| OpenMS 2.5.0

Classes | Namespaces
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>`

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.

Class Members
String | name |
String | version |

## ◆ OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence

struct OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence

Struct to hold the PeptideEvidence information.

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.

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.

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.

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.

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.

Class Members
DateTime | date |
String | location |
String | name |
String | version |