OpenMS
MzTab::CMMzTabStream Class Reference

#include <OpenMS/FORMAT/MzTab.h>

Collaboration diagram for MzTab::CMMzTabStream:
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Public Member Functions

 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")
 
const MzTabMetaDatagetMetaData () const
 
const std::vector< String > & getProteinOptionalColumnNames () const
 
const std::vector< String > & getPeptideOptionalColumnNames () const
 
const std::vector< String > & getPSMOptionalColumnNames () const
 
bool nextPRTRow (MzTabProteinSectionRow &row)
 
bool nextPEPRow (MzTabPeptideSectionRow &row)
 
bool nextPSMRow (MzTabPSMSectionRow &row)
 

Private Attributes

const ConsensusMapconsensus_map_
 
std::set< Stringprotein_hit_user_value_keys_
 
std::set< Stringconsensus_feature_user_value_keys_
 
std::set< Stringconsensus_feature_peptide_identification_user_value_keys_
 
std::set< Stringconsensus_feature_peptide_hit_user_value_keys_
 
std::map< Size, std::set< Size > > ind2prot_
 
std::map< Size, std::set< Size > > pg2prot_
 
std::map< String, size_t > idrunid_2_idrunindex_
 
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< std::pair< size_t, size_t >, size_t > map_id_run_fileidx_2_msfileidx_
 
std::map< std::pair< String, unsigned >, unsigned > path_label_to_assay_
 
std::vector< const ProteinIdentification * > prot_ids_
 
std::vector< const PeptideIdentification * > peptide_ids_
 
StringList ms_runs_
 
bool first_run_inference_
 
String filename_
 
StringList fixed_mods_
 
bool export_unidentified_features_
 
bool export_subfeatures_
 
bool export_empty_pep_ids_
 
bool export_all_psms_
 
size_t quant_study_variables_ = 0
 
size_t n_study_variables_ = 0
 
size_t PRT_STATE_ = 0
 
size_t prt_run_id_ = 0
 
size_t prt_hit_id_ = 0
 
size_t prt_group_id_ = 0
 
size_t prt_indistgroup_id_ = 0
 
size_t pep_id_ = 0
 
size_t pep_counter_ = 0
 
size_t psm_id_ = 0
 
size_t current_psm_idx_ = 0
 
MzTabString db_
 
MzTabString db_version_
 
std::vector< Stringprt_optional_column_names_
 
std::vector< Stringpep_optional_column_names_
 
std::vector< Stringpsm_optional_column_names_
 
MzTabMetaData meta_data_
 

Constructor & Destructor Documentation

◆ CMMzTabStream()

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" 
)

Member Function Documentation

◆ getMetaData()

const MzTabMetaData& getMetaData ( ) const

◆ getPeptideOptionalColumnNames()

const std::vector<String>& getPeptideOptionalColumnNames ( ) const

◆ getProteinOptionalColumnNames()

const std::vector<String>& getProteinOptionalColumnNames ( ) const

◆ getPSMOptionalColumnNames()

const std::vector<String>& getPSMOptionalColumnNames ( ) const

◆ nextPEPRow()

bool nextPEPRow ( MzTabPeptideSectionRow row)

◆ nextPRTRow()

bool nextPRTRow ( MzTabProteinSectionRow row)

◆ nextPSMRow()

bool nextPSMRow ( MzTabPSMSectionRow row)

Member Data Documentation

◆ consensus_feature_peptide_hit_user_value_keys_

std::set<String> consensus_feature_peptide_hit_user_value_keys_
private

◆ consensus_feature_peptide_identification_user_value_keys_

std::set<String> consensus_feature_peptide_identification_user_value_keys_
private

◆ consensus_feature_user_value_keys_

std::set<String> consensus_feature_user_value_keys_
private

◆ consensus_map_

const ConsensusMap& consensus_map_
private

◆ current_psm_idx_

size_t current_psm_idx_ = 0
private

◆ db_

MzTabString db_
private

◆ db_version_

MzTabString db_version_
private

◆ export_all_psms_

bool export_all_psms_
private

◆ export_empty_pep_ids_

bool export_empty_pep_ids_
private

◆ export_subfeatures_

bool export_subfeatures_
private

◆ export_unidentified_features_

bool export_unidentified_features_
private

◆ filename_

String filename_
private

◆ first_run_inference_

bool first_run_inference_
private

◆ fixed_mods_

StringList fixed_mods_
private

◆ idrunid_2_idrunindex_

std::map<String, size_t> idrunid_2_idrunindex_
private

◆ ind2prot_

std::map<Size, std::set<Size> > ind2prot_
private

◆ map_id_run_fileidx_2_msfileidx_

std::map<std::pair<size_t,size_t>,size_t> map_id_run_fileidx_2_msfileidx_
private

◆ meta_data_

MzTabMetaData meta_data_
private

◆ ms_runs_

StringList ms_runs_
private

◆ n_study_variables_

size_t n_study_variables_ = 0
private

◆ path_label_to_assay_

std::map<std::pair< String, unsigned >, unsigned> path_label_to_assay_
private

◆ pep_counter_

size_t pep_counter_ = 0
private

◆ pep_id_

size_t pep_id_ = 0
private

◆ pep_optional_column_names_

std::vector<String> pep_optional_column_names_
private

◆ peptide_ids_

std::vector<const PeptideIdentification*> peptide_ids_
private

◆ pg2prot_

std::map<Size, std::set<Size> > pg2prot_
private

◆ prot_ids_

std::vector<const ProteinIdentification*> prot_ids_
private

◆ protein_hit_user_value_keys_

std::set<String> protein_hit_user_value_keys_
private

◆ prt_group_id_

size_t prt_group_id_ = 0
private

◆ prt_hit_id_

size_t prt_hit_id_ = 0
private

◆ prt_indistgroup_id_

size_t prt_indistgroup_id_ = 0
private

◆ prt_optional_column_names_

std::vector<String> prt_optional_column_names_
private

◆ prt_run_id_

size_t prt_run_id_ = 0
private

◆ PRT_STATE_

size_t PRT_STATE_ = 0
private

◆ psm_id_

size_t psm_id_ = 0
private

◆ psm_optional_column_names_

std::vector<String> psm_optional_column_names_
private

◆ quant_study_variables_

size_t quant_study_variables_ = 0
private

◆ run_to_search_engines_

std::map<Size, std::vector<std::pair<String, String> > > run_to_search_engines_
private

◆ run_to_search_engines_settings_

std::map<Size, std::vector<std::vector<std::pair<String, String> > > > run_to_search_engines_settings_
private