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<a href="StatsHelpers_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: Witold Wolski $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Witold Wolski $</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_OPENSWATH_OPENSWATHALGO_ALGO_STATSHELPERS_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_OPENSWATH_OPENSWATHALGO_ALGO_STATSHELPERS_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 <cmath></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <numeric></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <boost/bind.hpp></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <complex></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <algorithm></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <cmath></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 <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include "<a class="code" href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h</a>"</span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="keyword">namespace </span>OpenSwath</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> {</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  OPENSWATHALGO_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">normalize</a>(<span class="keyword">const</span> std::vector<double>& intensities, <span class="keywordtype">double</span> normalization_factor, std::vector<double>& normalized_intensities);</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> T></div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="namespaceOpenSwath.html#ae0c53634415d6187fedbd4be63830087"> 62</a></span>  <span class="keywordtype">double</span> <a class="code" href="namespaceOpenSwath.html#ae0c53634415d6187fedbd4be63830087">norm</a>(T beg, T end)</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  {</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordtype">double</span> res = 0.0;</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keywordflow">for</span> (; beg != end; ++beg)</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  {</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordtype">double</span> tmp = *beg;</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  res += tmp * tmp;</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>  <span class="keywordflow">return</span> sqrt(res);</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  }</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="structOpenSwath_1_1mySqrt.html"> 73</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenSwath_1_1mySqrt.html">mySqrt</a> :</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  std::unary_function<double, double></div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  {</div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="structOpenSwath_1_1mySqrt.html#a8b01f5831c9306311d6385888986bd70"> 76</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenSwath_1_1mySqrt.html#a8b01f5831c9306311d6385888986bd70">operator()</a>(<span class="keywordtype">double</span> x)</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  {</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordflow">return</span> sqrt(x);</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> </div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  };</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> Texp, <span class="keyword">typename</span> Ttheo></div>
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="namespaceOpenSwath.html#a76a519ac5bb7019920e196b06bd05638"> 87</a></span>  <span class="keywordtype">double</span> <a class="code" href="namespaceOpenSwath.html#a76a519ac5bb7019920e196b06bd05638">dotProd</a>(Texp intExpBeg, Texp intExpEnd, Ttheo intTheo)</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  {</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  std::vector<double> res(std::distance(intExpBeg, intExpEnd));</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  std::transform(intExpBeg, intExpEnd, intTheo, res.begin(), std::multiplies<double>());</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="keywordtype">double</span> <a class="code" href="group__MathFunctionsStatistics.html#ga55edf7ee469b3d635c367d9c83fe87f5">sum</a> = std::accumulate(res.begin(), res.end(), 0.);</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordflow">return</span> <a class="code" href="group__MathFunctionsStatistics.html#ga55edf7ee469b3d635c367d9c83fe87f5">sum</a>;</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  }</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  OPENSWATHALGO_DLLAPI <span class="keywordtype">double</span> <a class="code" href="namespaceOpenSwath.html#a479125b149c88231a4e3a97d6a8c0576">dotprodScoring</a>(std::vector<double> intExp, std::vector<double> theorint);</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> </div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> Texp, <span class="keyword">typename</span> Ttheo></div>
<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="namespaceOpenSwath.html#a12b1bfedf1d2ca756e964e5dcbdb3543"> 108</a></span>  <span class="keywordtype">double</span> <a class="code" href="namespaceOpenSwath.html#a12b1bfedf1d2ca756e964e5dcbdb3543">manhattanDist</a>(Texp itExpBeg, Texp itExpEnd, Ttheo itTheo)</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  {</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordtype">double</span> <a class="code" href="group__MathFunctionsStatistics.html#ga55edf7ee469b3d635c367d9c83fe87f5">sum</a> = 0.0;</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordflow">for</span> (std::size_t i = 0; itExpBeg < itExpEnd; ++itExpBeg, ++itTheo, ++i)</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  {</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordtype">double</span> x = *itExpBeg - *itTheo;</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  x = fabs(x);</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  sum += x;</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>  <span class="keywordflow">return</span> <a class="code" href="group__MathFunctionsStatistics.html#ga55edf7ee469b3d635c367d9c83fe87f5">sum</a>;</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  }</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  OPENSWATHALGO_DLLAPI <span class="keywordtype">double</span> <a class="code" href="namespaceOpenSwath.html#a98920f3dc70b731b6b95d0abd070c34a">manhattanScoring</a>(std::vector<double> intExp, std::vector<double> theorint);</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> </div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> TInputIterator, <span class="keyword">typename</span> TInputIteratorY></div>
