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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>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<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>&#160;<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>&#160;<span class="comment">//</span></div>
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<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Witold Wolski  $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Witold Wolski $</span></div>
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<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<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>&#160;<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>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;cmath&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;numeric&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;boost/bind.hpp&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;complex&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;algorithm&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;cmath&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h</a>&quot;</span></div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="keyword">namespace </span>OpenSwath</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;{</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;  OPENSWATHALGO_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">normalize</a>(<span class="keyword">const</span> std::vector&lt;double&gt;&amp; intensities, <span class="keywordtype">double</span> normalization_factor, std::vector&lt;double&gt;&amp; normalized_intensities);</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">typename</span> T&gt;</div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="namespaceOpenSwath.html#ae0c53634415d6187fedbd4be63830087">   62</a></span>&#160;  <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>&#160;  {</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    <span class="keywordtype">double</span> res = 0.0;</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <span class="keywordflow">for</span> (; beg != end; ++beg)</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    {</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;      <span class="keywordtype">double</span> tmp = *beg;</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;      res += tmp * tmp;</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    }</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    <span class="keywordflow">return</span> sqrt(res);</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;  }</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="structOpenSwath_1_1mySqrt.html">   73</a></span>&#160;  <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>&#160;    std::unary_function&lt;double, double&gt;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;  {</div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="structOpenSwath_1_1mySqrt.html#a8b01f5831c9306311d6385888986bd70">   76</a></span>&#160;    <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>&#160;    {</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;      <span class="keywordflow">return</span> sqrt(x);</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    }</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;  };</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">typename</span> Texp, <span class="keyword">typename</span> Ttheo&gt;</div>
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="namespaceOpenSwath.html#a76a519ac5bb7019920e196b06bd05638">   87</a></span>&#160;  <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>&#160;  {</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    std::vector&lt;double&gt; res(std::distance(intExpBeg, intExpEnd));</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;    std::transform(intExpBeg, intExpEnd, intTheo, res.begin(), std::multiplies&lt;double&gt;());</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;    <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>&#160;    <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>&#160;  }</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;  OPENSWATHALGO_DLLAPI <span class="keywordtype">double</span> <a class="code" href="namespaceOpenSwath.html#a479125b149c88231a4e3a97d6a8c0576">dotprodScoring</a>(std::vector&lt;double&gt; intExp, std::vector&lt;double&gt; theorint);</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">typename</span> Texp, <span class="keyword">typename</span> Ttheo&gt;</div>
<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="namespaceOpenSwath.html#a12b1bfedf1d2ca756e964e5dcbdb3543">  108</a></span>&#160;  <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>&#160;  {</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    <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>&#160;    <span class="keywordflow">for</span> (std::size_t i = 0; itExpBeg &lt; itExpEnd; ++itExpBeg, ++itTheo, ++i)</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;    {</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;      <span class="keywordtype">double</span> x = *itExpBeg - *itTheo;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      x = fabs(x);</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      sum += x;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;    }</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;    <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>&#160;  }</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;  OPENSWATHALGO_DLLAPI <span class="keywordtype">double</span> <a class="code" href="namespaceOpenSwath.html#a98920f3dc70b731b6b95d0abd070c34a">manhattanScoring</a>(std::vector&lt;double&gt; intExp, std::vector&lt;double&gt; theorint);</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">typename</span> TInputIterator, <span class="keyword">typename</span> TInputIteratorY&gt;</div>
<div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="namespaceOpenSwath.html#ae9723e227cff096670229c72f6a2865e">  134</a></span>&#160;  <span class="keyword">typename</span> std::iterator_traits&lt;TInputIterator&gt;::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>&#160;    TInputIterator xBeg,</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;    TInputIterator xEnd,</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;    TInputIteratorY yBeg</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;    )</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;  {</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;    <span class="keyword">typedef</span> <span class="keyword">typename</span> std::iterator_traits&lt;TInputIterator&gt;::value_type value_type;</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;    value_type   m1, m2;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;    value_type   s1, s2;</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;    value_type   corr;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;    m1 = m2 = s1 = s2 = 0.0;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;    corr = 0.0;</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;    ptrdiff_t n = std::distance(xBeg, xEnd);</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;    value_type nd = <span class="keyword">static_cast&lt;</span>value_type<span class="keyword">&gt;</span>(n);</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;    <span class="keywordflow">for</span> (; xBeg != xEnd; ++xBeg, ++yBeg)</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;    {</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;      corr += *xBeg * *yBeg;</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;      m1 += *xBeg;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;      m2 += *yBeg;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;      s1 += *xBeg * *xBeg;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;      s2 += *yBeg * *yBeg;</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;    }</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;    m1 /= nd;</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;    m2 /= nd;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;    s1 -= m1 * m1 * nd;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;    s2 -= m2 * m2 * nd;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;    <span class="keywordflow">if</span> (s1 &lt; 1.0e-12 || s2 &lt; 1.0e-12)</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;      <span class="keywordflow">return</span> 0.0;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;    <span class="keywordflow">else</span></div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;    {</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;      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>&#160;      corr /= sqrt(s1 * s2);</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;      <span class="keywordflow">return</span> corr;</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;    }</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;  }</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno"><a class="line" href="classOpenSwath_1_1mean__and__stddev.html">  174</a></span>&#160;  <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>&#160;  {</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>&#160;    <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>&#160;    <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>&#160;<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>&#160;    <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>&#160;    <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>&#160;      m_(0.0), q_(0.0), c_(0u)</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;    {</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;    }</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;</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>&#160;    <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>&#160;    {</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;      <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>&#160;      m_ += delta / ++c_;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;      q_ += delta * (sample - m_);</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;    }</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;</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>&#160;    <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>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;      <span class="keywordflow">return</span> (c_ &gt; 1u) ? (q_ / (c_ - 1)) : 0;</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;    }</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;</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>&#160;    <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>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;      <span class="keywordflow">return</span> (c_ &gt; 1u) ? (q_ / c_) : 0;</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;    }</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;</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>&#160;    <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>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;      <span class="keywordflow">return</span> std::sqrt(sample_variance());</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;    }</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;</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>&#160;    <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>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;      <span class="keywordflow">return</span> std::sqrt(standard_variance());</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;    }</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;</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>&#160;    <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>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;      <span class="keywordflow">return</span> m_;</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;    }</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;</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>&#160;    <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>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;      <span class="keywordflow">return</span> c_;</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;    }</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;</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>&#160;    <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>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;      <span class="keywordflow">return</span> sample_variance();</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;    }</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;</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>&#160;    <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>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;      <span class="keywordflow">return</span> sample_stddev();</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;    }</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;</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>&#160;    <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>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;      <span class="keywordflow">return</span> stddev();</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;    }</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;  };</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;} <span class="comment">//end namespace OpenSwath</span></div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;<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&lt; double &gt; intExp, std::vector&lt; double &gt; 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&lt; double &gt; intExp, std::vector&lt; double &gt; 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&lt; double &gt; &amp;intensities, double normalization_factor, std::vector&lt; double &gt; &amp;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&lt; TInputIterator &gt;::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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