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TriqlerFile Class Reference
Format » File IO

File adapter for Triqler files. More...

#include <OpenMS/FORMAT/TriqlerFile.h>

Collaboration diagram for TriqlerFile:
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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.

Class Documentation

◆ OpenMS::TriqlerFile::AggregatedConsensusInfo

struct OpenMS::TriqlerFile::AggregatedConsensusInfo
Collaboration diagram for TriqlerFile::AggregatedConsensusInfo:
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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