#include <OpenMS/FORMAT/HANDLERS/MzXMLHandler.h>
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 ProgressLogger & | logger_ |
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. |
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] |
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.
void endElement | ( | const XMLCh *const | uri, | |
const XMLCh *const | localname, | |||
const XMLCh *const | qname | |||
) | [inline, virtual] |
void startElement | ( | const XMLCh *const | uri, | |
const XMLCh *const | localname, | |||
const XMLCh *const | qname, | |||
const xercesc::Attributes & | attrs | |||
) | [inline, virtual] |
void characters | ( | const XMLCh *const | chars, | |
const unsigned int | length | |||
) | [inline, virtual] |
void writeTo | ( | std::ostream & | os | ) | [inline, virtual] |
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)
MapType* exp_ [protected] |
map pointer for reading
const MapType* cexp_ [protected] |
map pointer for writing
PeakFileOptions options_ [protected] |
Options for loading and storing.
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.
Generated Tue Apr 1 15:36:49 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |