23 #pragma clang diagnostic push
24 #pragma clang diagnostic ignored "-Wnon-virtual-dtor"
76 std::vector<MzTabModification>
get()
const;
78 void set(
const std::vector<MzTabModification>& entries);
149 std::map<Size, MzTabString>
uri;
161 std::map<Size, MzTabMSRunMetaData>
ms_run;
165 std::map<Size, MzTabSampleMetaData>
sample;
167 std::map<Size, MzTabAssayMetaData>
assay;
171 std::map<Size, MzTabCVMetaData>
cv;
205 std::vector<MzTabOptionalColumnEntry>
opt_;
241 std::vector<MzTabOptionalColumnEntry>
opt_;
279 std::vector<MzTabOptionalColumnEntry>
opt_;
334 std::vector<MzTabOptionalColumnEntry>
opt_;
359 std::vector<MzTabOptionalColumnEntry>
opt_;
390 std::vector<MzTabOptionalColumnEntry>
opt_;
421 std::vector<MzTabOptionalColumnEntry>
opt_;
557 const std::vector<ProteinIdentification>& prot_ids,
560 bool first_run_inference_only,
561 bool export_empty_pep_ids =
false,
562 bool export_all_psms =
false,
563 const String& title =
"ID export from OpenMS");
590 const bool first_run_inference_only,
591 const bool export_unidentified_features,
592 const bool export_unassigned_ids,
593 const bool export_subfeatures,
594 const bool export_empty_pep_ids =
false,
595 const bool export_all_psms =
false,
596 const String& title =
"ConsensusMap export from OpenMS");
602 const std::vector<const ProteinIdentification*>& prot_ids,
603 const std::vector<const PeptideIdentification*>& peptide_ids,
605 bool first_run_inference_only,
606 bool export_empty_pep_ids =
false,
607 bool export_all_psms =
false,
608 const String& title =
"ID export from OpenMS");
645 size_t quant_study_variables_ = 0;
647 size_t PRT_STATE_ = 0;
648 size_t prt_run_id_ = 0;
649 size_t prt_hit_id_ = 0;
650 size_t prt_group_id_ = 0;
651 size_t prt_indistgroup_id_ = 0;
654 size_t current_psm_idx_ = 0;
670 const bool first_run_inference_only,
671 const bool export_unidentified_features,
672 const bool export_unassigned_ids,
673 const bool export_subfeatures,
674 const bool export_empty_pep_ids =
false,
675 const bool export_all_psms =
false,
676 const String& title =
"ConsensusMap export from OpenMS");
715 size_t quant_study_variables_ = 0;
716 size_t n_study_variables_ = 0;
717 size_t PRT_STATE_ = 0;
718 size_t prt_run_id_ = 0;
719 size_t prt_hit_id_ = 0;
720 size_t prt_group_id_ = 0;
721 size_t prt_indistgroup_id_ = 0;
723 size_t pep_counter_ = 0;
725 size_t current_psm_idx_ = 0;
743 std::vector<ProteinIdentification const*>
const& prot_id,
744 std::map<String, size_t>& idrun_2_run_index,
745 std::map<std::pair<size_t, size_t>,
size_t>& map_run_fileidx_2_msfileidx,
746 std::map<
Size, std::vector<std::pair<String, String>>>& run_to_search_engines,
747 Size const current_psm_idx,
751 bool const export_empty_pep_ids,
752 bool const export_all_psms);
758 const Size n_study_variables,
759 const std::set<String>& consensus_feature_user_value_keys,
760 const std::set<String>& peptide_identifications_user_value_keys,
761 const std::set<String>& peptide_hit_user_value_keys,
762 const std::map<String, size_t>& idrun_2_run_index,
763 const std::map<std::pair<size_t,size_t>,
size_t>& map_run_fileidx_2_msfileidx,
764 const std::map< std::pair< String, unsigned >,
unsigned>& path_label_to_assay,
765 const std::vector<String>& fixed_mods,
766 bool export_subfeatures);
770 const std::set<String>& feature_user_value_keys,
771 const std::set<String>& peptide_identifications_user_value_keys,
772 const std::set<String>& peptide_hit_user_value_keys,
773 const std::vector<String>& fixed_mods);
779 const std::set<String>& protein_hit_user_value_keys);
787 const std::vector<ProteinHit>& protein_hits,
790 const std::map<
Size, std::set<Size>>& ind2prot,
795 const std::map<size_t, String>& msrunindex_2_msfilename,
799 const std::vector<const ProteinIdentification*>& prot_ids,
801 std::map<String, size_t>& msfilename_2_msrunindex,
802 std::map<size_t, String>& msrunindex_2_msfilename);
810 std::set<String>& consensus_feature_user_value_keys,
811 std::set<String>& peptide_identification_user_value_keys,
812 std::set<String>& peptide_hit_user_value_keys);
815 std::set<String>& feature_user_value_keys,
816 std::set<String>& peptide_identification_user_value_keys,
817 std::set<String>& peptide_hit_user_value_keys);
820 const std::vector<const ProteinIdentification*>& prot_ids,
821 std::vector<const PeptideIdentification*>& peptide_ids_,
822 std::set<String>& protein_hit_user_value_keys,
823 std::set<String>& peptide_id_user_value_keys,
824 std::set<String>& peptide_hit_user_value_keys);
830 const std::vector<const ProteinIdentification*>& prot_ids,
831 const std::vector<const PeptideIdentification*>& pep_ids,
833 std::map<std::tuple<String, String, String>, std::set<Size>>& search_engine_to_runs,
834 std::map<
Size, std::vector<std::pair<String, String>>>& run_to_search_engines,
835 std::map<
Size, std::vector<std::vector<std::pair<String, String>>>>& run_to_search_engines_settings,
836 std::map<
String, std::vector<std::pair<String, String>>>& search_engine_to_settings);
839 const std::vector<ProteinIdentification::ProteinGroup>& groups,
840 const std::vector<ProteinHit>& proteins);
843 const std::vector<const ProteinIdentification*>& prot_ids,
844 const std::map<std::tuple<String, String, String>, std::set<Size>>& search_engine_to_runs,
845 const std::map<
String, std::vector<std::pair<String,String>>>& search_engine_to_settings,
847 bool first_run_inference_only);
850 const std::vector<const ProteinIdentification*>& prot_ids,
851 const std::map<String, size_t>& msfilename_2_msrunindex,
853 std::map<std::pair<size_t, size_t>,
size_t>& map_run_fileidx_2_msfileidx);
856 const std::vector<const ProteinIdentification*>& prot_ids,
881 #pragma clang diagnostic pop
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:45
A container for consensus elements.
Definition: ConsensusMap.h:68
A container for features.
Definition: FeatureMap.h:82
An LC-MS feature.
Definition: Feature.h:46
Definition: MzTabBase.h:361
Definition: MzTabBase.h:156
Definition: MzTabBase.h:79
Definition: MzTabBase.h:41
Definition: MzTabBase.h:101
void set(const std::vector< MzTabModification > &entries)
std::vector< MzTabModification > get() const
String toCellString() const
void fromCellString(const String &s)
~MzTabModificationList()=default
std::vector< MzTabModification > entries_
Definition: MzTab.h:82
Data model of MzTab files.
Definition: MzTab.h:38
MzTabString getModOrSubstIdentifier() const
String toCellString() const
void fromCellString(const String &s)
MzTabString mod_identifier_
Definition: MzTab.h:62
void setPositionsAndParameters(const std::vector< std::pair< Size, MzTabParameter > > &ppp)
set (potentially ambiguous) position(s) with associated parameter (might be null if not set)
std::vector< std::pair< Size, MzTabParameter > > pos_param_pairs_
Definition: MzTab.h:61
std::vector< std::pair< Size, MzTabParameter > > getPositionsAndParameters() const
~MzTabModification()=default
void setModificationIdentifier(const MzTabString &mod_id)
Definition: MzTabBase.h:243
Definition: MzTabBase.h:206
Definition: MzTabBase.h:292
String getSpecRef() const
Definition: MzTabBase.h:266
Definition: MzTabBase.h:180
std::vector< String > pep_optional_column_names_
Definition: MzTab.h:729
const ConsensusMap & consensus_map_
Definition: MzTab.h:689
std::map< Size, std::vector< std::pair< String, String > > > run_to_search_engines_
Definition: MzTab.h:699
std::map< std::pair< size_t, size_t >, size_t > map_id_run_fileidx_2_msfileidx_
Definition: MzTab.h:701
std::vector< const ProteinIdentification * > prot_ids_
Definition: MzTab.h:704
std::set< String > consensus_feature_peptide_identification_user_value_keys_
Definition: MzTab.h:692
String filename_
Definition: MzTab.h:709
std::map< Size, std::set< Size > > pg2prot_
Definition: MzTab.h:697
bool export_empty_pep_ids_
Definition: MzTab.h:713
bool nextPRTRow(MzTabProteinSectionRow &row)
bool export_unidentified_features_
Definition: MzTab.h:711
bool nextPEPRow(MzTabPeptideSectionRow &row)
const std::vector< String > & getProteinOptionalColumnNames() const
std::set< String > protein_hit_user_value_keys_
Definition: MzTab.h:690
std::vector< String > psm_optional_column_names_
Definition: MzTab.h:730
StringList fixed_mods_
Definition: MzTab.h:710
std::map< String, size_t > idrunid_2_idrunindex_
Definition: MzTab.h:698
bool export_all_psms_
Definition: MzTab.h:714
std::vector< const PeptideIdentification * > peptide_ids_
Definition: MzTab.h:705
std::map< Size, std::set< Size > > ind2prot_
Definition: MzTab.h:696
const MzTabMetaData & getMetaData() const
StringList ms_runs_
Definition: MzTab.h:707
bool nextPSMRow(MzTabPSMSectionRow &row)
