OpenMS
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XML DOM handler for MzIdentMLFile. More...
#include <OpenMS/FORMAT/HANDLERS/MzIdentMLDOMHandler.h>
Classes | |
struct | AnalysisSoftware |
Struct to hold the used analysis software for that file. More... | |
struct | DatabaseInput |
Struct to hold the information from the DatabaseInput xml tag. More... | |
struct | DBSequence |
Struct to hold the information from the DBSequence xml tag. More... | |
struct | ModificationParam |
Struct to hold the information from the ModificationParam xml tag. More... | |
struct | PeptideEvidence |
Struct to hold the PeptideEvidence information. More... | |
struct | SpectrumIdentification |
Struct to hold the information from the SpectrumIdentification xml tag. More... | |
struct | SpectrumIdentificationProtocol |
Struct to hold the information from the SpectrumIdentificationProtocol xml tag. More... | |
Constructors and destructor | |
const ProgressLogger & | logger_ |
Progress logger. More... | |
ControlledVocabulary | cv_ |
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) More... | |
ControlledVocabulary | unimod_ |
Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo) More... | |
std::vector< ProteinIdentification > * | pro_id_ = nullptr |
Internal +w Identification Item for proteins. More... | |
std::vector< PeptideIdentification > * | pep_id_ = nullptr |
Internal +w Identification Item for peptides. More... | |
const std::vector< ProteinIdentification > * | cpro_id_ = nullptr |
Internal -w Identification Item for proteins. More... | |
const std::vector< PeptideIdentification > * | cpep_id_ = nullptr |
Internal -w Identification Item for peptides. More... | |
const String | schema_version_ |
Internal version keeping. More... | |
MzIdentMLDOMHandler (const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_id, const String &version, const ProgressLogger &logger) | |
Constructor for a write-only handler for internal identification structures. More... | |
MzIdentMLDOMHandler (std::vector< ProteinIdentification > &pro_id, std::vector< PeptideIdentification > &pep_id, const String &version, const ProgressLogger &logger) | |
Constructor for a read-only handler for internal identification structures. More... | |
virtual | ~MzIdentMLDOMHandler () |
Destructor. More... | |
void | readMzIdentMLFile (const std::string &mzid_file) |
Provides the functionality of reading a mzid with a handler object. More... | |
void | writeMzIdentMLFile (const std::string &mzid_file) |
Provides the functionality to write a mzid with a handler object. More... | |
ControlledVocabulary::CVTerm | getChildWithName_ (const String &parent_accession, const String &name) const |
Looks up a child CV term of parent_accession with the name name . If no such term is found, an empty term is returned. More... | |
Helper functions to build a DOM tree from the internal id structures | |
XMLCh * | xml_root_tag_ptr_ |
XMLCh * | xml_cvparam_tag_ptr_ |
XMLCh * | xml_name_attr_ptr_ |
xercesc::XercesDOMParser | mzid_parser_ |
std::unique_ptr< XMLHandler > | xml_handler_ = nullptr |
String | search_engine_ |
String | search_engine_version_ |
std::map< String, AnalysisSoftware > | as_map_ |
mapping AnalysisSoftware id -> AnalysisSoftware More... | |
std::map< String, String > | sr_map_ |
mapping sourcefile id -> sourcefile location More... | |
std::map< String, String > | sd_map_ |
mapping spectradata id -> spectradata location More... | |
std::map< String, DatabaseInput > | db_map_ |
mapping database id -> DatabaseInput More... | |
std::map< String, SpectrumIdentification > | si_map_ |
mapping SpectrumIdentification id -> SpectrumIdentification (id refs) More... | |
std::map< String, size_t > | si_pro_map_ |
mapping SpectrumIdentificationList id -> index to ProteinIdentification in pro_id_ More... | |
std::map< String, SpectrumIdentificationProtocol > | sp_map_ |
mapping SpectrumIdentificationProtocol id -> SpectrumIdentificationProtocol More... | |
std::map< String, AASequence > | pep_map_ |
mapping Peptide id -> Sequence More... | |
std::map< String, PeptideEvidence > | pe_ev_map_ |
mapping PeptideEvidence id -> PeptideEvidence More... | |
