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<a href="OpenSwathHelper_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>
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<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Hannes Roest $</span></div>
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<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHHELPER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHHELPER_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="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.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="TargetedExperiment_8h.html">OpenMS/ANALYSIS/TARGETED/TargetedExperiment.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="TransitionExperiment_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/TransitionExperiment.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="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;{</div>
<div class="line"><a name="l00047"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OpenSwathHelper.html">   47</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1OpenSwathHelper.html">OpenSwathHelper</a></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;  {</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> selectSwathTransitions(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a>&amp; targeted_exp,</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;                                       <a class="code" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a>&amp; transition_exp_used, <span class="keywordtype">double</span> min_upper_edge_dist,</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;                                       <span class="keywordtype">double</span> lower, <span class="keywordtype">double</span> upper);</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> checkSwathMap(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment&lt;Peak1D&gt;</a>&amp; swath_map,</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;                              <span class="keywordtype">double</span>&amp; lower, <span class="keywordtype">double</span>&amp; upper);</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> selectSwathTransitions(<span class="keyword">const</span> <a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a>&amp; targeted_exp,</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;                                       <a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a>&amp; transition_exp_used, <span class="keywordtype">double</span> min_upper_edge_dist,</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;                                       <span class="keywordtype">double</span> lower, <span class="keywordtype">double</span> upper);</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> TargetedExperimentT&gt;</div>
<div class="line"><a name="l00067"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OpenSwathHelper.html#a58f5957aa8b970648d7cb611c76ed0f9">   67</a></span>&#160;    <span class="keyword">static</span> <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1OpenSwathHelper.html#a58f5957aa8b970648d7cb611c76ed0f9">checkSwathMapAndSelectTransitions</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment&lt;Peak1D&gt;</a>&amp; exp,</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;                                                  <span class="keyword">const</span> TargetedExperimentT&amp; targeted_exp, TargetedExperimentT&amp; transition_exp_used, <span class="keywordtype">double</span> min_upper_edge_dist)</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    {</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;      <span class="keywordflow">if</span> (exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() == 0 || exp[0].getPrecursors().<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() == 0)</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;      {</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;        std::cerr &lt;&lt; <span class="stringliteral">&quot;WARNING: File &quot;</span> &lt;&lt; exp.<a class="code" href="classOpenMS_1_1DocumentIdentifier.html#aee7ac99be667b810be1b096691c58efa">getLoadedFilePath</a>()</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;                  &lt;&lt; <span class="stringliteral">&quot; does not have any experiments or any precursors. Is it a SWATH map? &quot;</span></div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;                  &lt;&lt; <span class="stringliteral">&quot;I will move to the next map.&quot;</span></div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;                  &lt;&lt; std::endl;</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;      }</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;      <span class="keywordtype">double</span> upper, lower;</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;      <a class="code" href="classOpenMS_1_1OpenSwathHelper.html#ad407a5263ca24e0d1f66817ed1de792b">OpenSwathHelper::checkSwathMap</a>(exp, lower, upper);</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;      <a class="code" href="classOpenMS_1_1OpenSwathHelper.html#a36307242d32a7a1619073838a87ce671">OpenSwathHelper::selectSwathTransitions</a>(targeted_exp, transition_exp_used, min_upper_edge_dist, lower, upper);</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;      <span class="keywordflow">if</span> (transition_exp_used.getTransitions().size() == 0)</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;      {</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;        std::cerr &lt;&lt; <span class="stringliteral">&quot;WARNING: For File &quot;</span> &lt;&lt; exp.<a class="code" href="classOpenMS_1_1DocumentIdentifier.html#aee7ac99be667b810be1b096691c58efa">getLoadedFilePath</a>()</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;                  &lt;&lt; <span class="stringliteral">&quot; no transition were within the precursor window of &quot;</span> &lt;&lt; lower &lt;&lt; <span class="stringliteral">&quot; to &quot;</span> &lt;&lt; upper</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;                  &lt;&lt; <span class="stringliteral">&quot;I will move to the next map.&quot;</span></div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;                  &lt;&lt; std::endl;</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</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="keywordflow">return</span> <span class="keyword">true</span>;</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;</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;  };</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;}</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;<span class="preprocessor">#endif</span></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_1OpenSwathHelper_html"><div class="ttname"><a href="classOpenMS_1_1OpenSwathHelper.html">OpenMS::OpenSwathHelper</a></div><div class="ttdoc">A helper class that is used by several OpenSWATH tools. </div><div class="ttdef"><b>Definition:</b> OpenSwathHelper.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1DocumentIdentifier_html_aee7ac99be667b810be1b096691c58efa"><div class="ttname"><a href="classOpenMS_1_1DocumentIdentifier.html#aee7ac99be667b810be1b096691c58efa">OpenMS::DocumentIdentifier::getLoadedFilePath</a></div><div class="ttdeci">const String &amp; getLoadedFilePath() const </div><div class="ttdoc">get the file_name_ which is the absolute path to the file loaded from </div></div>
<div class="ttc" id="TransitionExperiment_8h_html"><div class="ttname"><a href="TransitionExperiment_8h.html">TransitionExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1OpenSwathHelper_html_a58f5957aa8b970648d7cb611c76ed0f9"><div class="ttname"><a href="classOpenMS_1_1OpenSwathHelper.html#a58f5957aa8b970648d7cb611c76ed0f9">OpenMS::OpenSwathHelper::checkSwathMapAndSelectTransitions</a></div><div class="ttdeci">static bool checkSwathMapAndSelectTransitions(const OpenMS::MSExperiment&lt; Peak1D &gt; &amp;exp, const TargetedExperimentT &amp;targeted_exp, TargetedExperimentT &amp;transition_exp_used, double min_upper_edge_dist)</div><div class="ttdef"><b>Definition:</b> OpenSwathHelper.h:67</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="TargetedExperiment_8h_html"><div class="ttname"><a href="TargetedExperiment_8h.html">TargetedExperiment.h</a></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="classOpenMS_1_1TargetedExperiment_html"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a></div><div class="ttdoc">This class stores an prediction of an SRM/MRM transition. </div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:53</div></div>
<div class="ttc" id="structOpenSwath_1_1LightTargetedExperiment_html"><div class="ttname"><a href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a></div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:120</div></div>
<div class="ttc" id="classOpenMS_1_1OpenSwathHelper_html_a36307242d32a7a1619073838a87ce671"><div class="ttname"><a href="classOpenMS_1_1OpenSwathHelper.html#a36307242d32a7a1619073838a87ce671">OpenMS::OpenSwathHelper::selectSwathTransitions</a></div><div class="ttdeci">static void selectSwathTransitions(const OpenMS::TargetedExperiment &amp;targeted_exp, OpenMS::TargetedExperiment &amp;transition_exp_used, double min_upper_edge_dist, double lower, double upper)</div><div class="ttdoc">Select transitions between lower and upper and write them into the new TargetedExperiment. </div></div>
<div class="ttc" id="classOpenMS_1_1OpenSwathHelper_html_ad407a5263ca24e0d1f66817ed1de792b"><div class="ttname"><a href="classOpenMS_1_1OpenSwathHelper.html#ad407a5263ca24e0d1f66817ed1de792b">OpenMS::OpenSwathHelper::checkSwathMap</a></div><div class="ttdeci">static void checkSwathMap(const OpenMS::MSExperiment&lt; Peak1D &gt; &amp;swath_map, double &amp;lower, double &amp;upper)</div><div class="ttdoc">Get the lower / upper offset for this SWATH map and do some sanity checks. </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 11:19:19 using doxygen 1.8.5</font></TD>
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