DTA2DFile Class Reference

DTA2D File adapter. More...

#include <OpenMS/FORMAT/DTA2DFile.h>

Inheritance diagram for DTA2DFile:

Collaboration diagram for DTA2DFile:

Public Member Functions
Constructors and Destructor
	DTA2DFile ()
	Default constructor. More...
	~DTA2DFile () override
	Destructor. More...
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...
template<typename MapType >
void	load (const String &filename, MapType &map)
	Loads a map from a DTA2D file. More...
template<typename MapType >
void	store (const String &filename, const MapType &map) const
	Stores a map in a DTA2D file. More...
template<typename MapType >
void	storeTIC (const String &filename, const MapType &map) const
	Stores the TIC of a map in a DTA2D file. More...
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...
virtual	~ProgressLogger ()
	Destructor. More...
	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...
LogType	getLogType () const
	Returns the type of progress log being used. More...
void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...
void	setProgress (SignedSize value) const
	Sets the current progress. More...
void	endProgress () const
	Ends the progress display. More...
void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Private Attributes
PeakFileOptions	options_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

DTA2D File adapter.

File adapter for files with three tab/space-separated columns.

The default format is: retention time (seconds) , m/z , intensity.

If the first line starts with '#', a different order is defined by the the order of the keywords 'MIN' (retention time in minutes) or 'SEC' (retention time in seconds), 'MZ', and 'INT'.

Example: '#MZ MIN INT'

Keywords can be lower/upper or mixed case, e.g. 'Int' or 'mz'.

The peaks of one retention time have to be in subsequent lines.

Constructor & Destructor Documentation

DTA2DFile()

DTA2DFile

(

)

Default constructor.

~DTA2DFile()

~DTA2DFile ( )

override

Destructor.

Member Function Documentation

getOptions() [1/2]

PeakFileOptions& getOptions

(

)

Mutable access to the options for loading/storing.

getOptions() [2/2]

const PeakFileOptions& getOptions

(

)

const

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

load()

void load ( const String &  filename, MapType &  map  )

inline

Loads a map from a DTA2D file.

Parameters

filename	The file from which the map should be loaded.
map	has to be a MSExperiment or have the same interface.

Exceptions

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

References MSExperiment::addSpectrum(), MSSpectrum::clear(), DRange< D >::encloses(), Peak1D::getIntensity(), PeakFileOptions::getIntensityRange(), Peak1D::getMZ(), PeakFileOptions::getMZRange(), MSSpectrum::getRT(), PeakFileOptions::getRTRange(), String::has(), PeakFileOptions::hasIntensityRange(), PeakFileOptions::hasMZRange(), String::hasPrefix(), PeakFileOptions::hasRTRange(), MSExperiment::reset(), Peak1D::setIntensity(), DocumentIdentifier::setLoadedFilePath(), DocumentIdentifier::setLoadedFileType(), Peak1D::setMZ(), SpectrumSettings::setNativeID(), MSSpectrum::setRT(), String::split(), String::substr(), OpenMS::StringUtils::toDouble(), OpenMS::StringUtils::toFloat(), String::toUpper(), and String::trim().

store()

void store ( const String &  filename, const MapType &  map  ) const

inline

Stores a map in a DTA2D file.

Parameters

filename	The name of the file where the map should be stored.
map	has to be a MSExperiment or have the same interface.

Exceptions

Exception::UnableToCreateFile

is thrown if the file could not be created

References MSExperiment::begin(), MSExperiment::end(), OpenMS::precisionWrapper(), and MSExperiment::size().

storeTIC()

void storeTIC ( const String &  filename, const MapType &  map  ) const

inline

Stores the TIC of a map in a DTA2D file.

Parameters

filename	The name of the file where the map should be stored.
map	has to be a MSExperiment or have the same interface.

Exceptions

Exception::UnableToCreateFile

is thrown if the file could not be created

References MSExperiment::calculateTIC(), OpenMS::precisionWrapper(), and MSExperiment::size().

Member Data Documentation

options_

PeakFileOptions options_

private