std::map< String, String > | pv_db_map_ |
mapping PeptideEvidence id -> DBSequence id More... | |
std::multimap< String, String > | p_pv_map_ |
mapping Peptide id -> PeptideEvidence id, multiple PeptideEvidences can have equivalent Peptides. More... | |
std::map< String, DBSequence > | db_sq_map_ |
mapping DBSequence id -> Sequence More... | |
std::list< std::list< String > > | hit_pev_ |
writing help only More... | |
bool | xl_ms_search_ |
is true when reading a file containing Cross-Linking MS search results More... | |
std::map< String, String > | xl_id_donor_map_ |
mapping Peptide id -> crosslink donor value More... | |
std::map< String, String > | xl_id_acceptor_map_ |
mapping peptide id of acceptor peptide -> crosslink acceptor value More... | |
std::map< String, SignedSize > | xl_donor_pos_map_ |
mapping donor value -> cross-link modification location More... | |
std::map< String, SignedSize > | xl_acceptor_pos_map_ |
mapping acceptor value -> cross-link modification location More... | |
std::map< String, double > | xl_mass_map_ |
mapping Peptide id -> cross-link mass More... | |
std::map< String, String > | xl_mod_map_ |
mapping peptide id -> cross-linking reagent name More... | |
void | buildCvList_ (xercesc::DOMElement *cvElements) |
void | buildAnalysisSoftwareList_ (xercesc::DOMElement *analysisSoftwareElements) |
void | buildSequenceCollection_ (xercesc::DOMElement *sequenceCollectionElements) |
void | buildAnalysisCollection_ (xercesc::DOMElement *analysisCollectionElements) |
void | buildAnalysisProtocolCollection_ (xercesc::DOMElement *protocolElements) |
void | buildInputDataCollection_ (xercesc::DOMElement *inputElements) |
void | buildEnclosedCV_ (xercesc::DOMElement *parentElement, const String &encel, const String &acc, const String &name, const String &cvref) |
void | buildAnalysisDataCollection_ (xercesc::DOMElement *analysisElements) |
MzIdentMLDOMHandler () | |
MzIdentMLDOMHandler (const MzIdentMLDOMHandler &rhs) | |
MzIdentMLDOMHandler & | operator= (const MzIdentMLDOMHandler &rhs) |
Helper functions to build the internal id structures from the DOM tree | |
std::pair< CVTermList, std::map< String, DataValue > > | parseParamGroup_ (xercesc::DOMNodeList *paramGroup) |
First: CVparams, Second: userParams (independent of each other) More... | |
CVTerm | parseCvParam_ (xercesc::DOMElement *param) |
std::pair< String, DataValue > | parseUserParam_ (xercesc::DOMElement *param) |
void | parseAnalysisSoftwareList_ (xercesc::DOMNodeList *analysisSoftwareElements) |
void | parseDBSequenceElements_ (xercesc::DOMNodeList *dbSequenceElements) |
void | parsePeptideElements_ (xercesc::DOMNodeList *peptideElements) |
AASequence | parsePeptideSiblings_ (xercesc::DOMElement *peptide) |
void | parsePeptideEvidenceElements_ (xercesc::DOMNodeList *peptideEvidenceElements) |
void | parseSpectrumIdentificationElements_ (xercesc::DOMNodeList *spectrumIdentificationElements) |
void | parseSpectrumIdentificationProtocolElements_ (xercesc::DOMNodeList *spectrumIdentificationProtocolElements) |
void | parseInputElements_ (xercesc::DOMNodeList *inputElements) |
void | parseSpectrumIdentificationListElements_ (xercesc::DOMNodeList *spectrumIdentificationListElements) |
void | parseSpectrumIdentificationItemSetXLMS (std::set< String >::const_iterator set_it, std::multimap< String, int > xl_val_map, xercesc::DOMElement *element_res, const String &spectrumID) |
void | parseSpectrumIdentificationItemElement_ (xercesc::DOMElement *spectrumIdentificationItemElement, PeptideIdentification &spectrum_identification, String &spectrumIdentificationList_ref) |
void | parseProteinDetectionHypothesisElement_ (xercesc::DOMElement *proteinDetectionHypothesisElement, ProteinIdentification &protein_identification) |
void | parseProteinAmbiguityGroupElement_ (xercesc::DOMElement *proteinAmbiguityGroupElement, ProteinIdentification &protein_identification) |
void | parseProteinDetectionListElements_ (xercesc::DOMNodeList *proteinDetectionListElements) |
static ProteinIdentification::SearchParameters | findSearchParameters_ (std::pair< CVTermList, std::map< String, DataValue > > as_params) |
XML DOM handler for MzIdentMLFile.
