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MzTabFile Class Reference

File adapter for MzTab files. More...

#include <OpenMS/FORMAT/MzTabFile.h>

Public Types

typedef std::map< std::pair
< String, String >
, std::vector< PeptideHit > > 
MapAccPepType
 

Public Member Functions

 MzTabFile ()
 Default constructor. More...
 
 ~MzTabFile ()
 Destructor. More...
 
void store (const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, String in, String document_id) const
 
void store (const String &filename, const MzTab &mz_tab) const
 
void load (const String &filename, MzTab &mz_tab)
 

Protected Member Functions

void generateMzTabMetaDataSection_ (const MzTabMetaData &map, StringList &sl) const
 
String generateMzTabProteinHeader_ (Int n_subsamples, const std::vector< String > &optional_protein_columns) const
 
String generateMzTabProteinSectionRow_ (const MzTabProteinSectionRow &row, const String &unit_id) const
 
void generateMzTabProteinSection_ (const MzTabProteinSectionData &map, StringList &sl) const
 
void generateMzTabPeptideSection_ (const MzTabPeptideSectionData &map, StringList &sl) const
 
void generateMzTabSmallMoleculeSection_ (const MzTabSmallMoleculeSectionData &map, StringList &sl) const
 
String generateMzTabPeptideHeader_ (Int n_subsamples, const std::vector< String > &optional_protein_columns) const
 
String generateMzTabPeptideSectionRow_ (const MzTabPeptideSectionRow &row, const String &unit_id) const
 
String generateMzTabSmallMoleculeHeader_ (Int n_subsamples, const std::vector< String > &optional_smallmolecule_columns) const
 
String generateMzTabSmallMoleculeSectionRow_ (const MzTabSmallMoleculeSectionRow &row, const String &unit_id) const
 

Static Protected Member Functions

static void sortPSM_ (std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end)
 
static void keepFirstPSM_ (std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end)
 
static void partitionIntoRuns_ (const std::vector< PeptideIdentification > &pep_ids, const std::vector< ProteinIdentification > &pro_ids, std::map< String, std::vector< PeptideIdentification > > &map_run_to_pepids, std::map< String, std::vector< ProteinIdentification > > &map_run_to_proids)
 Extract protein and peptide identifications for each run. maps are assumed empty. More...
 
static void createProteinToPeptideLinks_ (const std::map< String, std::vector< PeptideIdentification > > &map_run_to_pepids, MapAccPepType &map_run_accession_to_pephits)
 create links from protein to peptides More...
 
static String extractProteinAccession_ (const PeptideHit &peptide_hit)
 Extracts, if possible a unique protein accession for a peptide hit in mzTab format. Otherwise NA is returned. More...
 
static String extractPeptideModifications_ (const PeptideHit &peptide_hit)
 Extracts, modifications and positions of a peptide hit in mzTab format. More...
 
static String mapSearchEngineToCvParam_ (const String &openms_search_engine_name)
 Map search engine identifier to CV, param etc. More...
 
static String mapSearchEngineScoreToCvParam_ (const String &openms_search_engine_name, DoubleReal score, String score_type)
 
static String extractNumPeptides_ (const String &common_identifier, const String &protein_accession, const MapAccPepType &map_run_accesion_to_peptides)
 
static String extractNumPeptidesDistinct_ (String common_identifier, String protein_accession, const MapAccPepType &map_run_accesion_to_peptides)
 
static String extractNumPeptidesUnambiguous_ (String common_identifier, String protein_accession, const MapAccPepType &map_run_accesion_to_peptides)
 
static std::map< String, SizeextractNumberOfSubSamples_ (const std::map< String, std::vector< ProteinIdentification > > &map_run_to_proids)
 
static void writePeptideHeader_ (SVOutStream &output, std::map< String, Size > n_sub_samples)
 
static void writeProteinHeader_ (SVOutStream &output, std::map< String, Size > n_sub_samples)
 
static void writeProteinData_ (SVOutStream &output, const ProteinIdentification &prot_id, Size run_count, String input_filename, bool has_coverage, const MapAccPepType &map_run_accesion_to_peptides, const std::map< String, Size > &map_run_to_num_sub)
 

Detailed Description

File adapter for MzTab files.

Member Typedef Documentation

typedef std::map<std::pair<String, String>, std::vector<PeptideHit> > MapAccPepType

Constructor & Destructor Documentation

MzTabFile ( )

Default constructor.

~MzTabFile ( )

Destructor.

