OpenMS
2.6.0
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#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 IdentificationData::MoleculeParentMatch &match, MzTabOligonucleotideSectionRow &row) |
Helper function for exportPeptideOrOligoToMzTab_() - oligonucleotide variant. More... | |
static void | addMzTabMoleculeParentContext_ (const IdentificationData::MoleculeParentMatch &match, 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... | |
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staticprotected |
Helper function for exportPeptideOrOligoToMzTab_() - oligonucleotide variant.
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staticprotected |
Helper function for exportPeptideOrOligoToMzTab_() - peptide variant.
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staticprotected |
Helper function to add search engine score entries to MzTab's meta data section.
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staticprotected |
Helper function to export DB search parameters to legacy format.
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static |
Export to legacy peptide/protein identifications.
Referenced by NucleicAcidSearchEngine::main_().
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staticprotected |
Helper function to export (primary) MS run information to legacy format.
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static |
Export to mzTab format.
Referenced by NucleicAcidSearchEngine::main_().
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inlinestaticprotected |
Export a parent molecule (protein or nucleic acid) to mzTab.
References ParentMolecule::accession, ParentMolecule::coverage, ParentMolecule::description, ParentMolecule::sequence, and ScoredProcessingResult::steps_and_scores.
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inlinestaticprotected |
Export an identified sequence (peptide or oligonucleotide, but not small molecule/compound) to mzTab.
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inlinestaticprotected |
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.
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staticprotected |
Helper function to add processing steps (search engines) and their scores to MzTab.
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staticprotected |
Helper function to import DB search parameters from legacy format.
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static |
Import from legacy peptide/protein identifications.
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static |
Import FASTA sequences as parent molecules.
Referenced by NucleicAcidSearchEngine::main_().