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<HTML>
<HEAD>
<TITLE>MascotXMLFile 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_1MascotXMLFile.html">MascotXMLFile</a></li> </ul>
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<div class="header">
<div class="summary">
<a href="#pub-types">Public Types</a> |
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pub-static-methods">Static Public Member Functions</a> |
<a href="classOpenMS_1_1MascotXMLFile-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">MascotXMLFile Class Reference<div class="ingroups"><a class="el" href="group__FileIO.html">File IO</a></div></div> </div>
</div><!--header-->
<div class="contents">
<p>Used to load MascotXML files.
<a href="classOpenMS_1_1MascotXMLFile.html#details">More...</a></p>
<p><code>#include <<a class="el" href="MascotXMLFile_8h_source.html">OpenMS/FORMAT/MascotXMLFile.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for MascotXMLFile:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1MascotXMLFile.png" usemap="#MascotXMLFile_map" alt=""/>
<map id="MascotXMLFile_map" name="MascotXMLFile_map">
<area href="classOpenMS_1_1Internal_1_1XMLFile.html" title="Base class for loading/storing XML files that have a handler derived from XMLHandler. " alt="XMLFile" shape="rect" coords="0,0,101,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:a1f47840b5fb63cf1ad9f823ac2e12227"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6a5b7dd69471128e9cb680649b058f4f">Internal::MascotXMLHandler::RTMapping</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a></td></tr>
<tr class="separator:a1f47840b5fb63cf1ad9f823ac2e12227"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:ad2d1d74ff8feebb65c22e70b1f03ba76"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MascotXMLFile.html#ad2d1d74ff8feebb65c22e70b1f03ba76">MascotXMLFile</a> ()</td></tr>
<tr class="memdesc:ad2d1d74ff8feebb65c22e70b1f03ba76"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#ad2d1d74ff8feebb65c22e70b1f03ba76">More...</a><br/></td></tr>
<tr class="separator:ad2d1d74ff8feebb65c22e70b1f03ba76"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0c93745196d704459546675afaa970ac"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MascotXMLFile.html#a0c93745196d704459546675afaa970ac">load</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &protein_identification, std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &id_data, const <a class="el" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a> &rt_mapping=<a class="el" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a>(), const <a class="el" href="classOpenMS_1_1String.html">String</a> &scan_regex="")</td></tr>
<tr class="memdesc:a0c93745196d704459546675afaa970ac"><td class="mdescLeft"> </td><td class="mdescRight">loads data from a Mascot XML file <a href="#a0c93745196d704459546675afaa970ac">More...</a><br/></td></tr>
<tr class="separator:a0c93745196d704459546675afaa970ac"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a23387dae923d27e1c30da7cbb34ec501"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MascotXMLFile.html#a23387dae923d27e1c30da7cbb34ec501">load</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &protein_identification, std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &id_data, std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, std::vector< <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> > > &peptides, const <a class="el" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a> &rt_mapping=<a class="el" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a>(), const <a class="el" href="classOpenMS_1_1String.html">String</a> &scan_regex="")</td></tr>
<tr class="memdesc:a23387dae923d27e1c30da7cbb34ec501"><td class="mdescLeft"> </td><td class="mdescRight">loads data from a Mascot XML file <a href="#a23387dae923d27e1c30da7cbb34ec501">More...</a><br/></td></tr>
<tr class="separator:a23387dae923d27e1c30da7cbb34ec501"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1Internal_1_1XMLFile')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td></tr>
<tr class="memitem:a5288a663fb130ba112c205bd7c556fd4 inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#a5288a663fb130ba112c205bd7c556fd4">XMLFile</a> ()</td></tr>
<tr class="memdesc:a5288a663fb130ba112c205bd7c556fd4 inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a5288a663fb130ba112c205bd7c556fd4">More...</a><br/></td></tr>
<tr class="separator:a5288a663fb130ba112c205bd7c556fd4 inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab6a2f018df297124fba778512994282a inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#ab6a2f018df297124fba778512994282a">XMLFile</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &schema_location, const <a class="el" href="classOpenMS_1_1String.html">String</a> &version)</td></tr>
<tr class="memdesc:ab6a2f018df297124fba778512994282a inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="mdescLeft"> </td><td class="mdescRight">Constructor that sets the schema location. <a href="#ab6a2f018df297124fba778512994282a">More...</a><br/></td></tr>
<tr class="separator:ab6a2f018df297124fba778512994282a inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae64064342fc97bdd2008c5a91cd6d9de inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#ae64064342fc97bdd2008c5a91cd6d9de">~XMLFile</a> ()</td></tr>