CMMzTabStream(const ConsensusMap &consensus_map, const String &filename, const bool first_run_inference_only, const bool export_unidentified_features, const bool export_unassigned_ids, const bool export_subfeatures, const bool export_empty_pep_ids=false, const bool export_all_psms=false, const String &title="ConsensusMap export from OpenMS")
std::map< std::pair< String, unsigned >, unsigned > path_label_to_assay_
Definition: MzTab.h:702
bool first_run_inference_
Definition: MzTab.h:708
std::map< Size, std::vector< std::vector< std::pair< String, String > > > > run_to_search_engines_settings_
Definition: MzTab.h:700
const std::vector< String > & getPeptideOptionalColumnNames() const
bool export_subfeatures_
Definition: MzTab.h:712
std::vector< String > prt_optional_column_names_
Definition: MzTab.h:728
std::set< String > consensus_feature_user_value_keys_
Definition: MzTab.h:691
MzTabString db_
Definition: MzTab.h:726
const std::vector< String > & getPSMOptionalColumnNames() const
MzTabMetaData meta_data_
Definition: MzTab.h:732
std::set< String > consensus_feature_peptide_hit_user_value_keys_
Definition: MzTab.h:693
std::vector< String > pep_optional_column_names_
Definition: MzTab.h:658
std::map< Size, std::vector< std::pair< String, String > > > run_to_search_engines_
Definition: MzTab.h:628
std::map< std::pair< size_t, size_t >, size_t > map_id_run_fileidx_2_msfileidx_
Definition: MzTab.h:630
std::vector< const ProteinIdentification * > prot_ids_
Definition: MzTab.h:633
String filename_
Definition: MzTab.h:638
std::map< Size, std::set< Size > > pg2prot_
Definition: MzTab.h:626
bool export_empty_pep_ids_
Definition: MzTab.h:643
bool nextPRTRow(MzTabProteinSectionRow &row)
bool nextPEPRow(MzTabPeptideSectionRow &row)
const std::vector< String > & getProteinOptionalColumnNames() const
std::set< String > protein_hit_user_value_keys_
Definition: MzTab.h:620
std::vector< String > psm_optional_column_names_
Definition: MzTab.h:659
StringList fixed_mods_
Definition: MzTab.h:639
std::map< String, size_t > idrunid_2_idrunindex_
Definition: MzTab.h:627
bool export_all_psms_
Definition: MzTab.h:644
std::vector< const PeptideIdentification * > peptide_ids_
Definition: MzTab.h:634
std::map< Size, std::set< Size > > ind2prot_
Definition: MzTab.h:625
const MzTabMetaData & getMetaData() const
StringList ms_runs_
Definition: MzTab.h:636
bool nextPSMRow(MzTabPSMSectionRow &row)
std::map< std::pair< String, unsigned >, unsigned > path_label_to_assay_
Definition: MzTab.h:631
std::set< String > peptide_hit_user_value_keys_
Definition: MzTab.h:622
bool first_run_inference_
Definition: MzTab.h:637
std::map< Size, std::vector< std::vector< std::pair< String, String > > > > run_to_search_engines_settings_
Definition: MzTab.h:629
const std::vector< String > & getPeptideOptionalColumnNames() const
IDMzTabStream(const std::vector< const ProteinIdentification * > &prot_ids, const std::vector< const PeptideIdentification * > &peptide_ids, const String &filename, bool first_run_inference_only, bool export_empty_pep_ids=false, bool export_all_psms=false, const String &title="ID export from OpenMS")
std::vector< String > prt_optional_column_names_
Definition: MzTab.h:657
std::set< String > peptide_id_user_value_keys_
Definition: MzTab.h:621
MzTabString db_
Definition: MzTab.h:655
const std::vector< String > & getPSMOptionalColumnNames() const
MzTabMetaData meta_data_
Definition: MzTab.h:661
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:455
static void getSearchModifications_(const std::vector< const ProteinIdentification * > &prot_ids, StringList &var_mods, StringList &fixed_mods)
size_t getNumberOfPSMs() const
const std::map< Size, String > & getCommentRows() const
static MzTabString getModificationIdentifier_(const ResidueModification &r)
void setOligonucleotideSectionRows(const MzTabOligonucleotideSectionRows &onsd)
MzTabOSMSectionRows osm_data_
/ oligonucleotide-spectrum matches
Definition: MzTab.h:874
std::vector< Size > empty_rows_
index of empty rows
Definition: MzTab.h:875
MzTabSmallMoleculeSectionRows small_molecule_data_
Definition: MzTab.h:871
const std::vector< Size > & getEmptyRows() const
static void addMetaInfoToOptionalColumns(const std::set< String > &keys, std::vector< MzTabOptionalColumnEntry > &opt, const String &id, const MetaInfoInterface &meta)
std::vector< String > getSmallMoleculeOptionalColumnNames() const
Extract opt_ (custom, optional column names)
static MzTab exportConsensusMapToMzTab(const ConsensusMap &consensus_map, const String &filename, const bool first_run_inference_only, const bool export_unidentified_features, const bool export_unassigned_ids, const bool export_subfeatures, const bool export_empty_pep_ids=false, const bool export_all_psms=false, const String &title="ConsensusMap export from OpenMS")
export linked peptide features aka consensus map
std::vector< String > getOligonucleotideOptionalColumnNames() const
Extract opt_ (custom, optional column names)
MzTabOligonucleotideSectionRows oligonucleotide_data_
Definition: MzTab.h:873
static MzTabParameter getProteinScoreType_(const ProteinIdentification &prot_id)
MzTabPSMSectionRows & getPSMSectionRows()
static void addMSRunMetaData_(const std::map< size_t, String > &msrunindex_2_msfilename, MzTabMetaData &meta_data)
std::map< Size, String > comment_rows_
comments
Definition: MzTab.h:876
static MzTab exportIdentificationsToMzTab(const std::vector< ProteinIdentification > &prot_ids, const PeptideIdentificationList &peptide_ids, const String &filename, bool first_run_inference_only, bool export_empty_pep_ids=false, bool export_all_psms=false, const String &title="ID export from OpenMS")
Export peptide and protein identifications to mzTab.
const MzTabMetaData & getMetaData() const
const MzTabNucleicAcidSectionRows & getNucleicAcidSectionRows() const
static MzTabPeptideSectionRow peptideSectionRowFromConsensusFeature_(const ConsensusFeature &c, const ConsensusMap &consensus_map, const StringList &ms_runs, const Size n_study_variables, const std::set< String > &consensus_feature_user_value_keys, const std::set< String > &peptide_identifications_user_value_keys, const std::set< String > &peptide_hit_user_value_keys, const std::map< String, size_t > &idrun_2_run_index, const std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx, const std::map< std::pair< String, unsigned >, unsigned > &path_label_to_assay, const std::vector< String > &fixed_mods, bool export_subfeatures)
static std::optional< MzTabPSMSectionRow > PSMSectionRowFromPeptideID_(PeptideIdentification const &pid, std::vector< ProteinIdentification const * > const &prot_id, std::map< String, size_t > &idrun_2_run_index, std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx, std::map< Size, std::vector< std::pair< String, String >>> &run_to_search_engines, Size const current_psm_idx, Size const psm_id, MzTabString const &db, MzTabString const &db_version, bool const export_empty_pep_ids, bool const export_all_psms)
std::vector< String > getPeptideOptionalColumnNames() const
Extract opt_ (custom, optional column names)
std::vector< String > getOSMOptionalColumnNames() const
Extract opt_ (custom, optional column names)
void setNucleicAcidSectionRows(const MzTabNucleicAcidSectionRows &nasd)
static MzTabProteinSectionRow nextProteinSectionRowFromIndistinguishableGroup_(const std::vector< ProteinHit > &protein_hits, const ProteinIdentification::ProteinGroup &group, const size_t g, const std::map< Size, std::set< Size >> &ind2prot, const MzTabString &db, const MzTabString &db_version)
void setPeptideSectionRows(const MzTabPeptideSectionRows &psd)
static size_t getQuantStudyVariables_(const ProteinIdentification &pid)
static MzTabProteinSectionRow nextProteinSectionRowFromProteinGroup_(const ProteinIdentification::ProteinGroup &group, const MzTabString &db, const MzTabString &db_version)
static std::map< Size, std::set< Size > > mapGroupsToProteins_(const std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &proteins)
const MzTabPeptideSectionRows & getPeptideSectionRows() const
void setSmallMoleculeSectionRows(const MzTabSmallMoleculeSectionRows &smsd)
void setProteinSectionRows(const MzTabProteinSectionRows &psd)
std::vector< String > getNucleicAcidOptionalColumnNames() const
Extract opt_ (custom, optional column names)
void setMetaData(const MzTabMetaData &md)
MzTabPSMSectionRows psm_data_
Definition: MzTab.h:870
const MzTabPSMSectionRows & getPSMSectionRows() const
static MzTabParameter getMSRunSpectrumIdentifierType_(const std::vector< const PeptideIdentification * > &peptide_ids_)
const MzTabOligonucleotideSectionRows & getOligonucleotideSectionRows() const
