Facilitates file handling by file type recognition. More...

#include <OpenMS/FORMAT/FileHandler.h>

Collaboration diagram for FileHandler:

Public Member Functions
PeakFileOptions &	getOptions ()
	Mutable access to the options for loading/storing. More...

const PeakFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing. More...

void	setOptions (const PeakFileOptions &)
	set options for loading/storing More...

bool	loadExperiment (const String &filename, MSExperiment &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool rewrite_source_file=true, const bool compute_hash=true)
	Loads a file into an MSExperiment. More...

void	storeExperiment (const String &filename, const MSExperiment &exp, ProgressLogger::LogType log=ProgressLogger::NONE)
	Stores an MSExperiment to a file. More...

bool	loadFeatures (const String &filename, FeatureMap &map, FileTypes::Type force_type=FileTypes::UNKNOWN)
	Loads a file into a FeatureMap. More...

bool	storeFeatures (const String &filename, const FeatureMap &map)
	Store a FeatureMap. More...

bool	storeConsensusFeatures (const String &filename, const ConsensusMap &map)
	Store a ConsensFeatureMap. More...

bool	loadConsensusFeatures (const String &filename, ConsensusMap &map)
	Loads a file into a ConsensMap. More...

bool	loadIdentifications (const String &filename, std::vector< ProteinIdentification > additional_proteins, std::vector< PeptideIdentification > additional_peptides)

bool	storeTransitions (const String &filename, const TargetedExperiment &library)
	Store transitions of a spectral library. More...

Static Public Member Functions
static FileTypes::Type	getType (const String &filename)
	Tries to determine the file type (by name or content) More...

static FileTypes::Type	getTypeByFileName (const String &filename)
	Determines the file type from a file name. More...

static bool	hasValidExtension (const String &filename, const FileTypes::Type type)
	Check if `filename` has the extension `type`. More...

static String	stripExtension (const String &filename)
	If filename contains an extension, it will be removed (including the '.'). Special extensions, known to OpenMS, e.g. '.mzML.gz' will be recognized as well. More...

static String	swapExtension (const String &filename, const FileTypes::Type new_type)
	Tries to find and remove a known file extension, and append the new one. More...

static FileTypes::Type	getConsistentOutputfileType (const String &output_filename, const String &requested_type)
	Useful function for TOPP tools which have an 'out_type' parameter and want to know what output format to write. This function makes sure that the type derived from `output_filename` and `requested_type` are consistent, i.e. are either identical or one of them is UNKNOWN. Upon conflict, an error message is printed and the UNKNOWN type is returned. More...

static FileTypes::Type	getTypeByContent (const String &filename)
	Determines the file type of a file by parsing the first few lines. More...

static bool	isSupported (FileTypes::Type type)
	Returns if the file type is supported in this build of the library. More...

static String	computeFileHash (const String &filename)
	Computes a SHA-1 hash value for the content of the given file. More...

Private Attributes
PeakFileOptions	options_

Detailed Description

Facilitates file handling by file type recognition.

This class provides file type recognition from the file name and from the file content.

It also offer a common interface to load MSExperiment data and allows querying for supported file types.

See also: FileTypes

Member Function Documentation

◆ computeFileHash()

static String computeFileHash ( const String & filename )

static

Computes a SHA-1 hash value for the content of the given file.

Returns: The SHA-1 hash of the given file.

◆ getConsistentOutputfileType()

static FileTypes::Type getConsistentOutputfileType	(	const String &	output_filename,
		const String &	requested_type
	)

static

Useful function for TOPP tools which have an 'out_type' parameter and want to know what output format to write. This function makes sure that the type derived from output_filename and requested_type are consistent, i.e. are either identical or one of them is UNKNOWN. Upon conflict, an error message is printed and the UNKNOWN type is returned.

Parameters

output_filename	A full filename (with none, absolute or relative paths) whose type is determined using FileHandler::getTypeByFileName() internally
requested_type	A type as string, usually obtained from '-out_type', e.g. "FASTA" (case insensitive). The string can be empty (yields UNKNOWN for this type)

Returns: A consistent file type or UNKNOWN upon conflict

◆ getOptions() [1/2]

PeakFileOptions& getOptions ( )

Mutable access to the options for loading/storing.

Referenced by TOPPViewBase::metadataFileDialog().

◆ getOptions() [2/2]

const PeakFileOptions& getOptions ( ) const

Non-mutable access to the options for loading/storing.

◆ getType()

static FileTypes::Type getType ( const String & filename )

static

Tries to determine the file type (by name or content)

First the type is determined from the file name. If this fails, the type is determined from the file content.

Exceptions

Exception::FileNotFound is thrown if the file is not present

Referenced by TOPPViewBase::addDataFile(), and TOPPOpenSwathBase::performCalibration().

◆ getTypeByContent()

static FileTypes::Type getTypeByContent ( const String & filename )

static

Determines the file type of a file by parsing the first few lines.

Exceptions

Exception::FileNotFound is thrown if the file is not present

Referenced by InspectOutfile::getExperiment().

◆ getTypeByFileName()

static FileTypes::Type getTypeByFileName ( const String & filename )

static

Determines the file type from a file name.

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

◆ hasValidExtension()

static bool hasValidExtension	(	const String &	filename,
		const FileTypes::Type	type
	)

static

Check if filename has the extension type.

If the extension is not known (e.g. '.tmp') this is also allowed. However, if the extension is another one (neither type nor unknown), false is returned.

◆ isSupported()

static bool isSupported ( FileTypes::Type type )

static

Returns if the file type is supported in this build of the library.

◆ loadConsensusFeatures()

bool loadConsensusFeatures	(	const String &	filename,
		ConsensusMap &	map
	)

Loads a file into a ConsensMap.

