TriqlerFile Class Reference

File adapter for Triqler files. More...

#include <OpenMS/FORMAT/TriqlerFile.h>

Collaboration diagram for TriqlerFile:

Classes
struct	AggregatedConsensusInfo
class	TriqlerLine_

Public Member Functions
	TriqlerFile ()=default
	Default constructor. More...
	~TriqlerFile ()=default
	Destructor. More...
void	storeLFQ (const String &filename, const ConsensusMap &consensus_map, const ExperimentalDesign &design, const StringList &reannotate_filenames, const String &condition)
	store label free experiment More...

Private Types
typedef OpenMS::Peak2D::IntensityType	Intensity
typedef OpenMS::Peak2D::CoordinateType	Coordinate
using	MapSequenceToLines_ = std::map< String, std::set< TriqlerLine_ > >

Private Member Functions
TriqlerFile::AggregatedConsensusInfo	aggregateInfo_ (const ConsensusMap &consensus_map, const std::vector< String > &spectra_paths)
OpenMS::Peak2D::IntensityType	sumIntensity_ (const std::set< OpenMS::Peak2D::IntensityType > &intensities) const
OpenMS::Peak2D::IntensityType	meanIntensity_ (const std::set< OpenMS::Peak2D::IntensityType > &intensities) const
void	constructFile_ (TextFile &csv_out, const std::set< String > &peptideseq_quantifyable, const MapSequenceToLines_ &peptideseq_to_line) const
bool	isQuantifyable_ (const std::set< String > &accs, const std::unordered_map< String, const IndProtGrp * > &accession_to_group) const

Static Private Member Functions
static void	checkConditionLFQ_ (const ExperimentalDesign::SampleSection &sampleSection, const String &condition)
static void	assembleRunMap_ (std::map< std::pair< String, unsigned >, unsigned > &run_map, const ExperimentalDesign &design)
static bool	checkUnorderedContent_ (const std::vector< String > &first, const std::vector< String > &second)
static std::unordered_map< OpenMS::String, const IndProtGrp * >	getAccessionToGroupMap_ (const IndProtGrps &ind_prots)

Static Private Attributes
static const String	na_string_
static const char	delim_ = ','
static const char	accdelim_ = ';'
static const char	quote_ = '"'

Detailed Description

File adapter for Triqler files.

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Class Documentation

OpenMS::TriqlerFile::AggregatedConsensusInfo

struct OpenMS::TriqlerFile::AggregatedConsensusInfo

Collaboration diagram for TriqlerFile::AggregatedConsensusInfo:

Class Members
vector< vector< String > >	consensus_feature_filenames
vector< vector< Intensity > >	consensus_feature_intensities
vector< vector< unsigned > >	consensus_feature_labels
vector< vector< Coordinate > >	consensus_feature_retention_times
vector< BaseFeature >	features

Member Typedef Documentation

Coordinate

typedef OpenMS::Peak2D::CoordinateType Coordinate

private

Intensity

typedef OpenMS::Peak2D::IntensityType Intensity

private

MapSequenceToLines_

using MapSequenceToLines_ = std::map<String, std::set<TriqlerLine_> >

private

Constructor & Destructor Documentation

TriqlerFile()

TriqlerFile ( )

default

Default constructor.

~TriqlerFile()

~TriqlerFile ( )

default

Destructor.

Member Function Documentation

aggregateInfo_()

TriqlerFile::AggregatedConsensusInfo aggregateInfo_ ( const ConsensusMap &  consensus_map, const std::vector< String > &  spectra_paths  )

private

assembleRunMap_()

static void assembleRunMap_ ( std::map< std::pair< String, unsigned >, unsigned > &  run_map, const ExperimentalDesign &  design  )

staticprivate

checkConditionLFQ_()

static void checkConditionLFQ_ ( const ExperimentalDesign::SampleSection &  sampleSection, const String &  condition  )

staticprivate

checkUnorderedContent_()

static bool checkUnorderedContent_ ( const std::vector< String > &  first, const std::vector< String > &  second  )

staticprivate

constructFile_()

void constructFile_ ( TextFile &  csv_out, const std::set< String > &  peptideseq_quantifyable, const MapSequenceToLines_ &  peptideseq_to_line  ) const

private

getAccessionToGroupMap_()

static std::unordered_map<OpenMS::String, const IndProtGrp* > getAccessionToGroupMap_ ( const IndProtGrps &  ind_prots )

staticprivate

isQuantifyable_()

bool isQuantifyable_ ( const std::set< String > &  accs, const std::unordered_map< String, const IndProtGrp * > &  accession_to_group  ) const

private

meanIntensity_()

OpenMS::Peak2D::IntensityType meanIntensity_ ( const std::set< OpenMS::Peak2D::IntensityType > &  intensities ) const

inlineprivate

storeLFQ()

void storeLFQ	(	const String &	filename,
		const ConsensusMap &	consensus_map,
		const ExperimentalDesign &	design,
		const StringList &	reannotate_filenames,
		const String &	condition
	)

store label free experiment

sumIntensity_()

OpenMS::Peak2D::IntensityType sumIntensity_ ( const std::set< OpenMS::Peak2D::IntensityType > &  intensities ) const

inlineprivate

Member Data Documentation

accdelim_

const char accdelim_ = ';'

staticprivate

delim_

const char delim_ = ','

staticprivate

na_string_

const String na_string_

staticprivate

quote_

const char quote_ = '"'

staticprivate