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... | |
Public Member Functions | |
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... | |
Constructors and destructor | |
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... | |
Protected Member Functions | |
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 | |
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, String encel, String acc, String name, String cvref) |
void | buildAnalysisDataCollection_ (xercesc::DOMElement *analysisElements) |
Protected Attributes | |
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_ |
Internal +w Identification Item for proteins. More... | |
std::vector< PeptideIdentification > * | pep_id_ |
Internal +w Identification Item for peptides. More... | |
const std::vector< ProteinIdentification > * | cpro_id_ |
Internal -w Identification Item for proteins. More... | |
const std::vector< PeptideIdentification > * | cpep_id_ |
Internal -w Identification Item for peptides. More... | |
const String | schema_version_ |
Internal version keeping. More... | |
Private Member Functions | |
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) |
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, 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.
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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Looks up a child CV term of parent_accession
with the name name
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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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Internal -w Identification Item for peptides.
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Internal -w Identification Item for proteins.
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Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
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Progress logger.
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Internal +w Identification Item for peptides.
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Internal +w Identification Item for proteins.
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Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo)
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OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:14 using doxygen 1.8.13 |