FileHandler Class Reference

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

#include <OpenMS/FORMAT/FileHandler.h>

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...

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 the file extension of. 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.

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(), TOPPViewBase::annotateWithID(), TOPPXFDR::loadInputFile_(), 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 the file extension of.

Parameters

type	matches no other known FileType

This means that may match the extension of @type or any other unknown extension (e.g., '.tmp')

isSupported()

static bool isSupported ( FileTypes::Type  type )

static

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

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_().

setOptions()

void setOptions

(

const PeakFileOptions &

)

set options for loading/storing

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

Member Data Documentation

options_

PeakFileOptions options_

private