Member Function Documentation

static void createProteinToPeptideLinks_ ( const std::map< String, std::vector< PeptideIdentification > > &  map_run_to_pepids,
MapAccPepType map_run_accession_to_pephits 
)
staticprotected

create links from protein to peptides

static std::map<String, Size> extractNumberOfSubSamples_ ( const std::map< String, std::vector< ProteinIdentification > > &  map_run_to_proids)
staticprotected
static String extractNumPeptides_ ( const String common_identifier,
const String protein_accession,
const MapAccPepType map_run_accesion_to_peptides 
)
staticprotected
static String extractNumPeptidesDistinct_ ( String  common_identifier,
String  protein_accession,
const MapAccPepType map_run_accesion_to_peptides 
)
staticprotected
static String extractNumPeptidesUnambiguous_ ( String  common_identifier,
String  protein_accession,
const MapAccPepType map_run_accesion_to_peptides 
)
staticprotected
static String extractPeptideModifications_ ( const PeptideHit peptide_hit)
staticprotected

Extracts, modifications and positions of a peptide hit in mzTab format.

static String extractProteinAccession_ ( const PeptideHit peptide_hit)
staticprotected

Extracts, if possible a unique protein accession for a peptide hit in mzTab format. Otherwise NA is returned.

void generateMzTabMetaDataSection_ ( const MzTabMetaData map,
StringList sl 
) const
protected
String generateMzTabPeptideHeader_ ( Int  n_subsamples,
const std::vector< String > &  optional_protein_columns 
) const
protected
void generateMzTabPeptideSection_ ( const MzTabPeptideSectionData map,
StringList sl 
) const
protected
String generateMzTabPeptideSectionRow_ ( const MzTabPeptideSectionRow row,
const String unit_id 
) const
protected
String generateMzTabProteinHeader_ ( Int  n_subsamples,
const std::vector< String > &  optional_protein_columns 
) const
protected
void generateMzTabProteinSection_ ( const MzTabProteinSectionData map,
StringList sl 
) const
protected
String generateMzTabProteinSectionRow_ ( const MzTabProteinSectionRow row,
const String unit_id 
) const
protected
String generateMzTabSmallMoleculeHeader_ ( Int  n_subsamples,
const std::vector< String > &  optional_smallmolecule_columns 
) const
protected
void generateMzTabSmallMoleculeSection_ ( const MzTabSmallMoleculeSectionData map,
StringList sl 
) const
protected
String generateMzTabSmallMoleculeSectionRow_ ( const MzTabSmallMoleculeSectionRow row,
const String unit_id 
) const
protected
static void keepFirstPSM_ ( std::vector< PeptideIdentification >::iterator  begin,
std::vector< PeptideIdentification >::iterator  end 
)
staticprotected
void load ( const String filename,
MzTab mz_tab 
)
static String mapSearchEngineScoreToCvParam_ ( const String openms_search_engine_name,
DoubleReal  score,
String  score_type 
)
staticprotected
static String mapSearchEngineToCvParam_ ( const String openms_search_engine_name)
staticprotected

Map search engine identifier to CV, param etc.

static void partitionIntoRuns_ ( const std::vector< PeptideIdentification > &  pep_ids,
const std::vector< ProteinIdentification > &  pro_ids,
std::map< String, std::vector< PeptideIdentification > > &  map_run_to_pepids,
std::map< String, std::vector< ProteinIdentification > > &  map_run_to_proids 
)
staticprotected

Extract protein and peptide identifications for each run. maps are assumed empty.

static void sortPSM_ ( std::vector< PeptideIdentification >::iterator  begin,
std::vector< PeptideIdentification >::iterator  end 
)
staticprotected
void store ( const String filename,
const std::vector< ProteinIdentification > &  protein_ids,
const std::vector< PeptideIdentification > &  peptide_ids,
String  in,
String  document_id 
) const
void store ( const String filename,
const MzTab mz_tab 
) const
static void writePeptideHeader_ ( SVOutStream output,
std::map< String, Size n_sub_samples 
)
staticprotected
static void writeProteinData_ ( SVOutStream output,
const ProteinIdentification prot_id,
Size  run_count,
String  input_filename,
bool  has_coverage,
const MapAccPepType map_run_accesion_to_peptides,
const std::map< String, Size > &  map_run_to_num_sub 
)
staticprotected
static void writeProteinHeader_ ( SVOutStream output,
std::map< String, Size n_sub_samples 
)
staticprotected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5