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<a href="GaussFilter_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>
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<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>
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<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>
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<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: Alexandra Zerck $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Eva Lange $</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;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_FILTERING_SMOOTHING_GAUSSFILTER_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_SMOOTHING_GAUSSFILTER_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="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Constants_8h.html">OpenMS/CONCEPT/Constants.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="GaussFilterAlgorithm_8h.html">OpenMS/FILTERING/SMOOTHING/GaussFilterAlgorithm.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</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="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;{</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;<span class="comment">//#define DEBUG_FILTERING</span></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="classOpenMS_1_1GaussFilter.html">   73</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1GaussFilter.html">GaussFilter</a> :</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a>,</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></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;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    <a class="code" href="classOpenMS_1_1GaussFilter.html">GaussFilter</a>();</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1GaussFilter.html">GaussFilter</a>();</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> PeakType&gt;</div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GaussFilter.html#ab978eb8c2316573b1753199c8af2b041">   92</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1GaussFilter.html#ab978eb8c2316573b1753199c8af2b041">filter</a>(<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum&lt;PeakType&gt;</a> &amp; spectrum)</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;      <span class="keyword">typedef</span> std::vector&lt;double&gt; ContainerT;</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;      <span class="comment">// make sure the right data type is set</span></div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;      spectrum.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a7fd9d42016cc77134a5a518fc0478add">setType</a>(<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9ac4247d1d6a6d7690023932e58b441533">SpectrumSettings::RAWDATA</a>);</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;      <span class="keywordtype">bool</span> found_signal = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> data_size = spectrum.size();</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;      ContainerT mz_in(data_size), int_in(data_size), mz_out(data_size), int_out(data_size);</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;      <span class="comment">// copy spectrum to container</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> p = 0; p &lt; spectrum.size(); ++p)</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;        mz_in[p] = spectrum[p].getMZ();</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;        int_in[p] = spectrum[p].getIntensity();</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;      }</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;      <span class="comment">// apply filter</span></div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;      ContainerT::iterator mz_out_it = mz_out.begin();</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;      ContainerT::iterator int_out_it = int_out.begin();</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;      found_signal = gauss_algo_.filter(mz_in.begin(), mz_in.end(), int_in.begin(), mz_out_it, int_out_it);</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">// If all intensities are zero in the scan and the scan has a reasonable size, throw an exception.</span></div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      <span class="comment">// This is the case if the gaussian filter is smaller than the spacing of raw data</span></div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      <span class="keywordflow">if</span> (!found_signal &amp;&amp; spectrum.size() &gt;= 3)</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;        <a class="code" href="classOpenMS_1_1String.html">String</a> error_message = <span class="stringliteral">&quot;Found no signal. The gaussian width is probably smaller than the spacing in your profile data. Try to use a bigger width.&quot;</span>;</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;        <span class="keywordflow">if</span> (spectrum.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>() &gt; 0.0)</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;        {</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;          error_message += <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot; The error occured in the spectrum with retention time &quot;</span>) + spectrum.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>() + <span class="stringliteral">&quot;.\n&quot;</span>;</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;        std::cerr &lt;&lt; error_message;</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="keywordflow">else</span></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="comment">// copy the new data into the spectrum</span></div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;        ContainerT::iterator mz_it = mz_out.begin();</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;        ContainerT::iterator int_it = int_out.begin();</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; mz_it != mz_out.end(); mz_it++, int_it++, p++)</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;        {</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;          spectrum[p].setIntensity(*int_it);</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;          spectrum[p].setMZ(*mz_it);</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;      }</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;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> PeakType&gt;</div>
