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<a href="MassTraceDetection_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Erhan Kenar $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Erhan Kenar, Holger Franken $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FILTERING_DATAREDUCTION_MASSTRACEDETECTION_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FILTERING_DATAREDUCTION_MASSTRACEDETECTION_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="MassTrace_8h.html">OpenMS/KERNEL/MassTrace.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> {</div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MassTraceDetection.html"> 60</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MassTraceDetection.html">MassTraceDetection</a> :</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>,</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  {</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <a class="code" href="classOpenMS_1_1MassTraceDetection.html">MassTraceDetection</a>();</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1MassTraceDetection.html">MassTraceDetection</a>();</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordtype">void</span> updateIterativeWeightedMeanMZ(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> &, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> &, <a class="code" href="classdouble.html">DoubleReal</a> &, <a class="code" href="classdouble.html">DoubleReal</a> &, <a class="code" href="classdouble.html">DoubleReal</a> &);</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="comment">// void filterByPeakWidth(std::vector<MassTrace>&, std::vector<MassTrace>&);</span></div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordtype">void</span> run(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<Peak1D></a> &, std::vector<MassTrace> &);</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">void</span> run(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<Peak1D>::ConstAreaIterator</a> & begin, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<Peak1D>::ConstAreaIterator</a> & end, std::vector<MassTrace> & found_masstraces);</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="comment">// parameter stuff</span></div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MassTraceDetection.html#a975bbb72e95f7b92e1a2a1b508edddab"> 92</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MassTraceDetection.html#a975bbb72e95f7b92e1a2a1b508edddab">mass_error_ppm_</a>;</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MassTraceDetection.html#ad2875064bd79c6c81d73a00b78bf18f5"> 93</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MassTraceDetection.html#ad2875064bd79c6c81d73a00b78bf18f5">noise_threshold_int_</a>;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MassTraceDetection.html#a76c1c46fd8e4bd97b79b375db100a5ef"> 94</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MassTraceDetection.html#a76c1c46fd8e4bd97b79b375db100a5ef">chrom_peak_snr_</a>;</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MassTraceDetection.html#a2f99b62df5c6a6da9c518da68dbbb8fb"> 96</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MassTraceDetection.html#a2f99b62df5c6a6da9c518da68dbbb8fb">trace_termination_criterion_</a>;</div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MassTraceDetection.html#a5c95c345f9f9250b9a79bc7ccffec994"> 97</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1MassTraceDetection.html#a5c95c345f9f9250b9a79bc7ccffec994">trace_termination_outliers_</a>;</div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MassTraceDetection.html#a9b2be3129cd1400c52aa89bede427eae"> 98</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MassTraceDetection.html#a9b2be3129cd1400c52aa89bede427eae">min_sample_rate_</a>;</div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MassTraceDetection.html#a97524db7f0b46853fc93ccb0434054de"> 99</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MassTraceDetection.html#a97524db7f0b46853fc93ccb0434054de">min_trace_length_</a>;</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MassTraceDetection.html#a010b1c190db3c218f2b7347d479ce994"> 100</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MassTraceDetection.html#a010b1c190db3c218f2b7347d479ce994">max_trace_length_</a>;</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
