QuantitativeExperimentalDesign Class Reference

Merge files according to experimental design. More...

#include <OpenMS/ANALYSIS/QUANTITATION/QuantitativeExperimentalDesign.h>

Inheritance diagram for QuantitativeExperimentalDesign:

Public Member Functions
	QuantitativeExperimentalDesign ()
	Default constructor. More...
	~QuantitativeExperimentalDesign () override
void	applyDesign2Resolver (ProteinResolver &resolver, TextFile &file, StringList &fileNames)
	xxxxxxx More...
void	applyDesign2Quantifier (PeptideAndProteinQuant &quantifier, TextFile &file, StringList &fileNames)
	xxxxxxx More...
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...
virtual	~DefaultParamHandler ()
	Destructor. More...
virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...
void	setParameters (const Param &param)
	Sets the parameters. More...
const Param &	getParameters () const
	Non-mutable access to the parameters. More...
const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...
const String &	getName () const
	Non-mutable access to the name. More...
void	setName (const String &name)
	Mutable access to the name. More...
const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Private Member Functions
	QuantitativeExperimentalDesign (const QuantitativeExperimentalDesign &)
	Not implemented. More...
QuantitativeExperimentalDesign &	operator= (const QuantitativeExperimentalDesign &)
	Not implemented. More...
void	mergeFeatureMaps_ (FeatureMap &map, const String &experiment, StringList &file_paths)
void	mergeConsensusMaps_ (ConsensusMap &map, const String &experiment, StringList &file_paths)
void	mergeIDFiles_ (std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment, StringList &file_paths)
void	findRelevantFilePaths_ (std::map< String, StringList > &design2FileBaseName, std::map< String, StringList > &design2FilePath, StringList &filePaths)
void	analyzeHeader_ (UInt &expCol, UInt &fileCol, StringList &header)
	Analyze header, which column represents filename and experimental setting. More...
void	getSeparator_ (String &separator)
	Helper class to get separator of the experimental design text file. More...
void	mapFiles2Design_ (std::map< String, StringList > &experiments, TextFile &file)
	helper class. which file name belongs to which experimental setting More...

Additional Inherited Members
Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String	error_name_
	Name that is displayed in error messages during the parameter checking. More...
bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

Merge files according to experimental design.

This class

Constructor & Destructor Documentation

QuantitativeExperimentalDesign() [1/2]

QuantitativeExperimentalDesign

(

)

Default constructor.

~QuantitativeExperimentalDesign()

~QuantitativeExperimentalDesign ( )

override

QuantitativeExperimentalDesign() [2/2]

QuantitativeExperimentalDesign ( const QuantitativeExperimentalDesign &  )

private

Not implemented.

Member Function Documentation

analyzeHeader_()

void analyzeHeader_ ( UInt &  expCol, UInt &  fileCol, StringList &  header  )

private

Analyze header, which column represents filename and experimental setting.

applyDesign2Quantifier()

void applyDesign2Quantifier	(	PeptideAndProteinQuant &	quantifier,
		TextFile &	file,
		StringList &	fileNames
	)

xxxxxxx

Note

xxxxxx

applyDesign2Resolver()

void applyDesign2Resolver	(	ProteinResolver &	resolver,
		TextFile &	file,
		StringList &	fileNames
	)

xxxxxxx

Note

xxxxxx

findRelevantFilePaths_()

void findRelevantFilePaths_ ( std::map< String, StringList > &  design2FileBaseName, std::map< String, StringList > &  design2FilePath, StringList &  filePaths  )

private

getSeparator_()

void getSeparator_ ( String &  separator )

private

Helper class to get separator of the experimental design text file.

mapFiles2Design_()

void mapFiles2Design_ ( std::map< String, StringList > &  experiments, TextFile &  file  )

private

helper class. which file name belongs to which experimental setting

mergeConsensusMaps_()

void mergeConsensusMaps_ ( ConsensusMap &  map, const String &  experiment, StringList &  file_paths  )

private

mergeFeatureMaps_()

void mergeFeatureMaps_ ( FeatureMap &  map, const String &  experiment, StringList &  file_paths  )

private

mergeIDFiles_()

void mergeIDFiles_ ( std::vector< ProteinIdentification > &  proteins, std::vector< PeptideIdentification > &  peptides, const String &  experiment, StringList &  file_paths  )

private

operator=()

QuantitativeExperimentalDesign& operator= ( const QuantitativeExperimentalDesign &  )

private

Not implemented.