35 #ifndef OPENMS_FORMAT_MZTABFILE_H 36 #define OPENMS_FORMAT_MZTABFILE_H 40 #include <boost/math/special_functions/fpclassify.hpp> 62 typedef std::map<std::pair<String, String>, std::vector<PeptideHit> >
MapAccPepType;
65 void store(
const String& filename,
const MzTab& mz_tab)
const;
68 void storeProteinReliabilityColumn(
bool store);
69 void storePeptideReliabilityColumn(
bool store);
70 void storePSMReliabilityColumn(
bool store);
71 void storeSmallMoleculeReliabilityColumn(
bool store);
72 void storeProteinUriColumn(
bool store);
73 void storePeptideUriColumn(
bool store);
74 void storePSMUriColumn(
bool store);
75 void storeSmallMoleculeUriColumn(
bool store);
76 void storeProteinGoTerms(
bool store);
96 String generateMzTabProteinHeader_(
const MzTabProteinSectionRow& reference_row,
const Size n_best_search_engine_scores,
const std::vector<String>& optional_columns)
const;
102 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;
108 String generateMzTabPSMHeader_(
Size n_search_engine_scores,
const std::vector<String>& optional_columns)
const;
114 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;
120 static std::pair<int, int> extractIndexPairsFromBrackets_(
const String& s);
122 static void sortPSM_(std::vector<PeptideIdentification>::iterator begin, std::vector<PeptideIdentification>::iterator end);
124 static void keepFirstPSM_(std::vector<PeptideIdentification>::iterator begin, std::vector<PeptideIdentification>::iterator end);
127 static void partitionIntoRuns_(
const std::vector<PeptideIdentification>& pep_ids,
128 const std::vector<ProteinIdentification>& pro_ids,
129 std::map<
String, std::vector<PeptideIdentification> >& map_run_to_pepids,
130 std::map<
String, std::vector<ProteinIdentification> >& map_run_to_proids
135 static void createProteinToPeptideLinks_(
const std::map<
String, std::vector<PeptideIdentification> >& map_run_to_pepids, MapAccPepType& map_run_accession_to_pephits);
144 static String mapSearchEngineToCvParam_(
const String& openms_search_engine_name);
146 static String mapSearchEngineScoreToCvParam_(
const String& openms_search_engine_name,
double score,
String score_type);
148 static String extractNumPeptides_(
const String& common_identifier,
const String& protein_accession,
149 const MapAccPepType& map_run_accesion_to_peptides);
152 static String extractNumPeptidesDistinct_(
String common_identifier,
String protein_accession,
153 const MapAccPepType& map_run_accesion_to_peptides);
156 static String extractNumPeptidesUnambiguous_(
String common_identifier,
String protein_accession,
157 const MapAccPepType& map_run_accesion_to_peptides);
159 static std::map<String, Size> extractNumberOfSubSamples_(
const std::map<
String, std::vector<ProteinIdentification> >& map_run_to_proids);
161 static void writePeptideHeader_(
SVOutStream& output, std::map<String, Size> n_sub_samples);
163 static void writeProteinHeader_(
SVOutStream& output, std::map<String, Size> n_sub_samples);
170 const MapAccPepType& map_run_accesion_to_peptides,
171 const std::map<String, Size>& map_run_to_num_sub
178 #endif // OPENMS_FORMAT_MZTABFILE_H Representation of a protein identification run.
Definition: ProteinIdentification.h:61
bool store_protein_reliability_
Definition: MzTabFile.h:82
A more convenient string class.
Definition: String.h:57
bool store_smallmolecule_uri_
Definition: MzTabFile.h:89
std::vector< MzTabSmallMoleculeSectionRow > MzTabSmallMoleculeSectionRows
Definition: MzTab.h:692
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
bool store_protein_goterms_
Definition: MzTabFile.h:90
bool store_protein_uri_
Definition: MzTabFile.h:86
std::vector< MzTabProteinSectionRow > MzTabProteinSectionRows
Definition: MzTab.h:689
bool store_peptide_reliability_
Definition: MzTabFile.h:83
bool store_peptide_uri_
Definition: MzTabFile.h:87
bool store_psm_reliability_
Definition: MzTabFile.h:84
Representation of a peptide hit.
Definition: PeptideHit.h:55
File adapter for MzTab files.
Definition: MzTabFile.h:54
std::vector< MzTabPeptideSectionRow > MzTabPeptideSectionRows
Definition: MzTab.h:690
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:74
bool store_psm_uri_
Definition: MzTabFile.h:88
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:54
std::vector< MzTabPSMSectionRow > MzTabPSMSectionRows
Definition: MzTab.h:691
bool store_smallmolecule_reliability_
Definition: MzTabFile.h:85
std::map< std::pair< String, String >, std::vector< PeptideHit > > MapAccPepType
Definition: MzTabFile.h:62
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/.
Definition: MzTab.h:700