File: group__FileIO.html

package info (click to toggle)
openms 1.11.1-5
links: PTS, VCS
area: main
in suites: jessie, jessie-kfreebsd
size: 436,688 kB
ctags: 150,907
sloc: cpp: 387,126; xml: 71,547; python: 7,764; ansic: 2,626; php: 2,499; sql: 737; ruby: 342; sh: 325; makefile: 128
file content (386 lines) | stat: -rw-r--r-- 38,462 bytes
<HTML>
<HEAD>
<TITLE>File IO</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> &nbsp;&middot;
<A href="classes.html">Classes</A> &nbsp;&middot;
<A href="annotated.html">Annotated Classes</A> &nbsp;&middot;
<A href="modules.html">Modules</A> &nbsp;&middot;
<A href="functions_func.html">Members</A> &nbsp;&middot;
<A href="namespaces.html">Namespaces</A> &nbsp;&middot;
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
</div><!-- top -->
<div class="header">
  <div class="summary">
<a href="#nested-classes">Classes</a> &#124;
<a href="#enum-members">Enumerations</a> &#124;
<a href="#func-members">Functions</a>  </div>
  <div class="headertitle">
<div class="title">File IO<div class="ingroups"><a class="el" href="group__Format.html">Format</a></div></div>  </div>
</div><!--header-->
<div class="contents">

