MzTab::CMMzTabStream Class Reference

#include <OpenMS/FORMAT/MzTab.h>

Collaboration diagram for MzTab::CMMzTabStream:

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 MzTabMetaData &	getMetaData () 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 ConsensusMap &	consensus_map_
std::set< String >	protein_hit_user_value_keys_
std::set< String >	consensus_feature_user_value_keys_
std::set< String >	consensus_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< String >	prt_optional_column_names_
std::vector< String >	pep_optional_column_names_
std::vector< String >	psm_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_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