<div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="namespaceOpenSwath.html#ae9723e227cff096670229c72f6a2865e"> 134</a></span>  <span class="keyword">typename</span> std::iterator_traits<TInputIterator>::value_type <a class="code" href="namespaceOpenSwath.html#ae9723e227cff096670229c72f6a2865e">cor_pearson</a>(</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  TInputIterator xBeg,</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  TInputIterator xEnd,</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  TInputIteratorY yBeg</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>  {</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> std::iterator_traits<TInputIterator>::value_type value_type;</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  value_type m1, m2;</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  value_type s1, s2;</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  value_type corr;</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  m1 = m2 = s1 = s2 = 0.0;</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  corr = 0.0;</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  ptrdiff_t n = std::distance(xBeg, xEnd);</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  value_type nd = <span class="keyword">static_cast<</span>value_type<span class="keyword">></span>(n);</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="keywordflow">for</span> (; xBeg != xEnd; ++xBeg, ++yBeg)</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>  corr += *xBeg * *yBeg;</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  m1 += *xBeg;</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  m2 += *yBeg;</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  s1 += *xBeg * *xBeg;</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  s2 += *yBeg * *yBeg;</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  }</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  m1 /= nd;</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  m2 /= nd;</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  s1 -= m1 * m1 * nd;</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  s2 -= m2 * m2 * nd;</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> </div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="keywordflow">if</span> (s1 < 1.0e-12 || s2 < 1.0e-12)</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="keywordflow">return</span> 0.0;</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  {</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  corr -= m1 * m2 * (<a class="code" href="classdouble.html">double</a>)n;</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  corr /= sqrt(s1 * s2);</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordflow">return</span> corr;</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  }</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> </div>
<div class="line"><a name="l00174"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html"> 174</a></span>  <span class="keyword">class </span>OPENSWATHALGO_DLLAPI <a class="code" href="classOpenSwath_1_1mean__and__stddev.html">mean_and_stddev</a></div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  {</div>
<div class="line"><a name="l00176"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#aa1a5b8c948f80b8f9f4df5bf43a5ecad"> 176</a></span>  <span class="keywordtype">double</span> m_, <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#aa1a5b8c948f80b8f9f4df5bf43a5ecad">q_</a>;</div>
<div class="line"><a name="l00177"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a511ed50c3f82fc2c89b66c39cbacbc87"> 177</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a511ed50c3f82fc2c89b66c39cbacbc87">c_</a>;</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a32403829e9e5baa60c9fd58375e14842"> 179</a></span>  <span class="keyword">typedef</span> <span class="keywordtype">double</span> <a class="code" href="classdouble.html">argument_type</a>, <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a32403829e9e5baa60c9fd58375e14842">result_type</a>;</div>
<div class="line"><a name="l00180"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a3c8624f8975c2f086b20d4db65a34e93"> 180</a></span>  <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a3c8624f8975c2f086b20d4db65a34e93">mean_and_stddev</a>() :</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  m_(0.0), q_(0.0), c_(0u)</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  {</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> </div>
<div class="line"><a name="l00185"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#ae4eb0efbf43adb16dfd0519b87184225"> 185</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#ae4eb0efbf43adb16dfd0519b87184225">operator()</a>(<span class="keywordtype">double</span> sample)</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  {</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="keywordtype">double</span> <span class="keyword">const</span> delta = sample - m_;</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  m_ += delta / ++c_;</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  q_ += delta * (sample - m_);</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  }</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> </div>
<div class="line"><a name="l00192"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a83d588b08707b51ef0f5ce28e87458fd"> 192</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a83d588b08707b51ef0f5ce28e87458fd">sample_variance</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <span class="keywordflow">return</span> (c_ > 1u) ? (q_ / (c_ - 1)) : 0;</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</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"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a23177d026786da65c16cf53dde1dccdf"> 197</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a23177d026786da65c16cf53dde1dccdf">standard_variance</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="keywordflow">return</span> (c_ > 1u) ? (q_ / c_) : 0;</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> </div>