static void mapBetweenRunAndSearchEngines_(const std::vector< const ProteinIdentification * > &prot_ids, const std::vector< const PeptideIdentification * > &pep_ids, bool skip_first_run, std::map< std::tuple< String, String, String >, std::set< Size >> &search_engine_to_runs, std::map< Size, std::vector< std::pair< String, String >>> &run_to_search_engines, std::map< Size, std::vector< std::vector< std::pair< String, String >>>> &run_to_search_engines_settings, std::map< String, std::vector< std::pair< String, String >>> &search_engine_to_settings)
MzTabProteinSectionRows & getProteinSectionRows()
static void getFeatureMapMetaValues_(const FeatureMap &feature_map, std::set< String > &feature_user_value_keys, std::set< String > &peptide_identification_user_value_keys, std::set< String > &peptide_hit_user_value_keys)
MzTabNucleicAcidSectionRows nucleic_acid_data_
Definition: MzTab.h:872
static std::map< Size, MzTabModificationMetaData > generateMzTabStringFromVariableModifications(const std::vector< String > &mods)
MzTabProteinSectionRows protein_data_
Definition: MzTab.h:868
static std::map< Size, MzTabModificationMetaData > generateMzTabStringFromFixedModifications(const std::vector< String > &mods)
static std::map< String, Size > mapIDRunIdentifier2IDRunIndex_(const std::vector< const ProteinIdentification * > &prot_ids)
std::vector< String > getProteinOptionalColumnNames() const
Extract opt_ (custom, optional column names)
static void checkSequenceUniqueness_(const PeptideIdentificationList &curr_pep_ids)
void setEmptyRows(const std::vector< Size > &empty)
static MzTabPeptideSectionRow peptideSectionRowFromFeature_(const Feature &c, const std::set< String > &feature_user_value_keys, const std::set< String > &peptide_identifications_user_value_keys, const std::set< String > &peptide_hit_user_value_keys, const std::vector< String > &fixed_mods)
static MzTabModificationList extractModificationList(const PeptideHit &pep_hit, const std::vector< String > &fixed_mods, const std::vector< String > &localization_mods)
MzTabPeptideSectionRows peptide_data_
Definition: MzTab.h:869
const MzTabSmallMoleculeSectionRows & getSmallMoleculeSectionRows() const
static void mapIDRunFileIndex2MSFileIndex_(const std::vector< const ProteinIdentification * > &prot_ids, const std::map< String, size_t > &msfilename_2_msrunindex, bool skip_first_run, std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx)
MzTab()=default
Default constructor.
static void getIdentificationMetaValues_(const std::vector< const ProteinIdentification * > &prot_ids, std::vector< const PeptideIdentification * > &peptide_ids_, std::set< String > &protein_hit_user_value_keys, std::set< String > &peptide_id_user_value_keys, std::set< String > &peptide_hit_user_value_keys)
std::vector< String > getPSMOptionalColumnNames() const
Extract opt_ (custom, optional column names)
MzTabMetaData meta_data_
Definition: MzTab.h:867
const MzTabOSMSectionRows & getOSMSectionRows() const
static void mapBetweenMSFileNameAndMSRunIndex_(const std::vector< const ProteinIdentification * > &prot_ids, bool skip_first, std::map< String, size_t > &msfilename_2_msrunindex, std::map< size_t, String > &msrunindex_2_msfilename)
const MzTabProteinSectionRows & getProteinSectionRows() const
static std::map< Size, MzTabModificationMetaData > generateMzTabStringFromModifications(const std::vector< String > &mods)
MzTabPeptideSectionRows & getPeptideSectionRows()
void setCommentRows(const std::map< Size, String > &com)
void setPSMSectionRows(const MzTabPSMSectionRows &psd)
static void getConsensusMapMetaValues_(const ConsensusMap &consensus_map, std::set< String > &consensus_feature_user_value_keys, std::set< String > &peptide_identification_user_value_keys, std::set< String > &peptide_hit_user_value_keys)
static void addSearchMetaData_(const std::vector< const ProteinIdentification * > &prot_ids, const std::map< std::tuple< String, String, String >, std::set< Size >> &search_engine_to_runs, const std::map< String, std::vector< std::pair< String, String >>> &search_engine_to_settings, MzTabMetaData &meta_data, bool first_run_inference_only)
void setOSMSectionRows(const MzTabOSMSectionRows &osd)
static MzTabProteinSectionRow proteinSectionRowFromProteinHit_(const ProteinHit &hit, const MzTabString &db, const MzTabString &db_version, const std::set< String > &protein_hit_user_value_keys)
static MzTab exportFeatureMapToMzTab(const FeatureMap &feature_map, const String &filename)
Represents a single spectrum match (candidate) for a specific tandem mass spectrum (MS/MS).
