File IO [Format]

File IO classes. More...

Classes
class	ConsensusXMLFile
	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation. More...
class	CsvFile
	This class handles csv files. Currently only loading is implemented. More...
class	CVMappingFile
	Used to load CvMapping files. More...
class	DTA2DFile
	DTA2D File adapter. More...
class	DTAFile
	File adapter for DTA files. More...
class	EDTAFile
	File adapter for Enhanced DTA files. More...
class	FeatureXMLFile
	This class provides Input/Output functionality for feature maps. More...
class	FileHandler
	Facilitates file handling by file type recognition. More...
struct	FileTypes
	Centralizes the file types recognized by FileHandler. More...
class	IdXMLFile
	Used to load and store idXML files. More...
class	InspectInfile
	Inspect input file adapter. More...
class	InspectOutfile
	Representation of an Inspect outfile. More...
class	KroenikFile
	File adapter for Kroenik (HardKloer sibling) files. More...
class	MascotGenericFile
	Mascot input file adapter. More...
class	MascotInfile
	Mascot input file adapter. More...
class	MascotXMLFile
	Used to load MascotXML files. More...
class	MS2File
	MS2 input file adapter. More...
class	MsInspectFile
	File adapter for MsInspect files. More...
class	MSPFile
	File adapter for MSP files (NIST spectra library). More...
class	MzDataFile
	File adapter for MzData files. More...
class	MzIdentMLFile
	File adapter for MzIdentML files. More...
class	MzMLFile
	File adapter for MzML files. More...
class	MzQuantMLFile
	File adapter for MzQuantML files. More...
class	MzTabNAAbleInterface
	Data model of MzTab files. The format specification is in development and subject to change. Use at your own risk. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...
class	MzTab
	Data model of MzTab files. The format specification is in development and subject to change. Use at your own risk. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...
class	MzTabFile
	File adapter for MzTab files. More...
class	MzXMLFile
	File adapter for MzXML 2.1 files. More...
class	OMSSACSVFile
	File adapter for OMSSACSV files. More...
class	OMSSAXMLFile
	Used to load OMSSAXML files. More...
class	PepNovoInfile
	PepNovo input file adapter. More...
class	PepNovoOutfile
	Representation of a PepNovo output file. More...
class	PepXMLFile
	Used to load and store PepXML files. More...
class	PepXMLFileMascot
	Used to load Mascot PepXML files. More...
class	ProtXMLFile
	Used to load (storing not supported, yet) ProtXML files. More...
class	PTMXMLFile
	Used to load and store PTMXML files. More...
class	QcMLFile
	File adapter for QcML files. More...
class	SequestInfile
	Sequest input file adapter. More...
class	SequestOutfile
	Representation of a Sequest output file. More...
class	SpecArrayFile
	File adapter for SpecArray (.pepList) files. More...
class	TextFile
	This class provides some basic file handling methods for text files. More...
class	ToolDescriptionFile
	File adapter for ToolDescriptor files. More...
class	TraMLFile
	File adapter for HUPO PSI TraML files. More...
class	TransformationXMLFile
	Used to load and store TransformationXML files. More...
class	UnimodXMLFile
	Used to load XML files from unimod.org files. More...
class	XMLValidator
	Validator for XML files. More...
class	XMassFile
	File adapter for 'XMass Analysis (fid)' files. More...
class	XTandemInfile
	XTandem input file adapter. More...
class	XTandemXMLFile
	Used to load XTandemXML files. More...
Functions
void	load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true)
	loads data from a OMSSAXML file
void	load (const String &filename, std::vector< ResidueModification * > &modifications)
	loads data from unimod.xml file
void	load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data)
	loads data from a XTandemXML file

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Detailed Description

File IO classes.

This module contains all classes that are involved in file IO. Take a look at the FileHandler class!

Todo:

Implement reading of pepXML and protXML (Andreas)

Allow reading of zipped XML files (David, Hiwi)

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Function Documentation

void load	(	const String &	filename,
		ProteinIdentification &	protein_identification,
		std::vector< PeptideIdentification > &	id_data,
		bool	load_proteins = true
	)			[inherited]

loads data from a OMSSAXML file

Parameters:

	filename	the file to be loaded
	protein_identification	protein identifications belonging to the whole experiment
	id_data	the identifications with m/z and RT
	load_proteins	if this flag is set to false, the protein identifications are not loaded

This class serves to read in a OMSSAXML file. The information can be retrieved via the load function.

Exceptions:

	FileNotFound
	ParseError

void load	(	const String &	filename,
		ProteinIdentification &	protein_identification,
		std::vector< PeptideIdentification > &	id_data
	)			[inherited]

loads data from a XTandemXML file

Parameters:

	filename	the file to be loaded
	protein_identification	protein identifications belonging to the whole experiment
	id_data	the identifications with m/z and RT

This class serves to read in a XTandemXML file. The information can be retrieved via the load function.

void load	(	const String &	filename,
		std::vector< ResidueModification * > &	modifications
	)			[inherited]

loads data from unimod.xml file

Parameters:

	filename	the filename were the unimod xml file should be read from
	modifications	the modifications which are read from the file

Exceptions:

	FileNotFound	is thrown if the file could not be found
	ParseError	is thrown if the given file could not be parsed