35 #ifndef OPENMS_FORMAT_MZTABFILE_H 
   36 #define OPENMS_FORMAT_MZTABFILE_H 
   45 #include <boost/math/special_functions/fpclassify.hpp> 
   65     typedef std::map<std::pair<String, String>, std::vector<PeptideHit> > 
MapAccPepType;
 
   68     void store(
const String & filename, 
const std::vector<ProteinIdentification> & protein_ids, 
const std::vector<PeptideIdentification> & peptide_ids, 
String in, 
String document_id) 
const;
 
   71     void store(
const String & filename, 
const MzTab& mz_tab) 
const;
 
   79     String generateMzTabProteinHeader_(
Int n_subsamples, 
const std::vector<String>& optional_protein_columns) 
const;
 
   89     String generateMzTabPeptideHeader_(
Int n_subsamples, 
const std::vector<String>& optional_protein_columns) 
const;
 
   93     String generateMzTabSmallMoleculeHeader_(
Int n_subsamples, 
const std::vector<String>& optional_smallmolecule_columns) 
const;
 
   99     static void sortPSM_(std::vector<PeptideIdentification>::iterator begin, std::vector<PeptideIdentification>::iterator end);
 
  101     static void keepFirstPSM_(std::vector<PeptideIdentification>::iterator begin, std::vector<PeptideIdentification>::iterator end);
 
  104     static void partitionIntoRuns_(
const std::vector<PeptideIdentification> & pep_ids,
 
  105                                   const std::vector<ProteinIdentification> & pro_ids,
 
  106                                   std::map<
String, std::vector<PeptideIdentification> > & map_run_to_pepids,
 
  107                                   std::map<
String, std::vector<ProteinIdentification> > & map_run_to_proids
 
  112     static void createProteinToPeptideLinks_(
const std::map<
String, std::vector<PeptideIdentification> > & map_run_to_pepids, 
MapAccPepType & map_run_accession_to_pephits);
 
  121     static String mapSearchEngineToCvParam_(
const String & openms_search_engine_name);
 
  125     static String extractNumPeptides_(
const String & common_identifier, 
const String & protein_accession,
 
  129     static String extractNumPeptidesDistinct_(
String common_identifier, 
String protein_accession,
 
  133     static String extractNumPeptidesUnambiguous_(
String common_identifier, 
String protein_accession,
 
  136     static std::map<String, Size> extractNumberOfSubSamples_(
const std::map<
String, std::vector<ProteinIdentification> > & map_run_to_proids);
 
  138     static void writePeptideHeader_(
SVOutStream & output, std::map<String, Size> n_sub_samples);
 
  140     static void writeProteinHeader_(
SVOutStream & output, std::map<String, Size> n_sub_samples);
 
  142     static void writeProteinData_(
SVOutStream & output,
 
  148                                   const std::map<String, Size> & map_run_to_num_sub
 
  155 #endif // OPENMS_FORMAT_MZTABFILE_H 
Representation of a protein identification run. 
Definition: ProteinIdentification.h:61
std::map< String, MzTabProteinSectionRows > MzTabProteinSectionData
Definition: MzTab.h:1343
A more convenient string class. 
Definition: String.h:56
std::map< String, MzTabUnitIdMetaData > MzTabMetaData
Definition: MzTab.h:1341
std::map< String, MzTabSmallMoleculeSectionRows > MzTabSmallMoleculeSectionData
Definition: MzTab.h:1347
Representation of a peptide hit. 
Definition: PeptideHit.h:54
File adapter for MzTab files. 
Definition: MzTabFile.h:57
std::map< String, MzTabPeptideSectionRows > MzTabPeptideSectionData
Definition: MzTab.h:1345
String list. 
Definition: StringList.h:56
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
Stream class for writing to comma/tab/...-separated values files. 
Definition: SVOutStream.h:51
int Int
Signed integer type. 
Definition: Types.h:100
std::map< std::pair< String, String >, std::vector< PeptideHit > > MapAccPepType
Definition: MzTabFile.h:65
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. 
Definition: MzTab.h:1355