Definition: PeptideHit.h:50
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.h:66
Represents the set of candidates (SpectrumMatches) identified for a single precursor spectrum.
Definition: PeptideIdentification.h:63
Representation of a protein hit.
Definition: ProteinHit.h:34
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:106
Representation of a protein identification run.
Definition: ProteinIdentification.h:51
Representation of a modification on an amino acid residue.
Definition: ResidueModification.h:53
A more convenient string class.
Definition: String.h:34
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
const double c
Definition: Constants.h:188
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
MzTabInteger taxid
NEWT taxonomy for the species.
Definition: MzTab.h:319
MzTabInteger end
Definition: MzTab.h:389
MzTabSpectraRef spectra_ref
Spectra identifying the peptide.
Definition: MzTab.h:236
MzTabDouble calc_mass_to_charge
Precursor ion’s m/z.
Definition: MzTab.h:316
std::vector< MzTabPSMSectionRow > MzTabPSMSectionRows
Definition: MzTab.h:441
std::map< Size, MzTabDouble > smallmolecule_abundance_assay
Definition: MzTab.h:330
MzTabString position
Definition: MzTab.h:90
MzTabString modifications
Modifications identified on the small molecule.
Definition: MzTab.h:329
MzTabString sequence
The peptide’s sequence.
Definition: MzTab.h:221
std::map< Size, MzTabInteger > num_oligos_distinct_ms_run
Definition: MzTab.h:351
MzTabDoubleList retention_time
Time points in seconds. Semantics may vary.
Definition: MzTab.h:231
MzTabDoubleList retention_time_window
Definition: MzTab.h:232
MzTabParameterList fragmentation_method
Definition: MzTab.h:106
std::vector< int > sample_refs
Definition: MzTab.h:112
MzTabParameter format
Definition: MzTab.h:103
std::map< Size, MzTabDouble > smallmolecule_abundance_std_error_study_variable
Definition: MzTab.h:333
std::vector< MzTabProteinSectionRow > MzTabProteinSectionRows
Definition: MzTab.h:439
std::map< Size, MzTabDouble > best_search_engine_score
Search engine(s) score(s) for the peptide.
Definition: MzTab.h:227
MzTabString smiles
Molecular structure in SMILES format.
Definition: MzTab.h:312
MzTabBoolean unique
0=false, 1=true, null else: Peptide is unique for the protein.
Definition: MzTab.h:223
MzTabString uri
Location of the PSMs source entry.
Definition: MzTab.h:235
std::vector< int > assay_refs
Definition: MzTab.h:111
MzTabModificationList modifications
Modifications identified in the peptide.
Definition: MzTab.h:230
MzTabParameter id_format
Definition: MzTab.h:105
MzTabInteger charge
Precursor ion’s charge.
Definition: MzTab.h:233
std::map< Size, MzTabDouble > smallmolecule_abundance_stdev_study_variable
Definition: MzTab.h:332
MzTabString database_version
Version (and optionally # of entries).
Definition: MzTab.h:225
std::map< Size, MzTabModificationMetaData > quantification_mod
Definition: MzTab.h:96
MzTabString description
Definition: MzTab.h:113
MzTabStringList identifier
The small molecule’s identifier.
Definition: MzTab.h:310
std::vector< MzTabPeptideSectionRow > MzTabPeptideSectionRows
Definition: MzTab.h:440
std::map< Size, std::map< Size, MzTabDouble > > search_engine_score_ms_run
Definition: MzTab.h:228
MzTabString accession
The protein’s accession.
Definition: MzTab.h:222
MzTabStringList ambiguity_members
Alternative nucleic acid identifications.
Definition: MzTab.h:353
MzTabDouble mass_to_charge
Precursor ion’s m/z.
Definition: MzTab.h:234
MzTabDouble coverage
(0-1) Fraction of nucleic acid sequence identified.
