| OpenMS 2.5.0

Static Public Member Functions | Static Protected Member Functions | List of all members
IdentificationDataConverter Class Reference

`#include <OpenMS/METADATA/ID/IdentificationDataConverter.h>`

## Static Public Member Functions

static void | importIDs (IdentificationData &id_data, const std::vector< ProteinIdentification > &proteins, const std::vector< PeptideIdentification > &peptides)
| Import from legacy peptide/protein identifications. More...
static void | exportIDs (const IdentificationData &id_data, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, bool export_oligonucleotides=false)
| Export to legacy peptide/protein identifications. More...
static MzTab | exportMzTab (const IdentificationData &id_data)
| Export to mzTab format. More...
static void | importSequences (IdentificationData &id_data, const std::vector< FASTAFile::FASTAEntry > &fasta, IdentificationData::MoleculeType type=IdentificationData::MoleculeType::PROTEIN, const String &decoy_pattern="")
| Import FASTA sequences as parent molecules. More...

## Static Protected Member Functions

template<typename MzTabSectionRow >
static void | exportParentMoleculeToMzTab_ (const IdentificationData::ParentMolecule &parent, std::vector< MzTabSectionRow > &output, std::map< IdentificationData::ScoreTypeRef, Size > &score_map)
| Export a parent molecule (protein or nucleic acid) to mzTab. More...
template<typename MzTabSectionRow , typename IdentSeq >
static void | exportPeptideOrOligoToMzTab_ (const IdentSeq &identified, std::vector< MzTabSectionRow > &output, std::map< IdentificationData::ScoreTypeRef, Size > &score_map)
| Export an identified sequence (peptide or oligonucleotide, but not small molecule/compound) to mzTab. More...
template<typename MzTabSectionRow >
static void | exportQueryMatchToMzTab_ (const String &sequence, const IdentificationData::MoleculeQueryMatch &match, double calc_mass, std::vector< MzTabSectionRow > &output, std::map< IdentificationData::ScoreTypeRef, Size > &score_map, std::map< IdentificationData::InputFileRef, Size > &file_map)
| Export a molecule-query match (peptide- or oligonucleotide-spectrum match) to mzTab. More...
static void | exportStepsAndScoresToMzTab_ (const IdentificationData::AppliedProcessingSteps &steps_and_scores, MzTabParameterList &steps_out, std::map< Size, MzTabDouble > &scores_out, std::map< IdentificationData::ScoreTypeRef, Size > &score_map)
| Helper function to add processing steps (search engines) and their scores to MzTab. More...
static void | addMzTabSEScores_ (const std::map< IdentificationData::ScoreTypeRef, Size > &scores, std::map< Size, MzTabParameter > &output)
| Helper function to add search engine score entries to MzTab's meta data section. More...
static void | addMzTabMoleculeParentContext_ (const std::set< IdentificationData::MoleculeParentMatch > &matches, MzTabOligonucleotideSectionRow &row)
| Helper function for exportPeptideOrOligoToMzTab_() - oligonucleotide variant. More...
static void | addMzTabMoleculeParentContext_ (const std::set< IdentificationData::MoleculeParentMatch > &matches, MzTabPeptideSectionRow &row)
| Helper function for exportPeptideOrOligoToMzTab_() - peptide variant. More...
static IdentificationData::SearchParamRef | importDBSearchParameters_ (const ProteinIdentification::SearchParameters &pisp, IdentificationData &id_data)
| Helper function to import DB search parameters from legacy format. More...
static ProteinIdentification::SearchParameters | exportDBSearchParameters_ (IdentificationData::SearchParamRef ref)
| Helper function to export DB search parameters to legacy format. More...
static void | exportMSRunInformation_ (IdentificationData::ProcessingStepRef step_ref, ProteinIdentification &protein)
| Helper function to export (primary) MS run information to legacy format. More...

## Member Function Documentation

## ◆ addMzTabMoleculeParentContext_() [1/2]

static void addMzTabMoleculeParentContext_ | ( | const std::set< IdentificationData::MoleculeParentMatch > & | matches,
|  | MzTabOligonucleotideSectionRow & | row
| ) |  |

static protected

Helper function for exportPeptideOrOligoToMzTab_() - oligonucleotide variant.

## ◆ addMzTabMoleculeParentContext_() [2/2]

static void addMzTabMoleculeParentContext_ | ( | const std::set< IdentificationData::MoleculeParentMatch > & | matches,
|  | MzTabPeptideSectionRow & | row
| ) |  |

static protected

Helper function for exportPeptideOrOligoToMzTab_() - peptide variant.

