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MSstatsFile Class Reference
Format » File IO

File adapter for MSstats files. More...

#include <OpenMS/FORMAT/MSstatsFile.h>

Collaboration diagram for MSstatsFile:
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Classes

struct  AggregatedConsensusInfo
 
class  MSstatsLine_
 
class  MSstatsTMTLine_
 

Public Member Functions

 MSstatsFile ()=default
 Default constructor. More...
 
 ~MSstatsFile ()=default
 Destructor. More...
 
void storeLFQ (const String &filename, const ConsensusMap &consensus_map, const ExperimentalDesign &design, const StringList &reannotate_filenames, const bool is_isotope_label_type, const String &bioreplicate, const String &condition, const String &retention_time_summarization_method)
 store label free experiment (MSstats) More...
 
void storeISO (const String &filename, const ConsensusMap &consensus_map, const ExperimentalDesign &design, const StringList &reannotate_filenames, const String &bioreplicate, const String &condition, const String &mixture, const String &retention_time_summarization_method)
 store isobaric experiment (MSstatsTMT) More...
 

Private Types

typedef OpenMS::Peak2D::IntensityType Intensity
 
typedef OpenMS::Peak2D::CoordinateType Coordinate
 

Private Member Functions

MSstatsFile::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
 
template<class LineType >
void constructFile_ (const String &retention_time_summarization_method, const bool rt_summarization_manual, TextFile &csv_out, const std::set< String > &peptideseq_quantifyable, LineType &peptideseq_to_prefix_to_intensities) 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 &bioreplicate, const String &condition)
 
static void checkConditionISO_ (const ExperimentalDesign::SampleSection &sampleSection, const String &bioreplicate, const String &condition, const String &mixture)
 
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 MSstats files.

Class Documentation

◆ OpenMS::MSstatsFile::AggregatedConsensusInfo

struct OpenMS::MSstatsFile::AggregatedConsensusInfo
Collaboration diagram for MSstatsFile::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

Constructor & Destructor Documentation

◆ MSstatsFile()

MSstatsFile ( )
default

Default constructor.

◆ ~MSstatsFile()

~MSstatsFile ( )
default

Destructor.

Member Function Documentation

◆ aggregateInfo_()

MSstatsFile::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

◆ checkConditionISO_()

static void checkConditionISO_ ( const ExperimentalDesign::SampleSection &  sampleSection,
const String &  bioreplicate,
const String &  condition,
const String &  mixture 
)
staticprivate

◆ checkConditionLFQ_()

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

◆ checkUnorderedContent_()

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

◆ constructFile_()

void constructFile_ ( const String &  retention_time_summarization_method,
const bool  rt_summarization_manual,
TextFile &  csv_out,
const std::set< String > &  peptideseq_quantifyable,
LineType &  peptideseq_to_prefix_to_intensities 
) 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

◆ storeISO()

void storeISO ( const String &  filename,
const ConsensusMap &  consensus_map,
const ExperimentalDesign &  design,
const StringList &  reannotate_filenames,
const String &  bioreplicate,
const String &  condition,
const String &  mixture,
const String &  retention_time_summarization_method 
)

store isobaric experiment (MSstatsTMT)

◆ storeLFQ()

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

store label free experiment (MSstats)

◆ 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