File IO

File IO classes. More...

Collaboration diagram for File IO:

Classes
class	AbsoluteQuantitationMethodFile
	File adapter for AbsoluteQuantitationMethod files. More...
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. Does NOT support comment lines! 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	FLASHDeconvFeatureFile
	FLASHDeconv feature level output *.tsv, *.ms1ft (for Promex), *.feature (for TopPIC) file formats. More...
class	FLASHDeconvSpectrumFile
	FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats. More...
class	ConsensusXMLHandler
	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation. More...
class	FeatureXMLHandler
	This class provides Input/Output functionality for feature maps. More...
class	HDF5Connector
	File adapter for HDF5 files. 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
	Read/write Mascot generic files (MGF). More...
class	MascotInfile
	Mascot input file adapter. More...
class	MascotXMLFile
	Used to load Mascot XML files. More...
class	MRMFeatureQCFile
	File adapter for MRMFeatureQC 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	MSstatsFile
	File adapter for MSstats files. 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	MzQCFile
	File adapter for mzQC files used to load and store mzQC files. More...
class	MzQuantMLFile
	File adapter for MzQuantML files. More...
class	MzTabModification
	Data model of MzTab files. More...
class	MzTab
	Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...
class	MzTabFile
	File adapter for MzTab files. More...
struct	CompareMzTabMMatchRef
	Data model of MzTabM files. Please see the official MzTabM specification at https://github.com/HUPO-PSI/mzTab/tree/master/specification_document-releases/2_0-Metabolomics-Release. More...
class	MzTabMFile
	File adapter for MzTab-M files. More...
class	MzXMLFile
	File adapter for MzXML 3.1 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 used to load and store 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	SqliteConnector
	File adapter for Sqlite 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	TriqlerFile
	File adapter for Triqler 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	XQuestResultXMLFile
	Used to load and store xQuest result files. More...
class	XTandemInfile
	XTandem input file. More...
class	XTandemXMLFile
	Used to load XTandemXML files. More...

Enumerations
enum	MzTabCellStateType {   MZTAB_CELLSTATE_DEFAULT , MZTAB_CELLSTATE_NULL , MZTAB_CELLSTATE_NAN , MZTAB_CELLSTATE_INF ,   SIZE_OF_MZTAB_CELLTYPE }
	Base functionality to for MzTab data models. More...

Functions
void	load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true, bool load_empty_hits=true)
	loads data from a OMSSAXML file More...
void	load (const String &filename, std::vector< ResidueModification * > &modifications)
	loads data from unimod.xml file More...
void	load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, ModificationDefinitionsSet &mod_def_set)
	loads data from an X! Tandem XML file More...

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)

Enumeration Type Documentation

MzTabCellStateType

enum MzTabCellStateType

Base functionality to for MzTab data models.

MzTab supports null, NaN, Inf for cells with Integer or Double values. MzTabCellType explicitly defines the state of the cell for these types.

Enumerator
MZTAB_CELLSTATE_DEFAULT
MZTAB_CELLSTATE_NULL
MZTAB_CELLSTATE_NAN
MZTAB_CELLSTATE_INF
SIZE_OF_MZTAB_CELLTYPE

Function Documentation

load() [1/3]

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

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
load_empty_hits	Many spectra will not return a hit. Report empty peptide identifications?

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

Exceptions

FileNotFound
ParseError

load() [2/3]

void load	(	const String &	filename,
		ProteinIdentification &	protein_identification,
		std::vector< PeptideIdentification > &	id_data,
		ModificationDefinitionsSet &	mod_def_set
	)

loads data from an X! Tandem XML 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
mod_def_set	Fixed and variable modifications defined for the search. May be extended with additional (X! Tandem default) modifications if those are found in the file.

This class serves to read in an X! Tandem XML file. The information can be retrieved via the load function.

load() [3/3]

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

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