## ◆ addMzTabSEScores_()

static void addMzTabSEScores_ | ( | const std::map< IdentificationData::ScoreTypeRef, Size > & | scores,
|  | std::map< Size, MzTabParameter > & | output
| ) |  |

static protected

Helper function to add search engine score entries to MzTab's meta data section.

## ◆ exportDBSearchParameters_()

static ProteinIdentification::SearchParameters exportDBSearchParameters_ | ( | IdentificationData::SearchParamRef | ref | ) |

static protected

Helper function to export DB search parameters to legacy format.

## ◆ exportIDs()

static void exportIDs | ( | const IdentificationData & | id_data,
|  | std::vector< ProteinIdentification > & | proteins,
|  | std::vector< PeptideIdentification > & | peptides,
|  | bool | export_oligonucleotides = `false`
| ) |  |

static

Export to legacy peptide/protein identifications.

Referenced by NucleicAcidSearchEngine::main_().

## ◆ exportMSRunInformation_()

static void exportMSRunInformation_ | ( | IdentificationData::ProcessingStepRef | step_ref,
|  | ProteinIdentification & | protein
| ) |  |

static protected

Helper function to export (primary) MS run information to legacy format.

## ◆ exportMzTab()

static MzTab exportMzTab | ( | const IdentificationData & | id_data | ) |

static

Export to mzTab format.

Referenced by NucleicAcidSearchEngine::main_().

## ◆ exportParentMoleculeToMzTab_()

static void exportParentMoleculeToMzTab_ | ( | const IdentificationData::ParentMolecule & | parent,
|  | std::vector< MzTabSectionRow > & | output,
|  | std::map< IdentificationData::ScoreTypeRef, Size > & | score_map
| ) |  |

inline static protected

Export a parent molecule (protein or nucleic acid) to mzTab.

References ParentMolecule::accession, ParentMolecule::coverage, ParentMolecule::description, ParentMolecule::sequence, and ScoredProcessingResult::steps_and_scores.

## ◆ exportPeptideOrOligoToMzTab_()

static void exportPeptideOrOligoToMzTab_ | ( | const IdentSeq & | identified,
|  | std::vector< MzTabSectionRow > & | output,
|  | std::map< IdentificationData::ScoreTypeRef, Size > & | score_map
| ) |  |

inline static protected

Export an identified sequence (peptide or oligonucleotide, but not small molecule/compound) to mzTab.

## ◆ exportQueryMatchToMzTab_()

static void exportQueryMatchToMzTab_ | ( | const String & | sequence,
|  | const IdentificationData::MoleculeQueryMatch & | match,
|  | double | calc_mass,
|  | std::vector< MzTabSectionRow > & | output,
|  | std::map< IdentificationData::ScoreTypeRef, Size > & | score_map,
|  | std::map< IdentificationData::InputFileRef, Size > & | file_map
| ) |  |

inline static protected

Export a molecule-query match (peptide- or oligonucleotide-spectrum match) to mzTab.

References MoleculeQueryMatch::charge, DataQuery::data_id, MoleculeQueryMatch::data_query_ref, MetaInfoInterface::getMetaValue(), DataQuery::input_file_opt, MetaInfoInterface::metaValueExists(), DataQuery::mz, DataQuery::rt, and ScoredProcessingResult::steps_and_scores.

## ◆ exportStepsAndScoresToMzTab_()

static void exportStepsAndScoresToMzTab_ | ( | const IdentificationData::AppliedProcessingSteps & | steps_and_scores,
|  | MzTabParameterList & | steps_out,
|  | std::map< Size, MzTabDouble > & | scores_out,
|  | std::map< IdentificationData::ScoreTypeRef, Size > & | score_map
| ) |  |

static protected

Helper function to add processing steps (search engines) and their scores to MzTab.

## ◆ importDBSearchParameters_()

static IdentificationData::SearchParamRef importDBSearchParameters_ | ( | const ProteinIdentification::SearchParameters & | pisp,
|  | IdentificationData & | id_data
| ) |  |

static protected

Helper function to import DB search parameters from legacy format.

## ◆ importIDs()

static void importIDs | ( | IdentificationData & | id_data,
|  | const std::vector< ProteinIdentification > & | proteins,
|  | const std::vector< PeptideIdentification > & | peptides
| ) |  |

static

Import from legacy peptide/protein identifications.

## ◆ importSequences()

static void importSequences | ( | IdentificationData & | id_data,
|  | const std::vector< FASTAFile::FASTAEntry > & | fasta,
|  | IdentificationData::MoleculeType | type = `IdentificationData::MoleculeType::PROTEIN`,
|  | const String & | decoy_pattern = `""`
| ) |  |

static

Import FASTA sequences as parent molecules.

Referenced by NucleicAcidSearchEngine::main_().