FileHandler Class Reference [File IO]

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

#include <OpenMS/FORMAT/FileHandler.h>

List of all members.

Public Member Functions
PeakFileOptions &	getOptions ()
	Mutable access to the options for loading/storing.
const PeakFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing.
template<class PeakType >
bool	loadExperiment (const String &filename, MSExperiment< PeakType > &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE)
	Loads a file into an MSExperiment.
template<class PeakType >
void	storeExperiment (const String &filename, const MSExperiment< PeakType > &exp, ProgressLogger::LogType log=ProgressLogger::NONE)
	Stores an MSExperiment to a file.
template<class FeatureType >
bool	loadFeatures (const String &filename, FeatureMap< FeatureType > &map, FileTypes::Type force_type=FileTypes::UNKNOWN)
	Loads a file into a FeatureMap.
Static Public Member Functions
static FileTypes::Type	getType (const String &filename)
	Tries to determine the file type (by name or content).
static FileTypes::Type	getTypeByFileName (const String &filename)
	Determines the file type from a file name.
static FileTypes::Type	getTypeByContent (const String &filename)
	Determines the file type of a file by parsing the first few lines.
static bool	isSupported (FileTypes::Type type)
	Returns if the file type is supported in this build of the library.
Private Attributes
PeakFileOptions	options_

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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

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Member Function Documentation

PeakFileOptions& getOptions

(

)

Mutable access to the options for loading/storing.

Referenced by TOPPViewBase::metadataFileDialog().

const PeakFileOptions& getOptions

(

)

const

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

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 IDEvaluationBase::loadCurve().

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().

static FileTypes::Type getTypeByFileName

(

const String &

filename

)

[static]

Determines the file type from a file name.

static bool isSupported

(

FileTypes::Type

type

)

[static]

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

bool loadExperiment	(	const String &	filename,
		MSExperiment< PeakType > &	exp,
		FileTypes::Type	force_type = FileTypes::UNKNOWN,
		ProgressLogger::LogType	log = ProgressLogger::NONE
	)			[inline]

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 extention ( or from the content if that fails).
	log	Progress logging mode

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

References FileTypes::DTA, FileTypes::DTA2D, MzMLFile::getOptions(), MzDataFile::getOptions(), MzXMLFile::getOptions(), DTA2DFile::getOptions(), MS2File::load(), MascotGenericFile::load(), MzMLFile::load(), MzDataFile::load(), MzXMLFile::load(), DTA2DFile::load(), FileTypes::MGF, FileTypes::MS2, FileTypes::MZDATA, FileTypes::MZML, FileTypes::MZXML, MSExperiment< PeakT, ChromatogramPeakT >::reset(), ProgressLogger::setLogType(), FileTypes::UNKNOWN, and FileTypes::XMASS.

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

bool loadFeatures	(	const String &	filename,
		FeatureMap< FeatureType > &	map,
		FileTypes::Type	force_type = FileTypes::UNKNOWN
	)			[inline]

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 extention ( 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

References FileTypes::FEATUREXML, FileTypes::KROENIK, FileTypes::PEPLIST, FileTypes::TSV, and FileTypes::UNKNOWN.

void storeExperiment	(	const String &	filename,
		const MSExperiment< PeakType > &	exp,
		ProgressLogger::LogType	log = ProgressLogger::NONE
	)			[inline]

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

References FileTypes::DTA2D, MSExperiment< PeakT, ChromatogramPeakT >::getChromatograms(), MzMLFile::getOptions(), MzDataFile::getOptions(), MzXMLFile::getOptions(), DTA2DFile::getOptions(), FileTypes::MZDATA, FileTypes::MZXML, ProgressLogger::setLogType(), MzMLFile::store(), MzDataFile::store(), MzXMLFile::store(), and DTA2DFile::store().

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Member Data Documentation

PeakFileOptions options_ [private]