OpenMS
2.5.0
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#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>
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. | |
struct OpenMS::Internal::MzIdentMLDOMHandler::AnalysisSoftware |
struct OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence |
Struct to hold the PeptideEvidence information.
Class Members | ||
---|---|---|
bool | idec | |
char | post | |
char | pre | |
int | start | |
int | stop |
struct OpenMS::Internal::MzIdentMLDOMHandler::DBSequence |
Struct to hold the information from the DBSequence xml tag.
Class Members | ||
---|---|---|
String | accession | |
CVTermList | cvs | |
String | database_ref | |
String | sequence |
struct OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentification |
Struct to hold the information from the SpectrumIdentification xml tag.
Class Members | ||
---|---|---|
String | search_database_ref | |
String | spectra_data_ref | |
String | spectrum_identification_list_ref | |
String | spectrum_identification_protocol_ref |
struct OpenMS::Internal::MzIdentMLDOMHandler::ModificationParam |
Struct to hold the information from the ModificationParam xml tag.
Class Members | ||
---|---|---|
String | fixed_mod | |
long double | mass_delta | |
CVTermList | modification_param_cvs | |
String | residues | |
CVTermList | specificities |
struct OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol |
Struct to hold the information from the SpectrumIdentificationProtocol xml tag.
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 |
struct OpenMS::Internal::MzIdentMLDOMHandler::DatabaseInput |
Struct to hold the information from the DatabaseInput xml tag.
Class Members | ||
---|---|---|
DateTime | date | |
String | location | |
String | name | |
String | version |