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<a href="DataAccessHelper_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>
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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>
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<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</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>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Hannes Roest $</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_ANALYSIS_OPENSWATH_DATAACCESS_DATAACCESSHELPER_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_DATAACCESS_DATAACCESSHELPER_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;fstream&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;boost/numeric/conversion/cast.hpp&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;<a class="code" href="MSSpectrum_8h.html">OpenMS/KERNEL/MSSpectrum.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSChromatogram_8h.html">OpenMS/KERNEL/MSChromatogram.h</a>&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</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="l00045"></a><span class="lineno">   45</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="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h</a>&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;{</div>
<div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OpenSwathDataAccessHelper.html">   54</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1OpenSwathDataAccessHelper.html">OpenSwathDataAccessHelper</a></div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;  {</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> convertToOpenMSSpectrum(<span class="keyword">const</span> <a class="code" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> sptr, <a class="code" href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt;&gt;</a> &amp; spectrum);</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    <span class="keyword">static</span> <a class="code" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> convertToSpectrumPtr(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt;&gt;</a> &amp; spectrum);</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> convertToOpenMSChromatogram(<a class="code" href="classOpenMS_1_1MSChromatogram.html">OpenMS::MSChromatogram&lt;&gt;</a> &amp; chromatogram, <span class="keyword">const</span> <a class="code" href="namespaceOpenSwath.html#a159d76e81a041373752ffca5f953a5ca">OpenSwath::ChromatogramPtr</a> cptr);</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> convertTargetedExp(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> &amp; transition_exp_, <a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a> &amp; transition_exp);</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> convertPeptideToAASequence(<span class="keyword">const</span> <a class="code" href="structOpenSwath_1_1LightPeptide.html">OpenSwath::LightPeptide</a> &amp; peptide, <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> &amp; aa_sequence);</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;  };</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;} <span class="comment">//end namespace OpenMS</span></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="preprocessor">#endif</span></div>
<div class="ttc" id="namespaceOpenSwath_html_a159d76e81a041373752ffca5f953a5ca"><div class="ttname"><a href="namespaceOpenSwath.html#a159d76e81a041373752ffca5f953a5ca">OpenSwath::ChromatogramPtr</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI typedef boost::shared_ptr&lt; Chromatogram &gt; ChromatogramPtr</div><div class="ttdef"><b>Definition:</b> ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:152</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="TransitionExperiment_8h_html"><div class="ttname"><a href="TransitionExperiment_8h.html">TransitionExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1AASequence_html"><div class="ttname"><a href="classOpenMS_1_1AASequence.html">OpenMS::AASequence</a></div><div class="ttdoc">Representation of a peptide/protein sequence. </div><div class="ttdef"><b>Definition:</b> AASequence.h:84</div></div>
<div class="ttc" id="MSSpectrum_8h_html"><div class="ttname"><a href="MSSpectrum_8h.html">MSSpectrum.h</a></div></div>
<div class="ttc" id="structOpenSwath_1_1LightPeptide_html"><div class="ttname"><a href="structOpenSwath_1_1LightPeptide.html">OpenSwath::LightPeptide</a></div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:99</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt;&gt;</a></div></div>
<div class="ttc" id="namespaceOpenSwath_html_a93e7d6a13eb66ccae0357dbae6f33523"><div class="ttname"><a href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI typedef boost::shared_ptr&lt; Spectrum &gt; SpectrumPtr</div><div class="ttdef"><b>Definition:</b> ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:227</div></div>
<div class="ttc" id="classOpenMS_1_1OpenSwathDataAccessHelper_html"><div class="ttname"><a href="classOpenMS_1_1OpenSwathDataAccessHelper.html">OpenMS::OpenSwathDataAccessHelper</a></div><div class="ttdoc">Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interface...</div><div class="ttdef"><b>Definition:</b> DataAccessHelper.h:54</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_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="MSChromatogram_8h_html"><div class="ttname"><a href="MSChromatogram_8h.html">MSChromatogram.h</a></div></div>
<div class="ttc" id="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h_html"><div class="ttname"><a href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h.html">ISpectrumAccess.h</a></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>
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