<div class="line"><a name="l00139"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GaussFilter.html#aa2a2b837042a474a9e3bec99763ce306">  139</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1GaussFilter.html#aa2a2b837042a474a9e3bec99763ce306">filter</a>(<a class="code" href="classOpenMS_1_1MSChromatogram.html">MSChromatogram&lt;PeakType&gt;</a> &amp; chromatogram)</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;    {</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;      <span class="keywordflow">if</span> (param_.getValue(<span class="stringliteral">&quot;use_ppm_tolerance&quot;</span>).toBool())</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;      {</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalArgument.html">Exception::IllegalArgument</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, </div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;          <span class="stringliteral">&quot;GaussFilter: Cannot use ppm tolerance on chromatograms&quot;</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;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;      <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum&lt;PeakType&gt;</a> filter_spectra;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSChromatogram.html">MSChromatogram&lt;PeakType&gt;::const_iterator</a> it = chromatogram.begin(); it != chromatogram.end(); ++it)</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;        filter_spectra.push_back(*it);</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;      filter(filter_spectra);</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;      chromatogram.<a class="code" href="classOpenMS_1_1MSChromatogram.html#af072fc84225ae927f7527f208ea86cbd">clear</a>(<span class="keyword">false</span>);</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum&lt;PeakType&gt;::const_iterator</a> it = filter_spectra.begin(); it != filter_spectra.end(); ++it)</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;      {</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;        chromatogram.push_back(*it);</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;      }</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;    }</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> PeakType&gt;</div>
<div class="line"><a name="l00168"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GaussFilter.html#ad4b88e98d5f5de8b90ba2c68ecdddc1e">  168</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1GaussFilter.html#ad4b88e98d5f5de8b90ba2c68ecdddc1e">filterExperiment</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;PeakType&gt;</a> &amp; map)</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;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> progress = 0;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;      startProgress(0, map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() + map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>().size(), <span class="stringliteral">&quot;smoothing data&quot;</span>);</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++i)</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;        filter(map[i]);</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;        setProgress(++progress);</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;      }</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>().size(); ++i)</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;        filter(map.<a class="code" href="classOpenMS_1_1MSExperiment.html#ae9be60694b267dc26b3e79a125646e25">getChromatogram</a>(i));</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;        setProgress(++progress);</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;      }</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;      endProgress();</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">  185</span>&#160;<span class="keyword">protected</span>:</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"><a class="line" href="classOpenMS_1_1GaussFilter.html#afe07453148ee07d964015f6595d7b593">  187</a></span>&#160;    <a class="code" href="classOpenMS_1_1GaussFilterAlgorithm.html">GaussFilterAlgorithm</a> <a class="code" href="classOpenMS_1_1GaussFilter.html#afe07453148ee07d964015f6595d7b593">gauss_algo_</a>;</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;</div>