<p>File IO classes.  
<a href="#details">More...</a></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusXMLFile.html">ConsensusXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation.  <a href="classOpenMS_1_1ConsensusXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CsvFile.html">CsvFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">This class handles csv files. Currently only loading is implemented.  <a href="classOpenMS_1_1CsvFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CVMappingFile.html">CVMappingFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load CvMapping files.  <a href="classOpenMS_1_1CVMappingFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DTA2DFile.html">DTA2DFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">DTA2D <a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter.  <a href="classOpenMS_1_1DTA2DFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DTAFile.html">DTAFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for DTA files.  <a href="classOpenMS_1_1DTAFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EDTAFile.html">EDTAFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for Enhanced DTA files.  <a href="classOpenMS_1_1EDTAFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureXMLFile.html">FeatureXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">This class provides Input/Output functionality for feature maps.  <a href="classOpenMS_1_1FeatureXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html">FileHandler</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Facilitates file handling by file type recognition.  <a href="classOpenMS_1_1FileHandler.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1FileTypes.html">FileTypes</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Centralizes the file types recognized by <a class="el" href="classOpenMS_1_1FileHandler.html" title="Facilitates file handling by file type recognition. ">FileHandler</a>.  <a href="structOpenMS_1_1FileTypes.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IdXMLFile.html">IdXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load and store idXML files.  <a href="classOpenMS_1_1IdXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InspectInfile.html">InspectInfile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Inspect input file adapter.  <a href="classOpenMS_1_1InspectInfile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InspectOutfile.html">InspectOutfile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Representation of an Inspect outfile.  <a href="classOpenMS_1_1InspectOutfile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1KroenikFile.html">KroenikFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><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><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MascotGenericFile.html">MascotGenericFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Mascot input file adapter.  <a href="classOpenMS_1_1MascotGenericFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MascotInfile.html">MascotInfile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Mascot input file adapter.  <a href="classOpenMS_1_1MascotInfile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MascotXMLFile.html">MascotXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load MascotXML files.  <a href="classOpenMS_1_1MascotXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MS2File.html">MS2File</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">MS2 input file adapter.  <a href="classOpenMS_1_1MS2File.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MsInspectFile.html">MsInspectFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for MsInspect files.  <a href="classOpenMS_1_1MsInspectFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSPFile.html">MSPFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for MSP files (NIST spectra library)  <a href="classOpenMS_1_1MSPFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MzDataFile.html">MzDataFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for MzData files.  <a href="classOpenMS_1_1MzDataFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MzIdentMLFile.html">MzIdentMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for MzIdentML files.  <a href="classOpenMS_1_1MzIdentMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MzMLFile.html">MzMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for MzML files.  <a href="classOpenMS_1_1MzMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MzQuantMLFile.html">MzQuantMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for MzQuantML files.  <a href="classOpenMS_1_1MzQuantMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MzTab.html">MzTab</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Data model of <a class="el" href="classOpenMS_1_1MzTab.html" title="Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. ">MzTab</a> files. Please see the official <a class="el" href="classOpenMS_1_1MzTab.html" title="Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. ">MzTab</a> specification at <a href="https://code.google.com/p/mztab/">https://code.google.com/p/mztab/</a>.  <a href="classOpenMS_1_1MzTab.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MzTabFile.html">MzTabFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for <a class="el" href="classOpenMS_1_1MzTab.html" title="Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. ">MzTab</a> files.  <a href="classOpenMS_1_1MzTabFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MzXMLFile.html">MzXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for MzXML 2.1 files.  <a href="classOpenMS_1_1MzXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OMSSACSVFile.html">OMSSACSVFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for OMSSACSV files.  <a href="classOpenMS_1_1OMSSACSVFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OMSSAXMLFile.html">OMSSAXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load OMSSAXML files.  <a href="classOpenMS_1_1OMSSAXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">PepNovo input file adapter.  <a href="classOpenMS_1_1PepNovoInfile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoOutfile.html">PepNovoOutfile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Representation of a PepNovo output file.  <a href="classOpenMS_1_1PepNovoOutfile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load and store PepXML files.  <a href="classOpenMS_1_1PepXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepXMLFileMascot.html">PepXMLFileMascot</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load Mascot PepXML files.  <a href="classOpenMS_1_1PepXMLFileMascot.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProtXMLFile.html">ProtXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load (storing not supported, yet) ProtXML files.  <a href="classOpenMS_1_1ProtXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PTMXMLFile.html">PTMXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load and store PTMXML files.  <a href="classOpenMS_1_1PTMXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1QcMLFile.html">QcMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for QcML files.  <a href="classOpenMS_1_1QcMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SequestInfile.html">SequestInfile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sequest input file adapter.  <a href="classOpenMS_1_1SequestInfile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SequestOutfile.html">SequestOutfile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Representation of a Sequest output file.  <a href="classOpenMS_1_1SequestOutfile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SpecArrayFile.html">SpecArrayFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for SpecArray (.pepList) files.  <a href="classOpenMS_1_1SpecArrayFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TextFile.html">TextFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">This class provides some basic file handling methods for text files.  <a href="classOpenMS_1_1TextFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ToolDescriptionFile.html">ToolDescriptionFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for ToolDescriptor files.  <a href="classOpenMS_1_1ToolDescriptionFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraMLFile.html">TraMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for HUPO PSI TraML files.  <a href="classOpenMS_1_1TraMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationXMLFile.html">TransformationXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load and store TransformationXML files.  <a href="classOpenMS_1_1TransformationXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1UnimodXMLFile.html">UnimodXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load XML files from unimod.org files.  <a href="classOpenMS_1_1UnimodXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1XMLValidator.html">XMLValidator</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Validator for XML files.  <a href="classOpenMS_1_1XMLValidator.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1XMassFile.html">XMassFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> adapter for 'XMass Analysis (fid)' files.  <a href="classOpenMS_1_1XMassFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1XTandemInfile.html">XTandemInfile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">XTandem input file.  <a href="classOpenMS_1_1XTandemInfile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1XTandemXMLFile.html">XTandemXMLFile</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Used to load XTandemXML files.  <a href="classOpenMS_1_1XTandemXMLFile.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="enum-members"></a>
Enumerations</h2></td></tr>
<tr class="memitem:gabfb38d02724e669a1f4b254e8ae24e46"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__FileIO.html#gabfb38d02724e669a1f4b254e8ae24e46">MzTabCellStateType</a> { <br/>
&#160;&#160;<a class="el" href="group__FileIO.html#ggabfb38d02724e669a1f4b254e8ae24e46adfafdfb46f1c3154b17bc7cf3b494a55">MZTAB_CELLSTATE_DEFAULT</a>, 
<a class="el" href="group__FileIO.html#ggabfb38d02724e669a1f4b254e8ae24e46a48160ee797ee7286e648c0eb425554cb">MZTAB_CELLSTATE_NULL</a>, 
<a class="el" href="group__FileIO.html#ggabfb38d02724e669a1f4b254e8ae24e46a7e2b2fd9f8495ea858101b8f6b72ff0f">MZTAB_CELLSTATE_NAN</a>, 
<a class="el" href="group__FileIO.html#ggabfb38d02724e669a1f4b254e8ae24e46a6465258af6efd7218d121b8216e3b686">MZTAB_CELLSTATE_INF</a>, 
<br/>
&#160;&#160;<a class="el" href="group__FileIO.html#ggabfb38d02724e669a1f4b254e8ae24e46a337defb4c1e30fe3406a887131638714">SIZE_OF_MZTAB_CELLTYPE</a>
<br/>
 }</td></tr>
<tr class="memdesc:gabfb38d02724e669a1f4b254e8ae24e46"><td class="mdescLeft">&#160;</td><td class="mdescRight">Data model of MzTab files. Please see the official MzTab specification at <a href="https://code.google.com/p/mztab/">https://code.google.com/p/mztab/</a>.  <a href="group__FileIO.html#gabfb38d02724e669a1f4b254e8ae24e46">More...</a><br/></td></tr>
<tr class="separator:gabfb38d02724e669a1f4b254e8ae24e46"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:ga80d2c14e7be773ffeaee280fd1f4f133"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__FileIO.html#ga80d2c14e7be773ffeaee280fd1f4f133">load</a> (const String &amp;filename, ProteinIdentification &amp;protein_identification, std::vector&lt; PeptideIdentification &gt; &amp;id_data, bool load_proteins=true)</td></tr>
<tr class="memdesc:ga80d2c14e7be773ffeaee280fd1f4f133"><td class="mdescLeft">&#160;</td><td class="mdescRight">loads data from a OMSSAXML file  <a href="#ga80d2c14e7be773ffeaee280fd1f4f133">More...</a><br/></td></tr>
<tr class="separator:ga80d2c14e7be773ffeaee280fd1f4f133"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga80be5a8d8ba7265507d7a9853637a79a"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__FileIO.html#ga80be5a8d8ba7265507d7a9853637a79a">load</a> (const String &amp;filename, std::vector&lt; ResidueModification * &gt; &amp;modifications)</td></tr>
<tr class="memdesc:ga80be5a8d8ba7265507d7a9853637a79a"><td class="mdescLeft">&#160;</td><td class="mdescRight">loads data from unimod.xml file  <a href="#ga80be5a8d8ba7265507d7a9853637a79a">More...</a><br/></td></tr>
<tr class="separator:ga80be5a8d8ba7265507d7a9853637a79a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gae6ff0d806cf1b17fc837c6242f6a38b7"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__FileIO.html#gae6ff0d806cf1b17fc837c6242f6a38b7">load</a> (const String &amp;filename, ProteinIdentification &amp;protein_identification, std::vector&lt; PeptideIdentification &gt; &amp;id_data)</td></tr>
<tr class="memdesc:gae6ff0d806cf1b17fc837c6242f6a38b7"><td class="mdescLeft">&#160;</td><td class="mdescRight">loads data from a XTandemXML file  <a href="#gae6ff0d806cf1b17fc837c6242f6a38b7">More...</a><br/></td></tr>
<tr class="separator:gae6ff0d806cf1b17fc837c6242f6a38b7"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<p>File IO classes. </p>
<p>This module contains all classes that are involved in file IO. Take a look at the FileHandler class!</p>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000037">Todo:</a></b></dt><dd><p class="startdd">Implement reading of pepXML and protXML (Andreas) </p>
<p class="enddd">Allow reading of zipped XML files (David, Hiwi)</p>
</dd></dl>
<h2 class="groupheader">Enumeration Type Documentation</h2>
<a class="anchor" id="gabfb38d02724e669a1f4b254e8ae24e46"></a>
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">enum MzTabCellStateType</td>
        </tr>
      </table>
</div><div class="memdoc">

