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<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_cf999e13dd2b4cfaf0739996c075e697.html">FILTERING</a></li><li class="navelem"><a class="el" href="dir_62c1f31bb4b13c13dc21bb0b305cfde6.html">TRANSFORMERS</a></li>  </ul>
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<div class="title">MarkerMower.h</div>  </div>
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<a href="MarkerMower_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: $</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_MARKERMOWER_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_MARKERMOWER_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="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.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="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.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="PeakMarker_8h.html">OpenMS/FILTERING/TRANSFORMERS/PeakMarker.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;map&gt;</span></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;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;{</div>
<div class="line"><a name="l00052"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MarkerMower.html">   52</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MarkerMower.html">MarkerMower</a> :</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;  {</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;    <span class="comment">// @name Constructors and Destructors</span></div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;    <span class="comment">// @{</span></div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;<span class="comment"></span>    <a class="code" href="classOpenMS_1_1MarkerMower.html">MarkerMower</a>();</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1MarkerMower.html">MarkerMower</a>();</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <a class="code" href="classOpenMS_1_1MarkerMower.html">MarkerMower</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MarkerMower.html">MarkerMower</a> &amp; source);</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <a class="code" href="classOpenMS_1_1MarkerMower.html">MarkerMower</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MarkerMower.html">MarkerMower</a> &amp; source);</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <span class="comment">// @}</span></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="comment">// @name Accessors</span></div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;    <span class="comment">// @{</span></div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;<span class="comment"></span>    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> SpectrumType&gt;</div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MarkerMower.html#ac18ff4cbb43a342f27038ac8f4f99111">   74</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MarkerMower.html#ac18ff4cbb43a342f27038ac8f4f99111">filterSpectrum</a>(SpectrumType &amp; spectrum)</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">   76</span>&#160;      <span class="keyword">typedef</span> <span class="keyword">typename</span> SpectrumType::Iterator Iterator;</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;      std::map&lt;double, int&gt; marks;</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;      <span class="keywordflow">for</span> (std::vector&lt;PeakMarker *&gt;::const_iterator cvit = markers_.begin(); cvit != markers_.end(); ++cvit)</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;        std::map&lt;double, bool&gt; marked;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;        (*cvit)-&gt;apply(marked, spectrum);</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;        <span class="keywordflow">for</span> (std::map&lt;double, bool&gt;::const_iterator cmit = marked.begin(); cmit != marked.end(); ++cmit)</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;        {</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;          <span class="keywordflow">if</span> (cmit-&gt;second)</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;          {</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;            marks[cmit-&gt;first]++;</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;        }</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;      }</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      <span class="keywordflow">for</span> (Iterator it = spectrum.begin(); it != spectrum.end(); )</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="keywordflow">if</span> (marks[it-&gt;getMZ()] &gt; 0)</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;          ++it;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;        }</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;        <span class="keywordflow">else</span></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;          it = spectrum.erase(it);</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;      }</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;    }</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="keywordtype">void</span> filterPeakSpectrum(<a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; spectrum);</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;    <span class="keywordtype">void</span> filterPeakMap(<a class="code" href="classOpenMS_1_1MSExperiment.html">PeakMap</a> &amp; exp);</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"><a class="line" href="classOpenMS_1_1MarkerMower.html#af73fd15708e50e77665070023a09cc87">  109</a></span>&#160;    <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MarkerMower.html#af73fd15708e50e77665070023a09cc87">getProductName</a>()</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    {</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;      <span class="keywordflow">return</span> <span class="stringliteral">&quot;MarkerMower&quot;</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="l00115"></a><span class="lineno">  115</span>&#160;    <span class="keywordtype">void</span> insertmarker(<a class="code" href="classOpenMS_1_1PeakMarker.html">PeakMarker</a> * peak_marker);</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="comment">//TODO reimplement DefaultParamHandler::updateMembers_()</span></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;    <span class="comment">// @}</span></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;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MarkerMower.html#ad5dd2bd94eebf6bfb9cd05025dcf7d53">  123</a></span>&#160;    std::vector&lt;PeakMarker *&gt; <a class="code" href="classOpenMS_1_1MarkerMower.html#ad5dd2bd94eebf6bfb9cd05025dcf7d53">markers_</a>;</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;  };</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="preprocessor">#endif // OPENMS_COMPARISON_CLUSTERING_MARKERMOWER_H</span></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="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_1MarkerMower_html"><div class="ttname"><a href="classOpenMS_1_1MarkerMower.html">OpenMS::MarkerMower</a></div><div class="ttdoc">MarkerMower uses PeakMarker to find peaks, those that are not marked get removed. ...</div><div class="ttdef"><b>Definition:</b> MarkerMower.h:52</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_1PeakMarker_html"><div class="ttname"><a href="classOpenMS_1_1PeakMarker.html">OpenMS::PeakMarker</a></div><div class="ttdoc">PeakMarker marks peaks that seem to fulfill some criterion. </div><div class="ttdef"><b>Definition:</b> PeakMarker.h:48</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_1MarkerMower_html_ac18ff4cbb43a342f27038ac8f4f99111"><div class="ttname"><a href="classOpenMS_1_1MarkerMower.html#ac18ff4cbb43a342f27038ac8f4f99111">OpenMS::MarkerMower::filterSpectrum</a></div><div class="ttdeci">void filterSpectrum(SpectrumType &amp;spectrum)</div><div class="ttdef"><b>Definition:</b> MarkerMower.h:74</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="PeakMarker_8h_html"><div class="ttname"><a href="PeakMarker_8h.html">PeakMarker.h</a></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_1MarkerMower_html_ad5dd2bd94eebf6bfb9cd05025dcf7d53"><div class="ttname"><a href="classOpenMS_1_1MarkerMower.html#ad5dd2bd94eebf6bfb9cd05025dcf7d53">OpenMS::MarkerMower::markers_</a></div><div class="ttdeci">std::vector&lt; PeakMarker * &gt; markers_</div><div class="ttdoc">used peak markers </div><div class="ttdef"><b>Definition:</b> MarkerMower.h:123</div></div>
<div class="ttc" id="classOpenMS_1_1MarkerMower_html_af73fd15708e50e77665070023a09cc87"><div class="ttname"><a href="classOpenMS_1_1MarkerMower.html#af73fd15708e50e77665070023a09cc87">OpenMS::MarkerMower::getProductName</a></div><div class="ttdeci">static const String getProductName()</div><div class="ttdef"><b>Definition:</b> MarkerMower.h:109</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:16 using doxygen 1.8.5</font></TD>
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