<div class="line"><a name="l00202"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a6cafc108f630a861bf156b0627e95325"> 202</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a6cafc108f630a861bf156b0627e95325">sample_stddev</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keywordflow">return</span> std::sqrt(sample_variance());</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</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"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a572505563eb12c8803cf887f732ef6c3"> 207</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a572505563eb12c8803cf887f732ef6c3">standard_stddev</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  <span class="keywordflow">return</span> std::sqrt(standard_variance());</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> </div>
<div class="line"><a name="l00212"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a9921c567694a5f661302230feffb76d1"> 212</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a9921c567694a5f661302230feffb76d1">mean</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <span class="keywordflow">return</span> m_;</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"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#ad9eb3c6cef0ec1d7873fc9658d9cf344"> 217</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#ad9eb3c6cef0ec1d7873fc9658d9cf344">count</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="keywordflow">return</span> c_;</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  }</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a name="l00222"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a8ca2b77cf0a83e10d4dab0f029c8e526"> 222</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a8ca2b77cf0a83e10d4dab0f029c8e526">variance</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="keywordflow">return</span> sample_variance();</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  }</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span> </div>
<div class="line"><a name="l00227"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a4b46e55bb8bb93edaa8e5741177666ff"> 227</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a4b46e55bb8bb93edaa8e5741177666ff">stddev</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <span class="keywordflow">return</span> sample_stddev();</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  }</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span> </div>
<div class="line"><a name="l00232"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html#a8f9baeb5887be0f2b51bacc41dc1964f"> 232</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenSwath_1_1mean__and__stddev.html#a8f9baeb5887be0f2b51bacc41dc1964f">operator()</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <span class="keywordflow">return</span> stddev();</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  }</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>  };</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span> </div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span> } <span class="comment">//end namespace OpenSwath</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> <span class="preprocessor">#endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_STATSHELPERS_H</span></div>
<div class="ttc" id="namespaceOpenSwath_html_a12b1bfedf1d2ca756e964e5dcbdb3543"><div class="ttname"><a href="namespaceOpenSwath.html#a12b1bfedf1d2ca756e964e5dcbdb3543">OpenSwath::manhattanDist</a></div><div class="ttdeci">double manhattanDist(Texp itExpBeg, Texp itExpEnd, Ttheo itTheo)</div><div class="ttdoc">compute manhattan distance between Exp and Theo </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:108</div></div>
<div class="ttc" id="namespaceOpenSwath_html_a98920f3dc70b731b6b95d0abd070c34a"><div class="ttname"><a href="namespaceOpenSwath.html#a98920f3dc70b731b6b95d0abd070c34a">OpenSwath::manhattanScoring</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI double manhattanScoring(std::vector< double > intExp, std::vector< double > theorint)</div><div class="ttdoc">manhattan scoring </div></div>
<div class="ttc" id="group__MathFunctionsStatistics_html_ga55edf7ee469b3d635c367d9c83fe87f5"><div class="ttname"><a href="group__MathFunctionsStatistics.html#ga55edf7ee469b3d635c367d9c83fe87f5">OpenMS::Math::sum</a></div><div class="ttdeci">static DoubleReal sum(IteratorType begin, IteratorType end)</div><div class="ttdoc">Calculates the sum of a range of values. </div><div class="ttdef"><b>Definition:</b> StatisticFunctions.h:56</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a83d588b08707b51ef0f5ce28e87458fd"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a83d588b08707b51ef0f5ce28e87458fd">OpenSwath::mean_and_stddev::sample_variance</a></div><div class="ttdeci">double sample_variance() const </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:192</div></div>
<div class="ttc" id="namespaceOpenSwath_html_a479125b149c88231a4e3a97d6a8c0576"><div class="ttname"><a href="namespaceOpenSwath.html#a479125b149c88231a4e3a97d6a8c0576">OpenSwath::dotprodScoring</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI double dotprodScoring(std::vector< double > intExp, std::vector< double > theorint)</div><div class="ttdoc">the dot product scoring </div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_ae4eb0efbf43adb16dfd0519b87184225"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#ae4eb0efbf43adb16dfd0519b87184225">OpenSwath::mean_and_stddev::operator()</a></div><div class="ttdeci">void operator()(double sample)</div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:185</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a9921c567694a5f661302230feffb76d1"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a9921c567694a5f661302230feffb76d1">OpenSwath::mean_and_stddev::mean</a></div><div class="ttdeci">double mean() const </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:212</div></div>