Parameters

filename	the file name of the file to load.
map	The ConsensMap to load the data into.

Returns: true if the file could be loaded, false otherwise

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing

◆ loadExperiment()

bool loadExperiment	(	const String &	filename,
		MSExperiment &	exp,
		FileTypes::Type	force_type = `FileTypes::UNKNOWN`,
		ProgressLogger::LogType	log = `ProgressLogger::NONE`,
		const bool	rewrite_source_file = `true`,
		const bool	compute_hash = `true`
	)

Loads a file into an MSExperiment.

Parameters

filename	The file name of the file to load.
exp	The experiment to load the data into.
force_type	Forces to load the file with that file type. If no type is forced, it is determined from the extension (or from the content if that fails).
log	Progress logging mode
rewrite_source_file	Set's the SourceFile name and path to the current file. Note that this looses the link to the primary MS run the file originated from.
compute_hash	If source files are rewritten, this flag triggers a recomputation of hash values. A SHA1 string gets stored in the checksum member of SourceFile.

Returns: true if the file could be loaded, false otherwise

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::fileChanged_(), InspectOutfile::getExperiment(), and TOPPViewBase::metadataFileDialog().

◆ loadFeatures()

bool loadFeatures	(	const String &	filename,
		FeatureMap &	map,
		FileTypes::Type	force_type = `FileTypes::UNKNOWN`
	)

Loads a file into a FeatureMap.

Parameters

filename	the file name of the file to load.
map	The FeatureMap to load the data into.
force_type	Forces to load the file with that file type. If no type is forced, it is determined from the extension (or from the content if that fails).

Returns: true if the file could be loaded, false otherwise

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing

Referenced by TOPPViewBase::fileChanged_().

◆ loadIdentifications()

bool loadIdentifications	(	const String &	filename,
		std::vector< ProteinIdentification >	additional_proteins,
		std::vector< PeptideIdentification >	additional_peptides
	)

◆ setOptions()

void setOptions ( const PeakFileOptions & )

set options for loading/storing

◆ storeConsensusFeatures()

bool storeConsensusFeatures	(	const String &	filename,
		const ConsensusMap &	map
	)

Store a ConsensFeatureMap.

Parameters

filename	the file name of the file to write.
map	The ConsensusMap to store.

Returns: true if the file could be stored, false otherwise

Exceptions

Exception::UnableToCreateFile is thrown if the file could not be written

◆ storeExperiment()

void storeExperiment	(	const String &	filename,
		const MSExperiment &	exp,
		ProgressLogger::LogType	log = `ProgressLogger::NONE`
	)

Stores an MSExperiment to a file.

The file type to store the data in is determined by the file name. Supported formats for storing are mzML, mzXML, mzData and DTA2D. If the file format cannot be determined from the file name, the mzML format is used.

Parameters

filename	The name of the file to store the data in.
exp	The experiment to store.
log	Progress logging mode

Exceptions

Exception::UnableToCreateFile is thrown if the file could not be written

◆ storeFeatures()

bool storeFeatures	(	const String &	filename,
		const FeatureMap &	map
	)

Store a FeatureMap.

Parameters

filename	the file name of the file to write.
map	The FeatureMap to store.

Returns: true if the file could be stored, false otherwise

Exceptions

Exception::UnableToCreateFile is thrown if the file could not be written

◆ storeTransitions()

bool storeTransitions	(	const String &	filename,
		const TargetedExperiment &	library
	)

Store transitions of a spectral library.

Parameters

filename	the file name of the file to write.
map	The TargetedExperiment to store.

Returns: true if the file could be stored, false otherwise

Exceptions

Exception::UnableToCreateFile is thrown if the file could not be written

◆ stripExtension()

static String stripExtension ( const String & filename )

static

If filename contains an extension, it will be removed (including the '.'). Special extensions, known to OpenMS, e.g. '.mzML.gz' will be recognized as well.

E.g. 'experiment.featureXML' becomes 'experiment' and 'c:\files\data.mzML.gz' becomes 'c:\files\data' If the extension is unknown, the everything in the basename of the file after the last '.' is removed. E.g. 'future.newEnding' becomes 'future' If the filename does not contain '.', but the path (if any) does, nothing is removed, e.g. '/my.dotted.dir/filename' is returned unchanged.

Referenced by TOPPViewBase::addDataFile().

◆ swapExtension()

static String swapExtension	(	const String &	filename,
		const FileTypes::Type	new_type
	)

static

Tries to find and remove a known file extension, and append the new one.

Internally calls 'stripExtension()' and adds the new suffix to the result. E.g. 'experiment.featureXML'+ FileTypes::TRAFOXML becomes 'experiment.trafoXML' and 'c:\files\data.mzML.gz' + FileTypes::FEATUREXML becomes 'c:\files\data.featureXML' If the existing extension is unknown, the everything after the last '.' is removed, e.g. 'exp.tmp'+FileTypes::IDXML becomes 'exp.idXML'

Referenced by TOPPViewBase::addDataFile().

Member Data Documentation

◆ options_

PeakFileOptions options_

private

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Member Function Documentation

◆ computeFileHash()

◆ getConsistentOutputfileType()

◆ getOptions() [1/2]

◆ getOptions() [2/2]

◆ getType()

◆ getTypeByContent()

◆ getTypeByFileName()

◆ hasValidExtension()

◆ isSupported()

◆ loadConsensusFeatures()

◆ loadExperiment()

◆ loadFeatures()

◆ loadIdentifications()

◆ setOptions()

◆ storeConsensusFeatures()

◆ storeExperiment()

◆ storeFeatures()

◆ storeTransitions()

◆ stripExtension()

◆ swapExtension()

Member Data Documentation

◆ options_