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<a href="WindowMower_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>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<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>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Mathias Walzer $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Mathias Walzer, Timo Sachsenberg$</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_FILTERING_TRANSFORMERS_WINDOWMOWER_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_FILTERING_TRANSFORMERS_WINDOWMOWER_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;<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;</div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;set&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;{</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;</div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="classOpenMS_1_1WindowMower.html">   53</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1WindowMower.html">WindowMower</a> :</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;  {</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;    <span class="comment">// @name Constructors, destructors and assignment operators</span></div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;    <span class="comment">// @{</span></div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;<span class="comment"></span>    <a class="code" href="classOpenMS_1_1WindowMower.html">WindowMower</a>();</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1WindowMower.html">WindowMower</a>();</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    <a class="code" href="classOpenMS_1_1WindowMower.html">WindowMower</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1WindowMower.html">WindowMower</a>&amp; source);</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <a class="code" href="classOpenMS_1_1WindowMower.html">WindowMower</a>&amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1WindowMower.html">WindowMower</a>&amp; source);</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <span class="comment">// @}  </span></div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> SpectrumType&gt;</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1WindowMower.html#aa8b30830b576ce00361f3ebbe1bed658">   73</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1WindowMower.html#aa8b30830b576ce00361f3ebbe1bed658">filterPeakSpectrumForTopNInSlidingWindow</a>(SpectrumType&amp; spectrum)</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    {</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;      <span class="keyword">typedef</span> <span class="keyword">typename</span> SpectrumType::ConstIterator ConstIterator;</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;      windowsize_ = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)param_.getValue(<span class="stringliteral">&quot;windowsize&quot;</span>);</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;      peakcount_ = (<a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>)param_.getValue(<span class="stringliteral">&quot;peakcount&quot;</span>);</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;      <span class="comment">//copy spectrum</span></div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;      SpectrumType old_spectrum = spectrum;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;      old_spectrum.sortByPosition();</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;      <span class="comment">//find high peak positions</span></div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      <span class="keywordtype">bool</span> end  = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;      std::set&lt;double&gt; positions;</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;      <span class="keywordflow">for</span> (ConstIterator it = old_spectrum.begin(); it != old_spectrum.end(); ++it)</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;        <span class="comment">// copy the window from the spectrum</span></div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;        SpectrumType window;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;        <span class="keywordflow">for</span> (ConstIterator it2 = it; (it2-&gt;getPosition() - it-&gt;getPosition() &lt; windowsize_); )</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;        {</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;          window.push_back(*it2);</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;          <span class="keywordflow">if</span> (++it2 == old_spectrum.end())</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;          {</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;            end = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;            <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;          }</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;        }</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;        <span class="comment">//extract peakcount most intense peaks</span></div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;        window.sortByIntensity(<span class="keyword">true</span>);</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; peakcount_; ++i)</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;        {</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;          <span class="keywordflow">if</span> (i &lt; window.size())</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;          {</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;            positions.insert(window[i].getMZ());</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;          }</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="comment">//abort at the end of the spectrum</span></div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;        <span class="keywordflow">if</span> (end) <span class="keywordflow">break</span>;</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;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      <span class="comment">// replace the old peaks by the new ones</span></div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      spectrum.clear(<span class="keyword">false</span>);</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      <span class="keywordflow">for</span> (ConstIterator it = old_spectrum.begin(); it != old_spectrum.end(); ++it)</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;      {</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;        <span class="keywordflow">if</span> (positions.find(it-&gt;getMZ()) != positions.end())</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;        {</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;          spectrum.push_back(*it);</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;        }</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;      }</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;    }</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;    <span class="keywordtype">void</span> filterPeakSpectrum(<a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a>&amp; spectrum);</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;    <span class="keywordtype">void</span> filterPeakMap(<a class="code" href="classOpenMS_1_1MSExperiment.html">PeakMap</a>&amp; exp);</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;    <span class="comment">// jumping window version (faster)</span></div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> SpectrumType&gt;</div>
<div class="line"><a name="l00131"></a><span class="lineno"><a class="line" href="classOpenMS_1_1WindowMower.html#a0075845d43b498a236e1977a1e558301">  131</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1WindowMower.html#a0075845d43b498a236e1977a1e558301">filterPeakSpectrumForTopNInJumpingWindow</a>(SpectrumType&amp; spectrum)</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;    {</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;        <span class="keywordflow">if</span> (spectrum.empty())</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;        {</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;            <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;        }</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;        spectrum.sortByPosition();</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;        windowsize_ = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)param_.getValue(<span class="stringliteral">&quot;windowsize&quot;</span>);</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;        peakcount_ = (<a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>)param_.getValue(<span class="stringliteral">&quot;peakcount&quot;</span>);</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;        <span class="comment">// copy meta data</span></div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;        SpectrumType out = spectrum;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;        out.clear(<span class="keyword">false</span>);</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;        SpectrumType peaks_in_window;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> window_start = spectrum[0].getMZ();</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i != spectrum.size(); ++i)</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;        {</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;            <span class="keywordflow">if</span> (spectrum[i].getMZ() - window_start &lt; windowsize_)  <span class="comment">// collect peaks in window</span></div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;            {</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;                peaks_in_window.push_back(spectrum[i]);</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;            } <span class="keywordflow">else</span> <span class="comment">// step over window boundaries</span></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;                window_start = spectrum[i].getMZ(); <span class="comment">// as there might be large gaps between peaks resulting in empty windows, set new window start to next peak</span></div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;                <span class="comment">// copy N highest peaks to out</span></div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;                std::partial_sort(peaks_in_window.begin(), peaks_in_window.begin() + peakcount_, peaks_in_window.end(), <a class="code" href="namespaceOpenMS.html#a74e80d32be63268d8a46039297e18cc6">reverseComparator</a>(<span class="keyword">typename</span> SpectrumType::PeakType::IntensityLess()));</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;                <span class="keywordflow">if</span> (peaks_in_window.size() &gt; peakcount_)</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;                {</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;                    copy(peaks_in_window.begin(), peaks_in_window.begin() + peakcount_, back_inserter(out));</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;                    copy(peaks_in_window.begin(), peaks_in_window.end(), back_inserter(out));</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;                }</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;                peaks_in_window.clear(<span class="keyword">false</span>);</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;                peaks_in_window.push_back(spectrum[i]);</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="l00171"></a><span class="lineno">  171</span>&#160;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;        <span class="keywordflow">if</span> (peaks_in_window.empty())  <span class="comment">// last window is empty -&gt; no special handling needed</span></div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;        {</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;          out.sortByPosition();</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;          spectrum = out;</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;          <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;        }</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;        <span class="comment">// Note that the last window might be much smaller than windowsize.</span></div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;        <span class="comment">// Therefor the number of peaks copied from this window should be adapted accordingly.</span></div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;        <span class="comment">// Otherwise alot of noise peaks are copied from each end of a spectrum.