Definition: MzTab.h:358
MzTabParameter modification
Definition: MzTab.h:88
std::map< Size, MzTabInteger > num_oligos_unique_ms_run
Definition: MzTab.h:352
MzTabInteger start
Definition: MzTab.h:388
std::map< Size, MzTabDouble > peptide_abundance_std_error_study_variable
Definition: MzTab.h:240
MzTabString site
Definition: MzTab.h:89
MzTabString inchi_key
InChi Key of the identified compound.
Definition: MzTab.h:313
MzTabParameter quantification_reagent
Definition: MzTab.h:95
MzTabString location
Definition: MzTab.h:104
std::vector< MzTabOSMSectionRow > MzTabOSMSectionRows
Definition: MzTab.h:445
MzTabInteger reliability
(1-3) 0=null Identification reliability for the peptide.
Definition: MzTab.h:229
std::vector< int > ms_run_ref
Definition: MzTab.h:98
std::map< Size, MzTabInteger > num_osms_ms_run
Definition: MzTab.h:350
std::map< Size, MzTabDouble > search_engine_score
Search engine(s) score(s) for the match.
Definition: MzTab.h:412
MzTabStringList go_terms
List of GO terms for the nucleic acid.
Definition: MzTab.h:357
MzTabString pre
Definition: MzTab.h:386
MzTabDouble exp_mass_to_charge
Precursor ion’s m/z.
Definition: MzTab.h:315
std::map< Size, MzTabDouble > peptide_abundance_study_variable
Definition: MzTab.h:238
std::map< Size, MzTabDouble > smallmolecule_abundance_study_variable
Definition: MzTab.h:331
std::vector< MzTabOptionalColumnEntry > opt_
Optional columns must start with “opt_”.
Definition: MzTab.h:241
std::vector< MzTabOligonucleotideSectionRow > MzTabOligonucleotideSectionRows
Definition: MzTab.h:444
MzTabParameterList search_engine
Search engine(s) that identified the peptide.
Definition: MzTab.h:226
MzTabString post
Definition: MzTab.h:387
std::map< Size, MzTabDouble > peptide_abundance_stdev_study_variable
Definition: MzTab.h:239
std::map< Size, MzTabDouble > peptide_abundance_assay
Definition: MzTab.h:237
MzTabString chemical_formula
Chemical formula of the identified compound.
Definition: MzTab.h:311
MzTabString sample_ref
Definition: MzTab.h:97
std::vector< MzTabSmallMoleculeSectionRow > MzTabSmallMoleculeSectionRows
Definition: MzTab.h:442
MzTabString species
Human readable name of the species.
Definition: MzTab.h:320
std::vector< MzTabNucleicAcidSectionRow > MzTabNucleicAcidSectionRows
Definition: MzTab.h:443
MzTabString database
Name of the sequence database.
Definition: MzTab.h:224
NUC - Nucleic acid section (table-based)
Definition: MzTab.h:339
OSM - OSM (oligonucleotide-spectrum match) section (table-based)
Definition: MzTab.h:409
OLI - Oligonucleotide section (table-based)
Definition: MzTab.h:374
PEP - Peptide section (Table based)
Definition: MzTab.h:220
SML Small molecule section (table based)
Definition: MzTab.h:309
Comparison operator for sorting rows.
Definition: MzTab.h:363
bool operator()(const MzTabNucleicAcidSectionRow &row1, const MzTabNucleicAcidSectionRow &row2) const
Definition: MzTab.h:364
Comparison operator for sorting rows.
Definition: MzTab.h:425
bool operator()(const MzTabOSMSectionRow &row1, const MzTabOSMSectionRow &row2) const
Definition: MzTab.h:426
Comparison operator for sorting rows.
Definition: MzTab.h:394
bool operator()(const MzTabOligonucleotideSectionRow &row1, const MzTabOligonucleotideSectionRow &row2) const
Definition: MzTab.h:395
Comparison operator for sorting rows.
Definition: MzTab.h:290
bool operator()(const MzTabPSMSectionRow &row1, const MzTabPSMSectionRow &row2) const
Definition: MzTab.h:291
PSM - PSM section (Table based)
Definition: MzTab.h:258
MzTabSpectraRef spectra_ref
Spectrum for this PSM.
Definition: MzTab.h:274
MzTabDouble calc_mass_to_charge
The calculated m/z ratio of the experimental precursor ion.
Definition: MzTab.h:272
MzTabString start
(List of) Start positions in parent protein(s)
Definition: MzTab.h:277
MzTabString sequence
The peptide’s sequence.
Definition: MzTab.h:259
MzTabDoubleList retention_time
Time points in seconds. Semantics may vary.
Definition: MzTab.h:269
MzTabBoolean unique
0=false, 1=true, null else: Peptide is unique for the protein.