<tr class="memdesc:ae64064342fc97bdd2008c5a91cd6d9de inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#ae64064342fc97bdd2008c5a91cd6d9de">More...</a><br/></td></tr>
<tr class="separator:ae64064342fc97bdd2008c5a91cd6d9de inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2f3216da86d8ced03f1b102a5c2e886c inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#a2f3216da86d8ced03f1b102a5c2e886c">isValid</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, std::ostream &os=std::cerr)</td></tr>
<tr class="memdesc:a2f3216da86d8ced03f1b102a5c2e886c inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="mdescLeft"> </td><td class="mdescRight">Checks if a file validates against the XML schema. <a href="#a2f3216da86d8ced03f1b102a5c2e886c">More...</a><br/></td></tr>
<tr class="separator:a2f3216da86d8ced03f1b102a5c2e886c inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6b3b4b6857bc1987282e2f29611dd41 inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#ae6b3b4b6857bc1987282e2f29611dd41">getVersion</a> () const </td></tr>
<tr class="memdesc:ae6b3b4b6857bc1987282e2f29611dd41 inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="mdescLeft"> </td><td class="mdescRight">return the version of the schema <a href="#ae6b3b4b6857bc1987282e2f29611dd41">More...</a><br/></td></tr>
<tr class="separator:ae6b3b4b6857bc1987282e2f29611dd41 inherit pub_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:a12e63693edc162e721713985ef8ae0bf"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MascotXMLFile.html#a12e63693edc162e721713985ef8ae0bf">generateRTMapping</a> (const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><>::ConstIterator begin, const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><>::ConstIterator end, <a class="el" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a> &rt_mapping)</td></tr>
<tr class="memdesc:a12e63693edc162e721713985ef8ae0bf"><td class="mdescLeft"> </td><td class="mdescRight">Generates a mapping between scan numbers and retention times in raw data. <a href="#a12e63693edc162e721713985ef8ae0bf">More...</a><br/></td></tr>
<tr class="separator:a12e63693edc162e721713985ef8ae0bf"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1Internal_1_1XMLFile"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1Internal_1_1XMLFile')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td></tr>
<tr class="memitem:ab08cc6e67bde4d478045ece950deb32b inherit pro_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#ab08cc6e67bde4d478045ece950deb32b">parse_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, <a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a> *handler)</td></tr>
<tr class="memdesc:ab08cc6e67bde4d478045ece950deb32b inherit pro_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="mdescLeft"> </td><td class="mdescRight">Parses the XML file given by <code>filename</code> using the handler given by <code>handler</code>. <a href="#ab08cc6e67bde4d478045ece950deb32b">More...</a><br/></td></tr>
<tr class="separator:ab08cc6e67bde4d478045ece950deb32b inherit pro_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa99a8fa1726ecc3b865167eea1c17db7 inherit pro_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#aa99a8fa1726ecc3b865167eea1c17db7">save_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, <a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a> *handler) const </td></tr>
<tr class="memdesc:aa99a8fa1726ecc3b865167eea1c17db7 inherit pro_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="mdescLeft"> </td><td class="mdescRight">Stores the contents of the XML handler given by <code>handler</code> in the file given by <code>filename</code>. <a href="#aa99a8fa1726ecc3b865167eea1c17db7">More...</a><br/></td></tr>
<tr class="separator:aa99a8fa1726ecc3b865167eea1c17db7 inherit pro_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a97478c2a7b5ed960dae2ac5da0c03045 inherit pro_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#a97478c2a7b5ed960dae2ac5da0c03045">enforceEncoding_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &encoding)</td></tr>
<tr class="separator:a97478c2a7b5ed960dae2ac5da0c03045 inherit pro_methods_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1Internal_1_1XMLFile"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1Internal_1_1XMLFile')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td></tr>
<tr class="memitem:aea8dd5b28e6057c3e2b3f296966431c3 inherit pro_attribs_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#aea8dd5b28e6057c3e2b3f296966431c3">schema_location_</a></td></tr>
<tr class="memdesc:aea8dd5b28e6057c3e2b3f296966431c3 inherit pro_attribs_classOpenMS_1_1Internal_1_1XMLFile"><td class="mdescLeft"> </td><td class="mdescRight">XML schema file location. <a href="#aea8dd5b28e6057c3e2b3f296966431c3">More...</a><br/></td></tr>
<tr class="separator:aea8dd5b28e6057c3e2b3f296966431c3 inherit pro_attribs_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a33231ac1616a429e6533af15231951 inherit pro_attribs_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#a5a33231ac1616a429e6533af15231951">schema_version_</a></td></tr>
<tr class="memdesc:a5a33231ac1616a429e6533af15231951 inherit pro_attribs_classOpenMS_1_1Internal_1_1XMLFile"><td class="mdescLeft"> </td><td class="mdescRight">Version string. <a href="#a5a33231ac1616a429e6533af15231951">More...</a><br/></td></tr>