<p>Data model of <a class="el" href="classOpenMS_1_1MzTab.html" title="Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. ">MzTab</a> files. Please see the official <a class="el" href="classOpenMS_1_1MzTab.html" title="Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. ">MzTab</a> specification at <a href="https://code.google.com/p/mztab/">https://code.google.com/p/mztab/</a>. </p>
<table class="fieldtable">
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="ggabfb38d02724e669a1f4b254e8ae24e46adfafdfb46f1c3154b17bc7cf3b494a55"></a>MZTAB_CELLSTATE_DEFAULT</em>&nbsp;</td><td class="fielddoc">
</td></tr>
<tr><td class="fieldname"><em><a class="anchor" id="ggabfb38d02724e669a1f4b254e8ae24e46a48160ee797ee7286e648c0eb425554cb"></a>MZTAB_CELLSTATE_NULL</em>&nbsp;</td><td class="fielddoc">
</td></tr>
<tr><td class="fieldname"><em><a class="anchor" id="ggabfb38d02724e669a1f4b254e8ae24e46a7e2b2fd9f8495ea858101b8f6b72ff0f"></a>MZTAB_CELLSTATE_NAN</em>&nbsp;</td><td class="fielddoc">
</td></tr>
<tr><td class="fieldname"><em><a class="anchor" id="ggabfb38d02724e669a1f4b254e8ae24e46a6465258af6efd7218d121b8216e3b686"></a>MZTAB_CELLSTATE_INF</em>&nbsp;</td><td class="fielddoc">
</td></tr>
<tr><td class="fieldname"><em><a class="anchor" id="ggabfb38d02724e669a1f4b254e8ae24e46a337defb4c1e30fe3406a887131638714"></a>SIZE_OF_MZTAB_CELLTYPE</em>&nbsp;</td><td class="fielddoc">
</td></tr>
</table>