Definition: MzTab.h:262
MzTabString uri
Location of the PSM’s source entry.
Definition: MzTab.h:273
void addPepEvidenceToRows(const std::vector< PeptideEvidence > &peptide_evidences)
Gets peptide_evidences with data from internal structures adds their info to an MzTabPSMSectionRow (p...
MzTabModificationList modifications
Modifications identified in the peptide.
Definition: MzTab.h:268
MzTabInteger charge
The charge of the experimental precursor ion.
Definition: MzTab.h:270
MzTabString database_version
Version (and optionally # of entries).
Definition: MzTab.h:264
MzTabString accession
List of potential parent protein accessions as in the fasta DB.
Definition: MzTab.h:261
MzTabString end
(List of) Start positions in parent protein(s)
Definition: MzTab.h:278
MzTabInteger reliability
(1-3) 0=null Identification reliability for the peptide.
Definition: MzTab.h:267
std::map< Size, MzTabDouble > search_engine_score
Search engine(s) score(s) for the peptide.
Definition: MzTab.h:266
MzTabString pre
(List of) Amino acid in parent protein(s) before the start of the current PSM
Definition: MzTab.h:275
MzTabDouble exp_mass_to_charge
The observed m/z ratio of the experimental precursor ion (either directly from the raw data or correc...
Definition: MzTab.h:271
std::vector< MzTabOptionalColumnEntry > opt_
Optional columns must start with “opt_”.
Definition: MzTab.h:279
MzTabParameterList search_engine
Search engine(s) that identified the peptide.
Definition: MzTab.h:265
MzTabString post
(List of) Amino acid in parent protein(s) after the start of the current PSM
Definition: MzTab.h:276
MzTabInteger PSM_ID
A unique ID of a PSM line.
Definition: MzTab.h:260
MzTabString database
Name of the sequence database.
Definition: MzTab.h:263
Comparison operator for sorting rows.
Definition: MzTab.h:246
bool operator()(const MzTabPeptideSectionRow &row1, const MzTabPeptideSectionRow &row2) const
Definition: MzTab.h:247
Comparison operator for sorting rows.
Definition: MzTab.h:209
bool operator()(const MzTabProteinSectionRow &row1, const MzTabProteinSectionRow &row2) const
Definition: MzTab.h:210
PRT - Protein section (Table based)
Definition: MzTab.h:181
MzTabInteger taxid
NEWT taxonomy for the species.
Definition: MzTab.h:185
std::map< Size, MzTabDouble > protein_abundance_assay
Definition: MzTab.h:201
std::map< Size, MzTabDouble > best_search_engine_score
best_search_engine_score[1-n]
Definition: MzTab.h:190
MzTabString uri
Location of the protein’s source entry.
Definition: MzTab.h:198
std::map< Size, MzTabDouble > protein_abundance_std_error_study_variable
Definition: MzTab.h:204
MzTabModificationList modifications
Modifications identified in the protein.
Definition: MzTab.h:197
MzTabString database_version
String Version of the protein database.
Definition: MzTab.h:188
MzTabString description
Human readable description (i.e. the name)
Definition: MzTab.h:184
std::map< Size, MzTabInteger > num_peptides_distinct_ms_run
Definition: MzTab.h:194
std::map< Size, MzTabDouble > protein_abundance_study_variable
Definition: MzTab.h:202
std::map< Size, std::map< Size, MzTabDouble > > search_engine_score_ms_run
search_engine_score[index1]_ms_run[index2]
Definition: MzTab.h:191
MzTabString accession
The protein’s accession.
Definition: MzTab.h:183
MzTabStringList ambiguity_members
Alternative protein identifications.
Definition: MzTab.h:196
MzTabDouble coverage
(0-1) Amount of protein sequence identified.
Definition: MzTab.h:200
MzTabInteger reliability
Definition: MzTab.h:192
std::map< Size, MzTabInteger > num_psms_ms_run
Definition: MzTab.h:193
MzTabStringList go_terms
List of GO terms for the protein.
Definition: MzTab.h:199
std::map< Size, MzTabInteger > num_peptides_unique_ms_run
Definition: MzTab.h:195
std::map< Size, MzTabDouble > protein_abundance_stdev_study_variable
Definition: MzTab.h:203
std::vector< MzTabOptionalColumnEntry > opt_
Optional Columns must start with “opt_”
Definition: MzTab.h:205
MzTabParameterList search_engine
Search engine(s) identifying the protein.
Definition: MzTab.h:189
MzTabString species
Human readable name of the species.
Definition: MzTab.h:186
MzTabString database
Name of the protein database.
Definition: MzTab.h:187