IBSpectraFile Class Reference

Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results. More...

#include <OpenMS/FORMAT/IBSpectraFile.h>

Public Member Functions
	IBSpectraFile ()
	Constructor. More...
	IBSpectraFile (const IBSpectraFile &other)
	Copy constructor. More...
IBSpectraFile &	operator= (const IBSpectraFile &rhs)
	Assignment operator. More...
void	store (const String &filename, const ConsensusMap &cm)
	Writes the contents of the ConsensusMap cm into the file named by filename. More...

Private Member Functions
boost::shared_ptr< IsobaricQuantitationMethod >	guessExperimentType_ (const ConsensusMap &cm)
	Guesses the type of isobaric quantitation performed on the experiment. More...
StringList	constructHeader_ (const IsobaricQuantitationMethod &quantMethod)
	Constructs the matching file header for the given quantitation method. More...
String	getModifString_ (const AASequence &sequence)
	Generates the modification string for the given AASequence. More...

Detailed Description

Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results.

Constructor & Destructor Documentation

IBSpectraFile() [1/2]

IBSpectraFile

(

)

Constructor.

IBSpectraFile() [2/2]

IBSpectraFile

(

const IBSpectraFile &

other

)

Copy constructor.

Member Function Documentation

constructHeader_()

StringList constructHeader_ ( const IsobaricQuantitationMethod &  quantMethod )

private

Constructs the matching file header for the given quantitation method.

Parameters

quantMethod

The used quantitation method.

Returns

The header of the IBSpectra file for the given quantitation method.

getModifString_()

String getModifString_ ( const AASequence &  sequence )

private

Generates the modification string for the given AASequence.

Parameters

sequence

The sequence for which the modification string should be generated.

Returns

The modification string for the given sequence.

guessExperimentType_()

boost::shared_ptr<IsobaricQuantitationMethod> guessExperimentType_ ( const ConsensusMap &  cm )

private

Guesses the type of isobaric quantitation performed on the experiment.

Exceptions

Exception::InvalidParameter

if the ConsensusMap does not hold the result of an isobaric quantification experiment (e.g., itraq).

operator=()

IBSpectraFile& operator=

(

const IBSpectraFile &

rhs

)

Assignment operator.

store()

void store	(	const String &	filename,
		const ConsensusMap &	cm
	)

Writes the contents of the ConsensusMap cm into the file named by filename.

Parameters

filename	The name of the file where the contents of cm should be stored.
cm	The ConsensusMap that should be exported to filename.

Exceptions

Exception::InvalidParameter

if the ConsensusMap does not hold the result of an isobaric quantification experiment (e.g., itraq).

Referenced by extractCachedMetaFilename().