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

Inheritance diagram for MzDataHandler:

Collaboration diagram for MzDataHandler:

Constructors and destructor
typedef MapType::PeakType	PeakType
	Peak type. More...

typedef MSSpectrum	SpectrumType
	Spectrum type. More...

MapType *	exp_
	map pointer for reading More...

const MapType *	cexp_
	map pointer for writing More...

PeakFileOptions	options_
	Options that can be set for loading/storing. More...

	MzDataHandler (MapType &exp, const String &filename, const String &version, ProgressLogger &logger)
	Constructor for a write-only handler. More...

	MzDataHandler (const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler. More...

	~MzDataHandler () override
	Destructor. More...

void	endElement (const XMLCh const, const XMLCh const, const XMLCh *const qname) override

void	startElement (const XMLCh const, const XMLCh const, const XMLCh *const qname, const xercesc::Attributes &attributes) override

void	characters (const XMLCh *const chars, const XMLSize_t length) override

void	writeTo (std::ostream &os) override
	Writes the contents to a stream. More...

void	setOptions (const PeakFileOptions &options)
	Sets the options. More...

void	init_ ()

temporary datastructures to hold parsed data
UInt	peak_count_
	The number of peaks in the current spectrum (according to the length attribute – which should not be trusted) More...

SpectrumType	spec_
	The current spectrum. More...

std::vector< std::pair< String, MetaInfoDescription > >	meta_id_descs_
	An array of pairs MetaInfodescriptions and their ids. More...

std::vector< String >	data_to_decode_
	encoded data which is read and has to be decoded More...

std::vector< float >	data_to_encode_
	floating point numbers which have to be encoded and written More...

std::vector< std::vector< float > >	decoded_list_

std::vector< std::vector< double > >	decoded_double_list_

std::vector< String >	precisions_

std::vector< String >	endians_

bool	skip_spectrum_
	Flag that indicates whether this spectrum should be skipped (due to options) More...

const ProgressLogger &	logger_
	Progress logger. More...

void	fillData_ ()
	fills the current spectrum with peaks and meta data More...

cvParam and userParam handling methods (for mzData and featureXML)
boost::shared_ptr< DataProcessing >	data_processing_

void	writeCVS_ (std::ostream &os, double value, const String &acc, const String &name, UInt indent=4) const
	write cvParam containing strings to stream More...

void	writeCVS_ (std::ostream &os, const String &value, const String &acc, const String &name, UInt indent=4) const
	write cvParam containing strings to stream More...

void	writeCVS_ (std::ostream &os, UInt value, UInt map, const String &acc, const String &name, UInt indent=4)
	write cvParam element to stream More...

void	writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent=4)
	Writing the MetaInfo as UserParam to the file. More...

void	cvParam_ (const String &name, const String &value)
	read attributes of MzData's cvParamType More...

void	writeBinary_ (std::ostream &os, Size size, const String &tag, const String &name="", SignedSize id=-1)
	write binary data to stream (first one) More...

Additional Inherited Members
Public Types inherited from XMLHandler
enum	ActionMode { LOAD , STORE }
	Action to set the current mode (for error messages) More...

enum	LOADDETAIL { LD_ALLDATA , LD_RAWCOUNTS , LD_COUNTS_WITHOPTIONS }

Public Member Functions inherited from XMLHandler
	XMLHandler (const String &filename, const String &version)
	Default constructor. More...

	~XMLHandler () override
	Destructor. More...

void	reset ()
	Release internal memory used for parsing (call. More...

void	fatalError (const xercesc::SAXParseException &exception) override

void	error (const xercesc::SAXParseException &exception) override

void	warning (const xercesc::SAXParseException &exception) override

void	fatalError (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
	Fatal error handler. Throws a ParseError exception. More...

void	error (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
	Error handler for recoverable errors. More...

void	warning (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
	Warning handler. More...

void	characters (const XMLCh *const chars, const XMLSize_t length) override
	Parsing method for character data. More...

void	startElement (const XMLCh const uri, const XMLCh const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) override
	Parsing method for opening tags. More...

void	endElement (const XMLCh const uri, const XMLCh const localname, const XMLCh *const qname) override
	Parsing method for closing tags. More...

virtual LOADDETAIL	getLoadDetail () const
	handler which support partial loading, implement this method More...

virtual void	setLoadDetail (const LOADDETAIL d)
	handler which support partial loading, implement this method More...

DataValue	cvParamToValue (const ControlledVocabulary &cv, const String &parent_tag, const String &accession, const String &name, const String &value, const String &unit_accession) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit. More...