In read-mode, this class will parse an MzIdentML XML file and append the input identifications to the provided PeptideIdentifications and ProteinIdentifications.
struct OpenMS::Internal::MzIdentMLDOMHandler::AnalysisSoftware |
struct OpenMS::Internal::MzIdentMLDOMHandler::DatabaseInput |
struct OpenMS::Internal::MzIdentMLDOMHandler::DBSequence |
Struct to hold the information from the DBSequence xml tag.
Class Members | ||
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String | accession | |
CVTermList | cvs | |
String | database_ref | |
String | sequence |
struct OpenMS::Internal::MzIdentMLDOMHandler::ModificationParam |
Struct to hold the information from the ModificationParam xml tag.
Class Members | ||
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String | fixed_mod | |
long double | mass_delta | |
CVTermList | modification_param_cvs | |
String | residues | |
CVTermList | specificities |
struct OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence |
Struct to hold the PeptideEvidence information.
Class Members | ||
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bool | idec | |
char | post | |
char | pre | |
int | start | |
int | stop |
struct OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentification |
Struct to hold the information from the SpectrumIdentification xml tag.
Class Members | ||
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String | search_database_ref | |
String | spectra_data_ref | |
String | spectrum_identification_list_ref | |
String | spectrum_identification_protocol_ref |
struct OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol |
Struct to hold the information from the SpectrumIdentificationProtocol xml tag.
Class Members | ||
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String | enzyme | |
long double | fragment_tolerance | |
CVTermList | modification_parameter | |
CVTermList | parameter_cvs | |
map< String, DataValue > | parameter_ups | |
long double | precursor_tolerance | |
CVTerm | searchtype | |
CVTermList | threshold_cvs | |
map< String, DataValue > | threshold_ups |
MzIdentMLDOMHandler | ( | const std::vector< ProteinIdentification > & | pro_id, |
const std::vector< PeptideIdentification > & | pep_id, | ||
const String & | version, | ||
const ProgressLogger & | logger | ||
) |
Constructor for a write-only handler for internal identification structures.
MzIdentMLDOMHandler | ( | std::vector< ProteinIdentification > & | pro_id, |
std::vector< PeptideIdentification > & | pep_id, | ||
const String & | version, | ||
const ProgressLogger & | logger | ||
) |
Constructor for a read-only handler for internal identification structures.
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Destructor.
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Looks up a child CV term of parent_accession
with the name name
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First: CVparams, Second: userParams (independent of each other)
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void readMzIdentMLFile | ( | const std::string & | mzid_file | ) |
Provides the functionality of reading a mzid with a handler object.
void writeMzIdentMLFile | ( | const std::string & | mzid_file | ) |
Provides the functionality to write a mzid with a handler object.
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mapping AnalysisSoftware id -> AnalysisSoftware
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Internal -w Identification Item for peptides.
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protected |
Internal -w Identification Item for proteins.
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protected |
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
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private |
mapping database id -> DatabaseInput
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mapping DBSequence id -> Sequence
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writing help only
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Progress logger.
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mapping Peptide id -> PeptideEvidence id, multiple PeptideEvidences can have equivalent Peptides.
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mapping PeptideEvidence id -> PeptideEvidence
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Internal +w Identification Item for peptides.
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mapping Peptide id -> Sequence
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Internal +w Identification Item for proteins.
mapping PeptideEvidence id -> DBSequence id
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mapping SpectrumIdentification id -> SpectrumIdentification (id refs)
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mapping SpectrumIdentificationList id -> index to ProteinIdentification in pro_id_
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mapping SpectrumIdentificationProtocol id -> SpectrumIdentificationProtocol
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Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo)
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mapping acceptor value -> cross-link modification location
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mapping donor value -> cross-link modification location
mapping peptide id of acceptor peptide -> crosslink acceptor value
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private |
mapping Peptide id -> cross-link mass
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private |
is true when reading a file containing Cross-Linking MS search results
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private |
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private |
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private |
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