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<HTML>
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<TITLE>KroenikFile Class Reference</TITLE>
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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_1KroenikFile.html">KroenikFile</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">KroenikFile Class Reference<div class="ingroups"><a class="el" href="group__FileIO.html">File IO</a></div></div> </div>
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<p><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for Kroenik (HardKloer sibling) files.
<a href="classOpenMS_1_1KroenikFile.html#details">More...</a></p>
<p><code>#include <<a class="el" href="KroenikFile_8h_source.html">OpenMS/FORMAT/KroenikFile.h</a>></code></p>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:aeee13c477b49a7de55b33172104036eb"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1KroenikFile.html#aeee13c477b49a7de55b33172104036eb">KroenikFile</a> ()</td></tr>
<tr class="memdesc:aeee13c477b49a7de55b33172104036eb"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#aeee13c477b49a7de55b33172104036eb">More...</a><br/></td></tr>
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<tr class="memitem:af798906e07af5236c12eee30d63068a9"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1KroenikFile.html#af798906e07af5236c12eee30d63068a9">~KroenikFile</a> ()</td></tr>
<tr class="memdesc:af798906e07af5236c12eee30d63068a9"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#af798906e07af5236c12eee30d63068a9">More...</a><br/></td></tr>
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<tr class="memitem:aa4e73ca60efa3ca29e203f46b5187c6c"><td class="memTemplParams" colspan="2">template<typename FeatureMapType > </td></tr>
<tr class="memitem:aa4e73ca60efa3ca29e203f46b5187c6c"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1KroenikFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">load</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, FeatureMapType &feature_map)</td></tr>
<tr class="memdesc:aa4e73ca60efa3ca29e203f46b5187c6c"><td class="mdescLeft"> </td><td class="mdescRight">Loads a Kroenik file into a featureXML. <a href="#aa4e73ca60efa3ca29e203f46b5187c6c">More...</a><br/></td></tr>
<tr class="separator:aa4e73ca60efa3ca29e203f46b5187c6c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aad1400476baaa9e6ff74301f6395c5e8"><td class="memTemplParams" colspan="2">template<typename SpectrumType > </td></tr>
<tr class="memitem:aad1400476baaa9e6ff74301f6395c5e8"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1KroenikFile.html#aad1400476baaa9e6ff74301f6395c5e8">store</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, const SpectrumType &spectrum) const </td></tr>
<tr class="memdesc:aad1400476baaa9e6ff74301f6395c5e8"><td class="mdescLeft"> </td><td class="mdescRight">Stores a featureXML as a Kroenik file. <a href="#aad1400476baaa9e6ff74301f6395c5e8">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for Kroenik (HardKloer sibling) files. </p>
<p>The first line is the header and contains the column names:<br/>
<a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a>, First Scan, Last Scan, Num of Scans, Charge, Monoisotopic Mass, Base Isotope Peak, Best Intensity, Summed Intensity, First RTime, Last RTime, Best RTime, Best Correlation, Modifications</p>
<p>Every subsequent line is a feature.</p>
<p>All properties in the file are converted to <a class="el" href="classOpenMS_1_1Feature.html" title="An LC-MS feature. ">Feature</a> properties, whereas "First Scan", "Last Scan", "Num of Scans" and "Modifications" are stored as metavalues with the following names "FirstScan", "LastScan", "NumOfScans" and "AveragineModifications".</p>
<p>The width in m/z of the overall convex hull of each feature is set to 3 Th in lack of a value provided by the Kroenik file.</p>
<dl class="section note"><dt>Note</dt><dd>Kroenik files are Tab (\t) separated files. </dd></dl>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1KroenikFile.html">KroenikFile</a> </td>
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<p>Default constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1KroenikFile.html">KroenikFile</a> </td>
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<p>Destructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void load </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>filename</em>, </td>
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<td class="paramname"><em>feature_map</em> </td>
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<p>Loads a Kroenik file into a featureXML. </p>
<p>The content of the file is stored in <code>features</code>.</p>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1FileNotFound.html" title="File not found exception. ">Exception::FileNotFound</a></td><td>is thrown if the file could not be opened </td></tr>
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1ParseError.html" title="Parse Error exception. ">Exception::ParseError</a></td><td>is thrown if an error occurs during parsing </td></tr>
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<p>References <a class="el" href="classOpenMS_1_1ConvexHull2D.html#a2e47ab249f168435217f81800a63ea37">ConvexHull2D::addPoint()</a>, <a class="el" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">BaseFeature::getCharge()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">Peak2D::getMZ()</a>, <a class="el" href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a7a25c5ed4c5f83b23ded7014aef42ad4">OpenMS::Constants::PROTON_MASS_U</a>, <a class="el" href="classOpenMS_1_1BaseFeature.html#ab595724fe9b9eb5d37011f07d90b9e0b">BaseFeature::setCharge()</a>, <a class="el" href="classOpenMS_1_1Feature.html#a8d65806c4f009695ab7bcf61eaf5546a">Feature::setConvexHulls()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">Peak2D::setIntensity()</a>, <a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">MetaInfoInterface::setMetaValue()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">Peak2D::setMZ()</a>, <a class="el" href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">Feature::setOverallQuality()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">Peak2D::setRT()</a>, <a class="el" href="classOpenMS_1_1DPosition.html#a7682888cd6f2b9f849548fb952307011">DPosition< D, TCoordinateType >::setX()</a>, <a class="el" href="classOpenMS_1_1DPosition.html#af9bb559c966c59f89d73b704d05592ad">DPosition< D, TCoordinateType >::setY()</a>, and <a class="el" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">String::split()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FileHandler.html#a5bc5a0452855c2d30d125261783b55cf">FileHandler::loadFeatures()</a>.</p>
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<td class="memname">void store </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>filename</em>, </td>
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<td class="paramtype">const SpectrumType & </td>
<td class="paramname"><em>spectrum</em> </td>
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<p>Stores a featureXML as a Kroenik file. </p>
<p>NOT IMPLEMENTED</p>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1UnableToCreateFile.html" title="Unable to create file exception. ">Exception::UnableToCreateFile</a></td><td>is thrown if the file could not be created </td></tr>
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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 11:19:30 using doxygen 1.8.5</font></TD>
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