OpenMS  3.0.0
MzIdentMLDOMHandler.h File Reference
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/FORMAT/ControlledVocabulary.h>
#include <OpenMS/METADATA/ProteinHit.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CONCEPT/UniqueIdGenerator.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/CVTermList.h>
#include <xercesc/dom/DOM.hpp>
#include <xercesc/dom/DOMDocument.hpp>
#include <xercesc/dom/DOMDocumentType.hpp>
#include <xercesc/dom/DOMElement.hpp>
#include <xercesc/dom/DOMImplementation.hpp>
#include <xercesc/dom/DOMImplementationLS.hpp>
#include <xercesc/dom/DOMNodeIterator.hpp>
#include <xercesc/dom/DOMNodeList.hpp>
#include <xercesc/dom/DOMText.hpp>
#include <xercesc/util/OutOfMemoryException.hpp>
#include <xercesc/util/XMLString.hpp>
#include <xercesc/util/PlatformUtils.hpp>
#include <xercesc/framework/LocalFileFormatTarget.hpp>
#include <xercesc/parsers/XercesDOMParser.hpp>
#include <xercesc/util/XMLUni.hpp>
#include <xercesc/framework/psvi/XSValue.hpp>
#include <list>
#include <string>
#include <stdexcept>
#include <vector>
#include <map>
Include dependency graph for MzIdentMLDOMHandler.h:

Go to the source code of this file.

Classes

class  MzIdentMLDOMHandler
 XML DOM handler for MzIdentMLFile. More...
 
struct  MzIdentMLDOMHandler::AnalysisSoftware
 Struct to hold the used analysis software for that file. More...
 
struct  MzIdentMLDOMHandler::PeptideEvidence
 Struct to hold the PeptideEvidence information. More...
 
struct  MzIdentMLDOMHandler::DBSequence
 Struct to hold the information from the DBSequence xml tag. More...
 
struct  MzIdentMLDOMHandler::SpectrumIdentification
 Struct to hold the information from the SpectrumIdentification xml tag. More...
 
struct  MzIdentMLDOMHandler::ModificationParam
 Struct to hold the information from the ModificationParam xml tag. More...
 
struct  MzIdentMLDOMHandler::SpectrumIdentificationProtocol
 Struct to hold the information from the SpectrumIdentificationProtocol xml tag. More...
 
struct  MzIdentMLDOMHandler::DatabaseInput
 Struct to hold the information from the DatabaseInput xml tag. More...
 

Namespaces

 OpenMS
 Main OpenMS namespace.
 
 OpenMS::Internal
 Namespace used to hide implementation details from users.
 

Class Documentation

◆ OpenMS::Internal::MzIdentMLDOMHandler::AnalysisSoftware

struct OpenMS::Internal::MzIdentMLDOMHandler::AnalysisSoftware

Struct to hold the used analysis software for that file.

Collaboration diagram for MzIdentMLDOMHandler::AnalysisSoftware:
[legend]
Class Members
String name
String version

◆ OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence

struct OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence

Struct to hold the PeptideEvidence information.

Collaboration diagram for MzIdentMLDOMHandler::PeptideEvidence:
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Class Members
bool idec
char post
char pre
int start
int stop

◆ OpenMS::Internal::MzIdentMLDOMHandler::DBSequence

struct OpenMS::Internal::MzIdentMLDOMHandler::DBSequence

Struct to hold the information from the DBSequence xml tag.

Collaboration diagram for MzIdentMLDOMHandler::DBSequence:
[legend]
Class Members
String accession
CVTermList cvs
String database_ref
String sequence

◆ OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentification

struct OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentification

Struct to hold the information from the SpectrumIdentification xml tag.

Collaboration diagram for MzIdentMLDOMHandler::SpectrumIdentification:
[legend]
Class Members
String search_database_ref
String spectra_data_ref
String spectrum_identification_list_ref
String spectrum_identification_protocol_ref

◆ OpenMS::Internal::MzIdentMLDOMHandler::ModificationParam

struct OpenMS::Internal::MzIdentMLDOMHandler::ModificationParam

Struct to hold the information from the ModificationParam xml tag.

Collaboration diagram for MzIdentMLDOMHandler::ModificationParam:
[legend]
Class Members
String fixed_mod
long double mass_delta
CVTermList modification_param_cvs
String residues
CVTermList specificities

◆ OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol

struct OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol

Struct to hold the information from the SpectrumIdentificationProtocol xml tag.

Collaboration diagram for MzIdentMLDOMHandler::SpectrumIdentificationProtocol:
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Class Members
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

◆ OpenMS::Internal::MzIdentMLDOMHandler::DatabaseInput

struct OpenMS::Internal::MzIdentMLDOMHandler::DatabaseInput

Struct to hold the information from the DatabaseInput xml tag.

Collaboration diagram for MzIdentMLDOMHandler::DatabaseInput:
[legend]
Class Members
DateTime date
String location
String name
String version