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/CONCEPT/LogStream.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 <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.

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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:

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:

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:

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:

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:

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:

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:

Class Members
DateTime	date
String	location
String	name
String	version