<tr class="separator:a5a33231ac1616a429e6533af15231951 inherit pro_attribs_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6b0159bfc4bc3062d47825cccfeec9cd inherit pro_attribs_classOpenMS_1_1Internal_1_1XMLFile"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#a6b0159bfc4bc3062d47825cccfeec9cd">enforced_encoding_</a></td></tr>
<tr class="memdesc:a6b0159bfc4bc3062d47825cccfeec9cd inherit pro_attribs_classOpenMS_1_1Internal_1_1XMLFile"><td class="mdescLeft"> </td><td class="mdescRight">Encoding string that replaces the encoding (system dependend or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. <a href="#a6b0159bfc4bc3062d47825cccfeec9cd">More...</a><br/></td></tr>
<tr class="separator:a6b0159bfc4bc3062d47825cccfeec9cd inherit pro_attribs_classOpenMS_1_1Internal_1_1XMLFile"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Used to load MascotXML files. </p>
<p>This class is used to load documents that implement the schema of MascotXML files. </p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
<a class="anchor" id="a1f47840b5fb63cf1ad9f823ac2e12227"></a>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6a5b7dd69471128e9cb680649b058f4f">Internal::MascotXMLHandler::RTMapping</a> <a class="el" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a></td>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1MascotXMLFile.html">MascotXMLFile</a> </td>
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<p>Constructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">static void generateRTMapping </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><>::ConstIterator </td>
<td class="paramname"><em>begin</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a> & </td>
<td class="paramname"><em>rt_mapping</em> </td>
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<p>Generates a mapping between scan numbers and retention times in raw data. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">begin</td><td>Iterator to the first spectrum </td></tr>
<tr><td class="paramname">end</td><td>Iterator past the last spectrum </td></tr>
<tr><td class="paramname">rt_mapping</td><td>Output mapping</td></tr>
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<p>The mapping can be used to infer retention times of identifications when a Mascot XML file is loaded. </p>
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<td class="memname">void load </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> & </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a> & </td>
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<p>loads data from a Mascot XML file </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">filename</td><td>the file to be loaded </td></tr>
<tr><td class="paramname">protein_identification</td><td>protein identifications belonging to the whole experiment </td></tr>
<tr><td class="paramname">id_data</td><td>the identifications with m/z and RT </td></tr>
<tr><td class="paramname">rt_mapping</td><td>An optional mapping of scan indices to RT, in case the file only contains scan numbers </td></tr>
<tr><td class="paramname">scan_regex</td><td>An optional regular expression used to extract the scan numbers</td></tr>
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<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 does not exists. </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 the file does not suit to the standard.</td></tr>
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<p>This method serves to read in a Mascot XML file. The information can be retrieved via the load function. </p>
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<td class="memname">void load </td>
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<td class="paramtype">std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, std::vector< <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> > > & </td>
<td class="paramname"><em>peptides</em>, </td>
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<td class="paramname"><em>rt_mapping</em> = <code><a class="el" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a>()</code>, </td>
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<p>loads data from a Mascot XML file </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">filename</td><td>the file to be loaded </td></tr>
<tr><td class="paramname">protein_identification</td><td>protein identifications belonging to the whole experiment </td></tr>
<tr><td class="paramname">id_data</td><td>the identifications with m/z and RT </td></tr>
<tr><td class="paramname">peptides</td><td>a map of modified peptides identified by the <a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> title </td></tr>
<tr><td class="paramname">rt_mapping</td><td>An optional mapping of scan indices to RT, in case the file only contains scan numbers </td></tr>
<tr><td class="paramname">scan_regex</td><td>An optional regular expression used to extract the scan numbers</td></tr>
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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 does not exists. </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 the file does not suit to the standard.</td></tr>
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<p>This method serves to read in a Mascot XML file. The information can be retrieved via the load function. </p>
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