EDTAFile Class Reference

File adapter for Enhanced DTA files. More...

#include <OpenMS/FORMAT/EDTAFile.h>

Public Member Functions
	EDTAFile ()
	Default constructor. More...
virtual	~EDTAFile ()
	Destructor. More...
void	load (const String &filename, ConsensusMap &consensus_map)
	Loads a EDTA file into a consensusXML. More...
void	store (const String &filename, const ConsensusMap &map) const
	Stores a ConsensusMap as an enhanced DTA file. More...
void	store (const String &filename, const FeatureMap &map) const
	Stores a FeatureMap as an enhanced DTA file. More...

Private Member Functions
double	checkedToDouble_ (const std::vector< String > &parts, Size index, double def=-1)
Int	checkedToInt_ (const std::vector< String > &parts, Size index, Int def=-1)

Detailed Description

File adapter for Enhanced DTA files.

Input text file containing tab, space or comma separated columns. The separator between columns is checked in the first line in this order.

It supports three variants of this format.

• Columns are: RT, MZ, Intensity A header is optional.

• Columns are: RT, MZ, Intensity, Charge, <Meta-Data> columns{0,} A header is mandatory.

  Example:

  RT m/z Intensity charge mymeta1 mymeta2
  321 405.233 24543534 2 lala  lili
  321 406.207 4343344  2 blubb blabb

• Columns are: (RT, MZ, Intensity, Charge){1,}, <Meta-Data> columns{0,} Header is mandatory. First quadruplet is the consensus. All following quadruplets describe the sub-features. This variant is discerned from variant #2 by the name of the fifth column, which is required to be RT1 (or rt1). All other column names for sub-features are faithfully ignored.

  Example:

  RT MZ INT CHARGE RT1 MZ1 INT1 CHARGE1 RT2 MZ2 INT2 CHARGE2
  321 405 100 2 321 405 100 2 321 406 50 2
  323 406 200 2 323 406 200 2 323 407 100 2 323 407 50 2

Constructor & Destructor Documentation

EDTAFile()

EDTAFile

(

)

Default constructor.

~EDTAFile()

virtual ~EDTAFile ( )

virtual

Destructor.

Member Function Documentation

checkedToDouble_()

double checkedToDouble_ ( const std::vector< String > &  parts, Size  index, double  def = -1  )

private

Check if column exists and convert String into double.

checkedToInt_()

Int checkedToInt_ ( const std::vector< String > &  parts, Size  index, Int  def = -1  )

private

Check if column exists and convert String into Int.

load()

void load	(	const String &	filename,
		ConsensusMap &	consensus_map
	)

Loads a EDTA file into a consensusXML.

The content of the file is stored in features.

Exceptions

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

Referenced by extractCachedMetaFilename().

store() [1/2]

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

Stores a ConsensusMap as an enhanced DTA file.

NOT IMPLEMENTED

Exceptions

Exception::UnableToCreateFile

is thrown if the file could not be created

Referenced by extractCachedMetaFilename().

store() [2/2]

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

Stores a FeatureMap as an enhanced DTA file.

Creating columns: RT, m/z, intensity, charge

Exceptions

Exception::UnableToCreateFile

is thrown if the file could not be created