</span></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;        <a class="code" href="classdouble.html">DoubleReal</a> last_window_size = peaks_in_window.back().getMZ() - window_start;</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> last_window_size_fraction = last_window_size / windowsize_;</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> last_window_peakcount = last_window_size_fraction * peakcount_;</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="keywordflow">if</span> (last_window_peakcount)  <span class="comment">// handle single peak in last window (will produce no proper fraction)</span></div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;        {</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;          last_window_peakcount = 1;</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">  192</span>&#160;        <span class="comment">// sort for last_window_peakcount highest peaks</span></div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;        std::partial_sort(peaks_in_window.begin(), peaks_in_window.begin() + last_window_peakcount, peaks_in_window.end(), <a class="code" href="namespaceOpenMS.html#a74e80d32be63268d8a46039297e18cc6">reverseComparator</a>(<span class="keyword">typename</span> SpectrumType::PeakType::IntensityLess()));</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;        <span class="keywordflow">if</span> (peaks_in_window.size() &gt; last_window_peakcount)</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">  197</span>&#160;          std::copy(peaks_in_window.begin(), peaks_in_window.begin() + last_window_peakcount, back_inserter(out));</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;        } <span class="keywordflow">else</span></div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;        {</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;          std::copy(peaks_in_window.begin(), peaks_in_window.end(), std::back_inserter(out));</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">  202</span>&#160;</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;        out.sortByPosition();</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;        spectrum = out;</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;        <span class="keywordflow">return</span>;</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">  207</span>&#160;</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;    <span class="comment">//TODO reimplement DefaultParamHandler::updateMembers_()</span></div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;<span class="keyword">private</span>:          </div>
<div class="line"><a name="l00211"></a><span class="lineno"><a class="line" href="classOpenMS_1_1WindowMower.html#a18a2e5bc978a24852825630b70a99a98">  211</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1WindowMower.html#a18a2e5bc978a24852825630b70a99a98">windowsize_</a>;</div>
<div class="line"><a name="l00212"></a><span class="lineno"><a class="line" href="classOpenMS_1_1WindowMower.html#ab3ca0a2a86becb86bb9eb373af98ce06">  212</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1WindowMower.html#ab3ca0a2a86becb86bb9eb373af98ce06">peakcount_</a>;</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;  };</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;</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">  217</span>&#160;<span class="preprocessor">#endif //OPENMS_FILTERING_TRANSFORMERS_WINDOWMOWER_H</span></div>
<div class="ttc" id="classOpenMS_1_1WindowMower_html"><div class="ttname"><a href="classOpenMS_1_1WindowMower.html">OpenMS::WindowMower</a></div><div class="ttdoc">WindowMower augments the highest peaks in a sliding or jumping window. </div><div class="ttdef"><b>Definition:</b> WindowMower.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1WindowMower_html_a18a2e5bc978a24852825630b70a99a98"><div class="ttname"><a href="classOpenMS_1_1WindowMower.html#a18a2e5bc978a24852825630b70a99a98">OpenMS::WindowMower::windowsize_</a></div><div class="ttdeci">DoubleReal windowsize_</div><div class="ttdef"><b>Definition:</b> WindowMower.h:211</div></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="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
<div class="ttc" id="group__Concept_html_gaba0996d26f7be2572973245b51852757"><div class="ttname"><a href="group__Concept.html#gaba0996d26f7be2572973245b51852757">OpenMS::UInt</a></div><div class="ttdeci">unsigned int UInt</div><div class="ttdoc">Unsigned integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:92</div></div>
<div class="ttc" id="namespaceOpenMS_html_a74e80d32be63268d8a46039297e18cc6"><div class="ttname"><a href="namespaceOpenMS.html#a74e80d32be63268d8a46039297e18cc6">OpenMS::reverseComparator</a></div><div class="ttdeci">ReverseComparator&lt; Cmp &gt; reverseComparator(Cmp const &amp;cmp)</div><div class="ttdoc">Make-function to create a ReverseComparator from another comparator without the need to specify the t...</div><div class="ttdef"><b>Definition:</b> ComparatorUtils.h:261</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1WindowMower_html_aa8b30830b576ce00361f3ebbe1bed658"><div class="ttname"><a href="classOpenMS_1_1WindowMower.html#aa8b30830b576ce00361f3ebbe1bed658">OpenMS::WindowMower::filterPeakSpectrumForTopNInSlidingWindow</a></div><div class="ttdeci">void filterPeakSpectrumForTopNInSlidingWindow(SpectrumType &amp;spectrum)</div><div class="ttdoc">sliding window version (slower) </div><div class="ttdef"><b>Definition:</b> WindowMower.h:73</div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt; Peak1D &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1WindowMower_html_a0075845d43b498a236e1977a1e558301"><div class="ttname"><a href="classOpenMS_1_1WindowMower.html#a0075845d43b498a236e1977a1e558301">OpenMS::WindowMower::filterPeakSpectrumForTopNInJumpingWindow</a></div><div class="ttdeci">void filterPeakSpectrumForTopNInJumpingWindow(SpectrumType &amp;spectrum)</div><div class="ttdef"><b>Definition:</b> WindowMower.h:131</div></div>
<div class="ttc" id="classOpenMS_1_1WindowMower_html_ab3ca0a2a86becb86bb9eb373af98ce06"><div class="ttname"><a href="classOpenMS_1_1WindowMower.html#ab3ca0a2a86becb86bb9eb373af98ce06">OpenMS::WindowMower::peakcount_</a></div><div class="ttdeci">UInt peakcount_</div><div class="ttdef"><b>Definition:</b> WindowMower.h:212</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment&lt; Peak1D &gt;</a></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_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
<div class="ttc" id="group__Concept_html_gace75bfb1aba684e874dffee13738bd15"><div class="ttname"><a href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">OpenMS::DoubleReal</a></div><div class="ttdeci">double DoubleReal</div><div class="ttdoc">Double-precision real type. </div><div class="ttdef"><b>Definition:</b> Types.h:118</div></div>
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