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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a></li> </ul>
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<div class="title">ChromatogramTools Class Reference<div class="ingroups"><a class="el" href="group__Kernel.html">Kernel</a></div></div> </div>
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<p>Conversion class to interconvert chromatograms.
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<a href="classOpenMS_1_1ChromatogramTools.html#details">More...</a></p>
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<p><code>#include <<a class="el" href="ChromatogramTools_8h_source.html">OpenMS/KERNEL/ChromatogramTools.h</a>></code></p>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
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Public Member Functions</h2></td></tr>
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<tr><td colspan="2"><div class="groupHeader">Constructors and destructors</div></td></tr>
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<tr class="memitem:a41bd54ebbe20b4f33112d5a1e979a870"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramTools.html#a41bd54ebbe20b4f33112d5a1e979a870">ChromatogramTools</a> ()</td></tr>
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<tr class="memdesc:a41bd54ebbe20b4f33112d5a1e979a870"><td class="mdescLeft"> </td><td class="mdescRight">default constructor <a href="#a41bd54ebbe20b4f33112d5a1e979a870">More...</a><br/></td></tr>
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<tr class="memitem:afda6458ea9e5f8f923907a7afe8c9e63"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramTools.html#afda6458ea9e5f8f923907a7afe8c9e63">ChromatogramTools</a> (const <a class="el" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a> &)</td></tr>
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<tr class="memdesc:afda6458ea9e5f8f923907a7afe8c9e63"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#afda6458ea9e5f8f923907a7afe8c9e63">More...</a><br/></td></tr>
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<tr class="memitem:adc92fcb859234049c3cebcd178b41ff0"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramTools.html#adc92fcb859234049c3cebcd178b41ff0">~ChromatogramTools</a> ()</td></tr>
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<tr class="memdesc:adc92fcb859234049c3cebcd178b41ff0"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#adc92fcb859234049c3cebcd178b41ff0">More...</a><br/></td></tr>
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<tr><td colspan="2"><div class="groupHeader">Accessors</div></td></tr>
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<tr class="memitem:a180cb4974eaf3d4dea0de5326b132951"><td class="memTemplParams" colspan="2">template<typename ExperimentType > </td></tr>
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<tr class="memitem:a180cb4974eaf3d4dea0de5326b132951"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramTools.html#a180cb4974eaf3d4dea0de5326b132951">convertChromatogramsToSpectra</a> (ExperimentType &exp)</td></tr>
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<tr class="memdesc:a180cb4974eaf3d4dea0de5326b132951"><td class="mdescLeft"> </td><td class="mdescRight">converts the chromatogram to a list of spectra with instrument settings SRM <a href="#a180cb4974eaf3d4dea0de5326b132951">More...</a><br/></td></tr>
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<tr class="memitem:af3ff28dcfb8f80c33a57605672ebb0b1"><td class="memTemplParams" colspan="2">template<typename ExperimentType > </td></tr>
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<tr class="memitem:af3ff28dcfb8f80c33a57605672ebb0b1"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramTools.html#af3ff28dcfb8f80c33a57605672ebb0b1">convertSpectraToChromatograms</a> (ExperimentType &exp, bool remove_spectra=false)</td></tr>
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<tr class="memdesc:af3ff28dcfb8f80c33a57605672ebb0b1"><td class="mdescLeft"> </td><td class="mdescRight">converts e.g. SRM spectra to chromatograms <a href="#af3ff28dcfb8f80c33a57605672ebb0b1">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>Conversion class to interconvert chromatograms. </p>
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<p>There are basically two methods implemented, conversion of chromatograms into spectra representation and vice versa. </p>
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</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a> </td>
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<td class="paramname"></td><td>)</td>
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<p>default constructor </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a> & </td>
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<p>copy constructor </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a> </td>
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<td class="paramname"></td><td>)</td>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void convertChromatogramsToSpectra </td>
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<td class="paramtype">ExperimentType & </td>
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<td class="paramname"><em>exp</em></td><td>)</td>
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<p>converts the chromatogram to a list of spectra with instrument settings SRM </p>
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<p>This conversion may be necessary as most of the spectra formats do not support chromatograms, except of mzML. However, most formats support e.g. SRM chromatogram as a list of spectra with instrument settings SRM and a separate spectrum for each data point. The disadvantage of storing chromatograms in spectra is its exhaustive memory consumption. </p>
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<p>References <a class="el" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdace5f1115eae62ba8c2527d50f67548aa">ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM</a>, <a class="el" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">Peak2D::setMZ()</a>, <a class="el" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">InstrumentSettings::SIM</a>, and <a class="el" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FileHandler.html#a4a8354ef45f8a0eac5a5038b3a025f37">FileHandler::storeExperiment()</a>.</p>
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<td class="memname">void convertSpectraToChromatograms </td>
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<td class="paramtype">ExperimentType & </td>
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<td class="paramname"><em>exp</em>, </td>
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<td class="paramtype">bool </td>
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<td class="paramname"><em>remove_spectra</em> = <code>false</code> </td>
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<p>converts e.g. SRM spectra to chromatograms </p>
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<p>This conversion is necessary to convert chromatograms, e.g. from SRM or MRM experiments to real chromatograms. mzML 1.1.0 has support for chromatograms which can be stored much more efficiently than spectra based chromatograms. However, most other file formats do not support chromatograms.</p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">exp</td><td>the experiment to be converted. </td></tr>
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<tr><td class="paramname">remove_spectra</td><td>if set to true, the chromatogram spectra are removed from the experiment. </td></tr>
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<p>References <a class="el" href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a>, <a class="el" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a>, <a class="el" href="classOpenMS_1_1Product.html#a94893c6a36a1281bfd8ff45c0199bd35">Product::setMZ()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">Peak2D::setRT()</a>, and <a class="el" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FileHandler.html#a408091416e0e1f6019abd59bdb6a9269">FileHandler::loadExperiment()</a>.</p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5</font></TD>
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