<div class="ttc" id="namespaceOpenSwath_html_a546b9a9117f4207e3cfc9ef2ea4aad3d"><div class="ttname"><a href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">OpenSwath::normalize</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)</div><div class="ttdoc">Normalize intensities in vector by normalization_factor. </div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a511ed50c3f82fc2c89b66c39cbacbc87"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a511ed50c3f82fc2c89b66c39cbacbc87">OpenSwath::mean_and_stddev::c_</a></div><div class="ttdeci">unsigned long c_</div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:177</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a8ca2b77cf0a83e10d4dab0f029c8e526"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a8ca2b77cf0a83e10d4dab0f029c8e526">OpenSwath::mean_and_stddev::variance</a></div><div class="ttdeci">double variance() const </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:222</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_ad9eb3c6cef0ec1d7873fc9658d9cf344"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#ad9eb3c6cef0ec1d7873fc9658d9cf344">OpenSwath::mean_and_stddev::count</a></div><div class="ttdeci">unsigned long count() const </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:217</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a3c8624f8975c2f086b20d4db65a34e93"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a3c8624f8975c2f086b20d4db65a34e93">OpenSwath::mean_and_stddev::mean_and_stddev</a></div><div class="ttdeci">mean_and_stddev()</div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:180</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_aa1a5b8c948f80b8f9f4df5bf43a5ecad"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#aa1a5b8c948f80b8f9f4df5bf43a5ecad">OpenSwath::mean_and_stddev::q_</a></div><div class="ttdeci">double q_</div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:176</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a6cafc108f630a861bf156b0627e95325"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a6cafc108f630a861bf156b0627e95325">OpenSwath::mean_and_stddev::sample_stddev</a></div><div class="ttdeci">double sample_stddev() const </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:202</div></div>
<div class="ttc" id="structOpenSwath_1_1mySqrt_html"><div class="ttname"><a href="structOpenSwath_1_1mySqrt.html">OpenSwath::mySqrt</a></div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:73</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a572505563eb12c8803cf887f732ef6c3"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a572505563eb12c8803cf887f732ef6c3">OpenSwath::mean_and_stddev::standard_stddev</a></div><div class="ttdeci">double standard_stddev() const </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:207</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a4b46e55bb8bb93edaa8e5741177666ff"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a4b46e55bb8bb93edaa8e5741177666ff">OpenSwath::mean_and_stddev::stddev</a></div><div class="ttdeci">double stddev() const </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:227</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html">OpenSwath::mean_and_stddev</a></div><div class="ttdoc">functor to compute the mean and stddev of sequence using the std::foreach algorithm ...</div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:174</div></div>
<div class="ttc" id="namespaceOpenSwath_html_ae9723e227cff096670229c72f6a2865e"><div class="ttname"><a href="namespaceOpenSwath.html#ae9723e227cff096670229c72f6a2865e">OpenSwath::cor_pearson</a></div><div class="ttdeci">std::iterator_traits< TInputIterator >::value_type cor_pearson(TInputIterator xBeg, TInputIterator xEnd, TInputIteratorY yBeg)</div><div class="ttdoc">compute prearson correlation of vector x and y </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:134</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a23177d026786da65c16cf53dde1dccdf"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a23177d026786da65c16cf53dde1dccdf">OpenSwath::mean_and_stddev::standard_variance</a></div><div class="ttdeci">double standard_variance() const </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:197</div></div>
<div class="ttc" id="namespaceOpenSwath_html_ae0c53634415d6187fedbd4be63830087"><div class="ttname"><a href="namespaceOpenSwath.html#ae0c53634415d6187fedbd4be63830087">OpenSwath::norm</a></div><div class="ttdeci">double norm(T beg, T end)</div><div class="ttdoc">compute the norm of the vector </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:62</div></div>
<div class="ttc" id="namespaceOpenSwath_html_a76a519ac5bb7019920e196b06bd05638"><div class="ttname"><a href="namespaceOpenSwath.html#a76a519ac5bb7019920e196b06bd05638">OpenSwath::dotProd</a></div><div class="ttdeci">double dotProd(Texp intExpBeg, Texp intExpEnd, Ttheo intTheo)</div><div class="ttdoc">compute dotprod of vecotrs </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:87</div></div>
<div class="ttc" id="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h_html"><div class="ttname"><a href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h.html">ISpectrumAccess.h</a></div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a32403829e9e5baa60c9fd58375e14842"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a32403829e9e5baa60c9fd58375e14842">OpenSwath::mean_and_stddev::result_type</a></div><div class="ttdeci">double result_type</div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:179</div></div>
<div class="ttc" id="structOpenSwath_1_1mySqrt_html_a8b01f5831c9306311d6385888986bd70"><div class="ttname"><a href="structOpenSwath_1_1mySqrt.html#a8b01f5831c9306311d6385888986bd70">OpenSwath::mySqrt::operator()</a></div><div class="ttdeci">double operator()(double x)</div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:76</div></div>
<div class="ttc" id="classOpenSwath_1_1mean__and__stddev_html_a8f9baeb5887be0f2b51bacc41dc1964f"><div class="ttname"><a href="classOpenSwath_1_1mean__and__stddev.html#a8f9baeb5887be0f2b51bacc41dc1964f">OpenSwath::mean_and_stddev::operator()</a></div><div class="ttdeci">double operator()() const </div><div class="ttdef"><b>Definition:</b> StatsHelpers.h:232</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 11:19:21 using doxygen 1.8.5</font></TD>
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