<div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MassTraceDetection.html#ad0503b35c5440d9f490b0a47a176bdcd"> 102</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MassTraceDetection.html#ad0503b35c5440d9f490b0a47a176bdcd">reestimate_mt_sd_</a>;</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  };</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> }</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> <span class="preprocessor">#endif // OPENMS_FILTERING_DATAREDUCTION_MASSTRACEDETECTION_H</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="MassTrace_8h_html"><div class="ttname"><a href="MassTrace_8h.html">MassTrace.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MassTraceDetection_html_a975bbb72e95f7b92e1a2a1b508edddab"><div class="ttname"><a href="classOpenMS_1_1MassTraceDetection.html#a975bbb72e95f7b92e1a2a1b508edddab">OpenMS::MassTraceDetection::mass_error_ppm_</a></div><div class="ttdeci">DoubleReal mass_error_ppm_</div><div class="ttdef"><b>Definition:</b> MassTraceDetection.h:92</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="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1MassTraceDetection_html_a9b2be3129cd1400c52aa89bede427eae"><div class="ttname"><a href="classOpenMS_1_1MassTraceDetection.html#a9b2be3129cd1400c52aa89bede427eae">OpenMS::MassTraceDetection::min_sample_rate_</a></div><div class="ttdeci">DoubleReal min_sample_rate_</div><div class="ttdef"><b>Definition:</b> MassTraceDetection.h:98</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_1MassTraceDetection_html_a5c95c345f9f9250b9a79bc7ccffec994"><div class="ttname"><a href="classOpenMS_1_1MassTraceDetection.html#a5c95c345f9f9250b9a79bc7ccffec994">OpenMS::MassTraceDetection::trace_termination_outliers_</a></div><div class="ttdeci">Size trace_termination_outliers_</div><div class="ttdef"><b>Definition:</b> MassTraceDetection.h:97</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_1MassTraceDetection_html_a010b1c190db3c218f2b7347d479ce994"><div class="ttname"><a href="classOpenMS_1_1MassTraceDetection.html#a010b1c190db3c218f2b7347d479ce994">OpenMS::MassTraceDetection::max_trace_length_</a></div><div class="ttdeci">DoubleReal max_trace_length_</div><div class="ttdef"><b>Definition:</b> MassTraceDetection.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1MassTraceDetection_html_ad0503b35c5440d9f490b0a47a176bdcd"><div class="ttname"><a href="classOpenMS_1_1MassTraceDetection.html#ad0503b35c5440d9f490b0a47a176bdcd">OpenMS::MassTraceDetection::reestimate_mt_sd_</a></div><div class="ttdeci">bool reestimate_mt_sd_</div><div class="ttdef"><b>Definition:</b> MassTraceDetection.h:102</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment< Peak1D ></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_1MassTraceDetection_html_a76c1c46fd8e4bd97b79b375db100a5ef"><div class="ttname"><a href="classOpenMS_1_1MassTraceDetection.html#a76c1c46fd8e4bd97b79b375db100a5ef">OpenMS::MassTraceDetection::chrom_peak_snr_</a></div><div class="ttdeci">DoubleReal chrom_peak_snr_</div><div class="ttdef"><b>Definition:</b> MassTraceDetection.h:94</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_1MassTraceDetection_html_a97524db7f0b46853fc93ccb0434054de"><div class="ttname"><a href="classOpenMS_1_1MassTraceDetection.html#a97524db7f0b46853fc93ccb0434054de">OpenMS::MassTraceDetection::min_trace_length_</a></div><div class="ttdeci">DoubleReal min_trace_length_</div><div class="ttdef"><b>Definition:</b> MassTraceDetection.h:99</div></div>
<div class="ttc" id="classOpenMS_1_1MassTraceDetection_html_a2f99b62df5c6a6da9c518da68dbbb8fb"><div class="ttname"><a href="classOpenMS_1_1MassTraceDetection.html#a2f99b62df5c6a6da9c518da68dbbb8fb">OpenMS::MassTraceDetection::trace_termination_criterion_</a></div><div class="ttdeci">String trace_termination_criterion_</div><div class="ttdef"><b>Definition:</b> MassTraceDetection.h:96</div></div>
<div class="ttc" id="classOpenMS_1_1MassTraceDetection_html"><div class="ttname"><a href="classOpenMS_1_1MassTraceDetection.html">OpenMS::MassTraceDetection</a></div><div class="ttdoc">A mass trace extraction method that gathers peaks similar in m/z and moving along retention time...</div><div class="ttdef"><b>Definition:</b> MassTraceDetection.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1MassTraceDetection_html_ad2875064bd79c6c81d73a00b78bf18f5"><div class="ttname"><a href="classOpenMS_1_1MassTraceDetection.html#ad2875064bd79c6c81d73a00b78bf18f5">OpenMS::MassTraceDetection::noise_threshold_int_</a></div><div class="ttdeci">DoubleReal noise_threshold_int_</div><div class="ttdef"><b>Definition:</b> MassTraceDetection.h:93</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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