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OpenMS
2.4.0
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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 MzTab &mz_tab) const |
void | storeProteinReliabilityColumn (bool store) |
void | storePeptideReliabilityColumn (bool store) |
void | storePSMReliabilityColumn (bool store) |
void | storeSmallMoleculeReliabilityColumn (bool store) |
void | storeProteinUriColumn (bool store) |
void | storePeptideUriColumn (bool store) |
void | storePSMUriColumn (bool store) |
void | storeSmallMoleculeUriColumn (bool store) |
void | storeProteinGoTerms (bool store) |
void | load (const String &filename, MzTab &mz_tab) |
Protected Member Functions | |
void | generateMzTabMetaDataSection_ (const MzTabMetaData &map, StringList &sl) const |
void | generateMzTabProteinSection_ (const MzTabProteinSectionRows &rows, StringList &sl, const std::vector< String > &optional_columns) const |
String | generateMzTabProteinHeader_ (const MzTabProteinSectionRow &reference_row, const Size n_best_search_engine_scores, const std::vector< String > &optional_columns) const |
String | generateMzTabProteinSectionRow_ (const MzTabProteinSectionRow &row, const std::vector< String > &optional_columns) const |
void | generateMzTabPeptideSection_ (const MzTabPeptideSectionRows &rows, StringList &sl, const std::vector< String > &optional_columns) const |
String | generateMzTabPeptideHeader_ (Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_score, Size assays, Size study_variables, const std::vector< String > &optional_columns) const |
String | generateMzTabPeptideSectionRow_ (const MzTabPeptideSectionRow &row, const std::vector< String > &optional_columns) const |
void | generateMzTabPSMSection_ (const MzTabPSMSectionRows &rows, StringList &sl, const std::vector< String > &optional_columns) const |
String | generateMzTabPSMHeader_ (Size n_search_engine_scores, const std::vector< String > &optional_columns) const |
String | generateMzTabPSMSectionRow_ (const MzTabPSMSectionRow &row, const std::vector< String > &optional_columns) const |
void | generateMzTabSmallMoleculeSection_ (const MzTabSmallMoleculeSectionRows &map, StringList &sl, const std::vector< String > &optional_columns) const |
String | generateMzTabSmallMoleculeHeader_ (Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_score, Size assays, Size study_variables, const std::vector< String > &optional_columns) const |
String | generateMzTabSmallMoleculeSectionRow_ (const MzTabSmallMoleculeSectionRow &row, const std::vector< String > &optional_columns) const |
Static Protected Member Functions | |
static std::pair< int, int > | extractIndexPairsFromBrackets_ (const String &s) |
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, double score, String score_type) |
static String | extractNumPeptides_ (const String &common_identifier, const String &protein_accession, const MapAccPepType &map_run_accession_to_peptides) |
static String | extractNumPeptidesDistinct_ (String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides) |
static String | extractNumPeptidesUnambiguous_ (String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides) |
static std::map< String, Size > | extractNumberOfSubSamples_ (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_accession_to_peptides, const std::map< String, Size > &map_run_to_num_sub) |
Protected Attributes | |
bool | store_protein_reliability_ |
bool | store_peptide_reliability_ |
bool | store_psm_reliability_ |
bool | store_smallmolecule_reliability_ |
bool | store_protein_uri_ |
bool | store_peptide_uri_ |
bool | store_psm_uri_ |
bool | store_smallmolecule_uri_ |
bool | store_protein_goterms_ |
typedef std::map<std::pair<String, String>, std::vector<PeptideHit> > MapAccPepType |
MzTabFile | ( | ) |
Default constructor.
~MzTabFile | ( | ) |
Destructor.
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create links from protein to peptides
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Extracts, modifications and positions of a peptide hit in mzTab format.
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Extracts, if possible a unique protein accession for a peptide hit in mzTab format. Otherwise NA is returned.
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Map search engine identifier to CV, param etc.
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Extract protein and peptide identifications for each run. maps are assumed empty.
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void storePeptideReliabilityColumn | ( | bool | store | ) |
void storePeptideUriColumn | ( | bool | store | ) |
void storeProteinGoTerms | ( | bool | store | ) |
void storeProteinReliabilityColumn | ( | bool | store | ) |
void storeProteinUriColumn | ( | bool | store | ) |
void storePSMReliabilityColumn | ( | bool | store | ) |
void storePSMUriColumn | ( | bool | store | ) |
void storeSmallMoleculeReliabilityColumn | ( | bool | store | ) |
void storeSmallMoleculeUriColumn | ( | bool | store | ) |
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