div></div>
<div class="ttc" id="classOpenMS_1_1LocalLinearMap_html_a18092568340f5be7e5023be1ca2890d5"><div class="ttname"><a href="classOpenMS_1_1LocalLinearMap.html#a18092568340f5be7e5023be1ca2890d5">OpenMS::LocalLinearMap::A_</a></div><div class="ttdeci">Matrix< DoubleReal > A_</div><div class="ttdoc">linear mappings </div><div class="ttdef"><b>Definition:</b> LocalLinearMap.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1LocalLinearMap_html_a114b8fab16086dbe2d9b8a607ae62008"><div class="ttname"><a href="classOpenMS_1_1LocalLinearMap.html#a114b8fab16086dbe2d9b8a607ae62008">OpenMS::LocalLinearMap::param_</a></div><div class="ttdeci">LLMParam param_</div><div class="ttdoc">parameters of the model </div><div class="ttdef"><b>Definition:</b> LocalLinearMap.h:98</div></div>
<div class="ttc" id="classOpenMS_1_1LocalLinearMap_html"><div class="ttname"><a href="classOpenMS_1_1LocalLinearMap.html">OpenMS::LocalLinearMap</a></div><div class="ttdoc">Trained Local Linear Map (LLM) model for peak intensity prediction. </div><div class="ttdef"><b>Definition:</b> LocalLinearMap.h:57</div></div>
<div class="ttc" id="Matrix_8h_html"><div class="ttname"><a href="Matrix_8h.html">Matrix.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1LocalLinearMap_1_1LLMParam_html_a5ba495b5ed499e9340ba75999ec131b4"><div class="ttname"><a href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html#a5ba495b5ed499e9340ba75999ec131b4">OpenMS::LocalLinearMap::LLMParam::radius</a></div><div class="ttdeci">DoubleReal radius</div><div class="ttdef"><b>Definition:</b> LocalLinearMap.h:73</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_1LocalLinearMap_html_aea0fcf699ccc353515587f409dd2acdf"><div class="ttname"><a href="classOpenMS_1_1LocalLinearMap.html#aea0fcf699ccc353515587f409dd2acdf">OpenMS::LocalLinearMap::wout_</a></div><div class="ttdeci">std::vector< DoubleReal > wout_</div><div class="ttdoc">linear bias </div><div class="ttdef"><b>Definition:</b> LocalLinearMap.h:101</div></div>
<div class="ttc" id="structOpenMS_1_1LocalLinearMap_1_1LLMParam_html_ab8c6a65d159dbdaf9cbcdeb65b9eae21"><div class="ttname"><a href="structOpenMS_1_1LocalLinearMap_1_1LLMParam.html#ab8c6a65d159dbdaf9cbcdeb65b9eae21">OpenMS::LocalLinearMap::LLMParam::ydim</a></div><div class="ttdeci">UInt ydim</div><div class="ttdef"><b>Definition:</b> LocalLinearMap.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1Matrix_html"><div class="ttname"><a href="classOpenMS_1_1Matrix.html">OpenMS::Matrix</a></div><div class="ttdoc">A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access...</div><div class="ttdef"><b>Definition:</b> Matrix.h:79</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:16 using doxygen 1.8.5</font></TD>
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