</div>
</div>
<h2 class="groupheader">Function Documentation</h2>
<a class="anchor" id="ga80be5a8d8ba7265507d7a9853637a79a"></a>
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">void load </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;&#160;</td>
          <td class="paramname"><em>filename</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1ResidueModification.html">ResidueModification</a> * &gt; &amp;&#160;</td>
          <td class="paramname"><em>modifications</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
      </table>
</div><div class="memdoc">

<p>loads data from unimod.xml file </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">filename</td><td>the filename were the unimod xml file should be read from </td></tr>
    <tr><td class="paramname">modifications</td><td>the modifications which are read from the file </td></tr>
  </table>
  </dd>
</dl>
<dl class="exception"><dt>Exceptions</dt><dd>
  <table class="exception">
    <tr><td class="paramname">FileNotFound</td><td>is thrown if the file could not be found </td></tr>
    <tr><td class="paramname">ParseError</td><td>is thrown if the given file could not be parsed </td></tr>
  </table>
  </dd>
</dl>

</div>
</div>
<a class="anchor" id="gae6ff0d806cf1b17fc837c6242f6a38b7"></a>
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">void load </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;&#160;</td>
          <td class="paramname"><em>filename</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &amp;&#160;</td>
          <td class="paramname"><em>protein_identification</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>id_data</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
      </table>
</div><div class="memdoc">

<p>loads data from a XTandemXML file </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <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>
  </table>
  </dd>
</dl>
<p>This class serves to read in a XTandemXML file. The information can be retrieved via the load function. </p>

</div>
</div>
<a class="anchor" id="ga80d2c14e7be773ffeaee280fd1f4f133"></a>
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">void load </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;&#160;</td>
          <td class="paramname"><em>filename</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &amp;&#160;</td>
          <td class="paramname"><em>protein_identification</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>id_data</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>load_proteins</em> = <code>true</code>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
      </table>
</div><div class="memdoc">

<p>loads data from a OMSSAXML file </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <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">load_proteins</td><td>if this flag is set to false, the protein identifications are not loaded</td></tr>
  </table>
  </dd>
</dl>
<p>This class serves to read in a OMSSAXML file. The information can be retrieved via the load function.</p>
<dl class="exception"><dt>Exceptions</dt><dd>
  <table class="exception">
    <tr><td class="paramname">FileNotFound</td><td></td></tr>
    <tr><td class="paramname">ParseError</td><td></td></tr>
  </table>
  </dd>
</dl>

</div>
</div>
</div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<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 11:19:25 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>