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

Inheritance diagram for MzDataHandler< MapType >:

Public Member Functions
virtual void	endElement (const XMLCh const , const XMLCh const , const XMLCh *const qname)
	Parsing method for closing tags.
virtual void	startElement (const XMLCh const , const XMLCh const , const XMLCh *const qname, const xercesc::Attributes &attributes)
	Parsing method for opening tags.
virtual void	characters (const XMLCh *const chars, const XMLSize_t length)
	Parsing method for character data.
void	writeTo (std::ostream &os)
	Writes the contents to a stream.
void	setOptions (const PeakFileOptions &options)
	Sets the options.
Constructors and destructor

	MzDataHandler (MapType &exp, const String &filename, const String &version, ProgressLogger &logger)
	Constructor for a write-only handler.
	MzDataHandler (const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler.
virtual	~MzDataHandler ()
	Destructor.
Protected Types
typedef MapType::PeakType	PeakType
	Peak type.
typedef MSSpectrum< PeakType >	SpectrumType
	Spectrum type.
Protected Member Functions
void	fillData_ ()
	fills the current spectrum with peaks and meta data
void	writeBinary_ (std::ostream &os, Size size, const String &tag, const String &name="", SignedSize id=-1)
	write binary data to stream (first one)
cvParam and userParam handling methods (for mzData and featureXML)

void	writeCVS_ (std::ostream &os, DoubleReal value, const String &acc, const String &name, UInt indent=4) const
	write cvParam containing strings to stream
void	writeCVS_ (std::ostream &os, const String &value, const String &acc, const String &name, UInt indent=4) const
	write cvParam containing strings to stream
void	writeCVS_ (std::ostream &os, UInt value, UInt map, const String &acc, const String &name, UInt indent=4)
	write cvParam element to stream
void	writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent=4)
	Writing the MetaInfo as UserParam to the file.
void	cvParam_ (const String &name, const String &value)
	read attributes of MzData's cvParamType
Protected Attributes
MapType *	exp_
	map pointer for reading
const MapType *	cexp_
	map pointer for writing
PeakFileOptions	options_
	Options that can be set for loading/storing.
Base64	decoder_
	Decoder/Encoder for Base64-data in MzData.
bool	skip_spectrum_
	Flag that indicates whether this spectrum should be skipped (due to options).
const ProgressLogger &	logger_
	Progress logger.
DataProcessing	data_processing_
temporary datastructures to hold parsed data

UInt	peak_count_
	The number of peaks in the current spectrum.
SpectrumType	spec_
	The current spectrum.
std::vector< std::pair< String, MetaInfoDescription > >	meta_id_descs_
	An array of pairs MetaInfodescriptions and their ids.
std::vector< String >	data_to_decode_
	encoded data which is read and has to be decoded
std::vector< Real >	data_to_encode_
	floating point numbers which have to be encoded and written
std::vector< std::vector< Real > >	decoded_list_
std::vector< std::vector < DoubleReal > >	decoded_double_list_
std::vector< String >	precisions_
std::vector< String >	endians_
Private Member Functions
void	init_ ()

Detailed Description

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

XML handler for MzDataFile.

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

Improvement:: Add implementation and tests of 'supDataArray' to store IntegerDataArray and StringDataArray of MSSpectrum (Hiwi)

Member Typedef Documentation

typedef MapType::PeakType PeakType [protected]

Peak type.

typedef MSSpectrum<PeakType> SpectrumType [protected]

Spectrum type.

Constructor & Destructor Documentation

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

Constructor for a write-only handler.

References MzDataHandler< MapType >::init_().

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

Constructor for a read-only handler.

References MzDataHandler< MapType >::init_().

virtual ~MzDataHandler ( ) [inline, virtual]

Destructor.

Member Function Documentation

void characters	(	const XMLCh *const	chars,
		const XMLSize_t	length
	)			`[virtual]`

Parsing method for character data.

Reimplemented from XMLHandler.

References StringManager::convert(), MzDataHandler< MapType >::data_processing_, MzDataHandler< MapType >::data_to_decode_, MzDataHandler< MapType >::exp_, MSSpectrum< PeakT >::getFloatDataArrays(), DataProcessing::getSoftware(), XMLHandler::LOAD, XMLHandler::open_tags_, SpectrumSettings::setComment(), MetaInfoInterface::setMetaValue(), Software::setName(), Software::setVersion(), MzDataHandler< MapType >::skip_spectrum_, XMLHandler::sm_, MzDataHandler< MapType >::spec_, String::trim(), and XMLHandler::warning().

void cvParam_	(	const String &	name,
		const String &	value
	)			`[protected]`

read attributes of MzData's cvParamType

Example: <cvParam cvLabel="psi" accession="PSI:1000001" name="@p name" value="@p value"/> name and sometimes value are defined in the MzData ontology.

Referenced by MzDataHandler< MapType >::startElement().

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

Parsing method for closing tags.

Reimplemented from XMLHandler.

void fillData_ ( ) [protected]

fills the current spectrum with peaks and meta data

Referenced by MzDataHandler< MapType >::endElement().

void init_ ( ) [inline, private]

References XMLHandler::cv_terms_.

Referenced by MzDataHandler< MapType >::MzDataHandler().

void setOptions ( const PeakFileOptions & options ) [inline]

Sets the options.

References MzDataHandler< MapType >::options_.

Referenced by MzDataFile::load(), and MzDataFile::store().

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

Parsing method for opening tags.

Reimplemented from XMLHandler.

void writeBinary_	(	std::ostream &	os,
		Size	size,
		const String &	tag,
		const String &	name = `""`,
		SignedSize	id = `-1`
	)			`[inline, protected]`

write binary data to stream (first one)

The name and id are only used if the tag is supDataArrayBinary or supDataArray.

References Base64::BYTEORDER_LITTLEENDIAN, MzDataHandler< MapType >::data_to_encode_, MzDataHandler< MapType >::decoder_, and Base64::encode().

Referenced by MzDataHandler< MapType >::writeTo().

void writeCVS_	(	std::ostream &	os,
		DoubleReal	value,
		const String &	acc,
		const String &	name,
		UInt	indent = `4`
	)			const `[inline, protected]`

write cvParam containing strings to stream

value string value acc accession number defined by ontology name term defined by ontology indent number of tabs used in front of tag

Example: <cvParam cvLabel="psi" accession="PSI:@p acc" name="@p name" value="@p value"/>

Referenced by MzDataHandler< MapType >::writeCVS_(), and MzDataHandler< MapType >::writeTo().

void writeCVS_	(	std::ostream &	os,
		const String &	value,
		const String &	acc,
		const String &	name,
		UInt	indent = `4`
	)			const `[inline, protected]`

write cvParam containing strings to stream

value string value acc accession number defined by ontology name term defined by ontology indent number of tabs used in front of tag

Example: <cvParam cvLabel="psi" accession="PSI:@p acc" name="@p name" value="@p value"/>

void writeCVS_	(	std::ostream &	os,
		UInt	value,
		UInt	map,
		const String &	acc,
		const String &	name,
		UInt	indent = `4`
	)			`[inline, protected]`

write cvParam element to stream

os Output stream value enumeration value map index if the terms in cv_terms_ acc accession number defined by ontology name term defined by ontology indent number of tabs used in front of tag

Example: <cvParam cvLabel="psi" accession="PSI:@p acc" name="@p name" value=""/>

References XMLHandler::cv_terms_, XMLHandler::STORE, XMLHandler::warning(), and MzDataHandler< MapType >::writeCVS_().

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

Writes the contents to a stream.

Reimplemented from XMLHandler.