<div class="line"><a name="l00190"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GaussFilter.html#a511870c7bb018e452eff999d65bc02a5">  190</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1GaussFilter.html#a511870c7bb018e452eff999d65bc02a5">spacing_</a>;</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">// Docu in base class</span></div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> updateMembers_();</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;</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1MSChromatogram_html"><div class="ttname"><a href="classOpenMS_1_1MSChromatogram.html">OpenMS::MSChromatogram</a></div><div class="ttdoc">The representation of a chromatogram. </div><div class="ttdef"><b>Definition:</b> MSChromatogram.h:53</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilter_html_aa2a2b837042a474a9e3bec99763ce306"><div class="ttname"><a href="classOpenMS_1_1GaussFilter.html#aa2a2b837042a474a9e3bec99763ce306">OpenMS::GaussFilter::filter</a></div><div class="ttdeci">void filter(MSChromatogram&lt; PeakType &gt; &amp;chromatogram)</div><div class="ttdef"><b>Definition:</b> GaussFilter.h:139</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="GaussFilterAlgorithm_8h_html"><div class="ttname"><a href="GaussFilterAlgorithm_8h.html">GaussFilterAlgorithm.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ab7b974cef152e339967fce62f49de0d9ac4247d1d6a6d7690023932e58b441533"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9ac4247d1d6a6d7690023932e58b441533">OpenMS::SpectrumSettings::RAWDATA</a></div><div class="ttdoc">Raw data (also called profile data) </div><div class="ttdef"><b>Definition:</b> SpectrumSettings.h:75</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="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt; PeakType &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1IllegalArgument_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1IllegalArgument.html">OpenMS::Exception::IllegalArgument</a></div><div class="ttdoc">A method or algorithm argument contains illegal values. </div><div class="ttdef"><b>Definition:</b> Exception.h:634</div></div>
<div class="ttc" id="Constants_8h_html"><div class="ttname"><a href="Constants_8h.html">Constants.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ae9be60694b267dc26b3e79a125646e25"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ae9be60694b267dc26b3e79a125646e25">OpenMS::MSExperiment::getChromatogram</a></div><div class="ttdeci">MSChromatogram&lt; ChromatogramPeakType &gt; &amp; getChromatogram(Size id)</div><div class="ttdoc">returns a single chromatogram </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:774</div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilter_html_afe07453148ee07d964015f6595d7b593"><div class="ttname"><a href="classOpenMS_1_1GaussFilter.html#afe07453148ee07d964015f6595d7b593">OpenMS::GaussFilter::gauss_algo_</a></div><div class="ttdeci">GaussFilterAlgorithm gauss_algo_</div><div class="ttdef"><b>Definition:</b> GaussFilter.h:187</div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilterAlgorithm_html"><div class="ttname"><a href="classOpenMS_1_1GaussFilterAlgorithm.html">OpenMS::GaussFilterAlgorithm</a></div><div class="ttdoc">This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform prof...</div><div class="ttdef"><b>Definition:</b> GaussFilterAlgorithm.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilter_html_a511870c7bb018e452eff999d65bc02a5"><div class="ttname"><a href="classOpenMS_1_1GaussFilter.html#a511870c7bb018e452eff999d65bc02a5">OpenMS::GaussFilter::spacing_</a></div><div class="ttdeci">DoubleReal spacing_</div><div class="ttdoc">The spacing of the pre-tabulated kernel coefficients. </div><div class="ttdef"><b>Definition:</b> GaussFilter.h:190</div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilter_html"><div class="ttname"><a href="classOpenMS_1_1GaussFilter.html">OpenMS::GaussFilter</a></div><div class="ttdoc">This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform prof...</div><div class="ttdef"><b>Definition:</b> GaussFilter.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_a7fd9d42016cc77134a5a518fc0478add"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#a7fd9d42016cc77134a5a518fc0478add">OpenMS::SpectrumSettings::setType</a></div><div class="ttdeci">void setType(SpectrumType type)</div><div class="ttdoc">sets the spectrum type </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_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<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="classOpenMS_1_1MSSpectrum_html_a3da529bd3240fa0d7148484bbef0b9d7"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">OpenMS::MSSpectrum::getRT</a></div><div class="ttdeci">DoubleReal getRT() const </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:215</div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilter_html_ad4b88e98d5f5de8b90ba2c68ecdddc1e"><div class="ttname"><a href="classOpenMS_1_1GaussFilter.html#ad4b88e98d5f5de8b90ba2c68ecdddc1e">OpenMS::GaussFilter::filterExperiment</a></div><div class="ttdeci">void filterExperiment(MSExperiment&lt; PeakType &gt; &amp;map)</div><div class="ttdoc">Smoothes an MSExperiment containing profile data. </div><div class="ttdef"><b>Definition:</b> GaussFilter.h:168</div></div>
<div class="ttc" id="classOpenMS_1_1MSChromatogram_html_af072fc84225ae927f7527f208ea86cbd"><div class="ttname"><a href="classOpenMS_1_1MSChromatogram.html#af072fc84225ae927f7527f208ea86cbd">OpenMS::MSChromatogram::clear</a></div><div class="ttdeci">void clear(bool clear_meta_data)</div><div class="ttdoc">Clears all data and meta data. </div><div class="ttdef"><b>Definition:</b> MSChromatogram.h:564</div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilter_html_ab978eb8c2316573b1753199c8af2b041"><div class="ttname"><a href="classOpenMS_1_1GaussFilter.html#ab978eb8c2316573b1753199c8af2b041">OpenMS::GaussFilter::filter</a></div><div class="ttdeci">void filter(MSSpectrum&lt; PeakType &gt; &amp;spectrum)</div><div class="ttdoc">Smoothes an MSSpectrum containing profile data. </div><div class="ttdef"><b>Definition:</b> GaussFilter.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a02fccfed86a20f8bd0f6b98c23fadb2e"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">OpenMS::MSExperiment::getChromatograms</a></div><div class="ttdeci">const std::vector&lt; MSChromatogram&lt; ChromatogramPeakType &gt; &gt; &amp; getChromatograms() const </div><div class="ttdoc">returns the chromatogram list </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:768</div></div>
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