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MzXMLHandler Class Template Reference

#include <OpenMS/FORMAT/HANDLERS/MzXMLHandler.h>

Inheritance diagram for MzXMLHandler:

XMLHandler xercesc::DefaultHandler

List of all members.


Detailed Description

template<typename MapType>
class OpenMS::Internal::MzXMLHandler< MapType >

XML handlers for MzXMLFile.

MapType has to be a MSExperiment or have the same interface. Do not use this class. It is only needed in MzXMLFile.

Public Member Functions

virtual void endElement (const XMLCh *const uri, const XMLCh *const local_name, const XMLCh *const qname)
 Parsing method for closing tags.
virtual void startElement (const XMLCh *const uri, const XMLCh *const local_name, const XMLCh *const qname, const xercesc::Attributes &attributes)
 Parsing method for opening tags.
virtual void characters (const XMLCh *const chars, const unsigned int length)
 Parsing method for character data.
void writeTo (std::ostream &os)
 Write the contents to a stream.
void setOptions (const PeakFileOptions &opt)
 Sets options for loading and storing.
Constructors and destructor
 MzXMLHandler (MapType &exp, const String &filename, const String &version, ProgressLogger &logger)
 Constructor for a write-only handler.
 MzXMLHandler (const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)
 Constructor for a read-only handler.
virtual ~MzXMLHandler ()
 Destructor.

Protected Types

typedef MapType::PeakType PeakType
 Peak type.
typedef MSSpectrum< PeakType,
std::allocator< PeakType > > 
SpectrumType
 Spectrum type.
typedef SpectrumType::Iterator PeakIterator
typedef
SpectrumType::PrecursorPeakType 
PrecursorPeakType

Protected Member Functions

void writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, int indent=4, String tag="nameValue")
 write metaInfo to xml (usually in nameValue-tag)

Protected Attributes

MapType * exp_
 map pointer for reading
const MapType * cexp_
 map pointer for writing
PeakFileOptions options_
 Options for loading and storing.
bool skip_spectrum_
 Flag that indicates that the current spectrum should be skipped.
UInt spec_write_counter_
 spectrum counter (spectra without peaks are not written)
const ProgressLoggerlogger_
 Progress logging class.
temporary datastructures to hold parsed data
Base64 decoder_
UInt peak_count_
String precision_
String char_rest_

Private Member Functions

 MzXMLHandler ()
 Not implemented.


Member Typedef Documentation

typedef MapType::PeakType PeakType [protected]

Peak type.

typedef MSSpectrum<PeakType, std::allocator<PeakType> > SpectrumType [protected]

Spectrum type.

typedef SpectrumType::Iterator PeakIterator [protected]

typedef SpectrumType::PrecursorPeakType PrecursorPeakType [protected]


Constructor & Destructor Documentation

MzXMLHandler ( MapType &  exp,
const String filename,
const String version,
ProgressLogger logger 
) [inline]

Constructor for a write-only handler.

MzXMLHandler ( const MapType &  exp,
const String filename,
const String version,
const ProgressLogger logger 
) [inline]

Constructor for a read-only handler.

virtual ~MzXMLHandler (  )  [inline, virtual]

Destructor.

MzXMLHandler (  )  [private]

Not implemented.


Member Function Documentation

void endElement ( const XMLCh *const   uri,
const XMLCh *const   localname,
const XMLCh *const   qname 
) [inline, virtual]

Parsing method for closing tags.

Reimplemented from XMLHandler.

void startElement ( const XMLCh *const   uri,
const XMLCh *const   localname,
const XMLCh *const   qname,
const xercesc::Attributes &  attrs 
) [inline, virtual]

Parsing method for opening tags.

Reimplemented from XMLHandler.

void characters ( const XMLCh *const   chars,
const unsigned int  length 
) [inline, virtual]

Parsing method for character data.

Reimplemented from XMLHandler.

void writeTo ( std::ostream &  os  )  [inline, virtual]

Write the contents to a stream.

Reimplemented from XMLHandler.

void setOptions ( const PeakFileOptions opt  )  [inline]

Sets options for loading and storing.

void writeUserParam_ ( std::ostream &  os,
const MetaInfoInterface meta,
int  indent = 4,
String  tag = "nameValue" 
) [inline, protected]

write metaInfo to xml (usually in nameValue-tag)


Member Data Documentation

MapType* exp_ [protected]

map pointer for reading

const MapType* cexp_ [protected]

map pointer for writing

PeakFileOptions options_ [protected]

Options for loading and storing.

Base64 decoder_ [protected]

UInt peak_count_ [protected]

String precision_ [protected]

String char_rest_ [protected]

bool skip_spectrum_ [protected]

Flag that indicates that the current spectrum should be skipped.

UInt spec_write_counter_ [protected]

spectrum counter (spectra without peaks are not written)

const ProgressLogger& logger_ [protected]

Progress logging class.


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:49 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1