DataValue	cvParamToValue (const ControlledVocabulary &cv, const CVTerm &raw_term) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit. More...

void	checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) const

Static Public Member Functions inherited from XMLHandler
static String	writeXMLEscape (const String &to_escape)
	Escapes a string and returns the escaped string. More...

static DataValue	fromXSDString (const String &type, const String &value)
	Convert an XSD type (e.g. 'xsd:double') to a DataValue. More...

Protected Member Functions inherited from XMLHandler
void	writeUserParam_ (const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes the content of MetaInfoInterface to the file. More...

Int	asInt_ (const String &in) const
	Conversion of a String to an integer value. More...

Int	asInt_ (const XMLCh *in) const
	Conversion of a Xerces string to an integer value. More...

UInt	asUInt_ (const String &in) const
	Conversion of a String to an unsigned integer value. More...

double	asDouble_ (const String &in) const
	Conversion of a String to a double value. More...

float	asFloat_ (const String &in) const
	Conversion of a String to a float value. More...

bool	asBool_ (const String &in) const
	Conversion of a string to a boolean value. More...

DateTime	asDateTime_ (String date_string) const
	Conversion of a xs:datetime string to a DateTime value. More...

bool	equal_ (const XMLCh a, const XMLCh b) const
	Returns if two Xerces strings are equal. More...

SignedSize	cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0)

String	attributeAsString_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a String. More...

Int	attributeAsInt_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a Int. More...

double	attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a double. More...

DoubleList	attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a DoubleList. More...

IntList	attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to an IntList. More...

StringList	attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to an StringList. More...

bool	optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the String value if the attribute is present. More...

bool	optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the Int value if the attribute is present. More...

bool	optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the UInt value if the attribute is present. More...

bool	optionalAttributeAsDouble_ (double &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the double value if the attribute is present. More...

bool	optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present. More...

bool	optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the StringList value if the attribute is present. More...

bool	optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the IntList value if the attribute is present. More...

String	attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a String. More...

Int	attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a Int. More...

double	attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a double. More...

DoubleList	attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a DoubleList. More...

IntList	attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a IntList. More...

StringList	attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a StringList. More...

bool	optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the String value if the attribute is present. More...

bool	optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the Int value if the attribute is present. More...

bool	optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the UInt value if the attribute is present. More...

bool	optionalAttributeAsDouble_ (double &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the double value if the attribute is present. More...

bool	optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present. More...

bool	optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the IntList value if the attribute is present. More...

bool	optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the StringList value if the attribute is present. More...

Protected Attributes inherited from XMLHandler
String	file_
	File name. More...

String	version_
	Schema version. More...

StringManager	sm_
	Helper class for string conversion. More...

std::vector< String >	open_tags_
	Stack of open XML tags. More...

LOADDETAIL	load_detail_
	parse only until total number of scans and chroms have been determined from attributes More...

std::vector< std::vector< String > >	cv_terms_
	Array of CV term lists (one sublist denotes one term and it's children) More...

Member Typedef Documentation

◆ PeakType

typedef MapType::PeakType PeakType

protected

Peak type.

◆ SpectrumType

typedef MSSpectrum SpectrumType

protected

Spectrum type.

Constructor & Destructor Documentation

◆ MzDataHandler() [1/2]

MzDataHandler	(	MapType &	exp,
		const String &	filename,
		const String &	version,
		ProgressLogger &	logger
	)

Constructor for a write-only handler.

◆ MzDataHandler() [2/2]

MzDataHandler	(	const MapType &	exp,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a read-only handler.

◆ ~MzDataHandler()

~MzDataHandler ( )

inlineoverride

Destructor.

Member Function Documentation

◆ characters()

void characters	(	const XMLCh *const	chars,
		const XMLSize_t	length
	)

override

◆ cvParam_()

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.

◆ endElement()

void endElement	(	const XMLCh * const	,
		const XMLCh * const	,
		const XMLCh *const	qname
	)

override

◆ fillData_()

void fillData_ ( )

protected

fills the current spectrum with peaks and meta data

◆ init_()

void init_ ( )

private

◆ setOptions()

void setOptions ( const PeakFileOptions & options )

inline

Sets the options.

◆ startElement()

void startElement	(	const XMLCh * const	,
		const XMLCh * const	,
		const XMLCh *const	qname,
		const xercesc::Attributes &	attributes
	)

override

◆ writeBinary_()

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

inlineprotected

write binary data to stream (first one)

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

◆ writeCVS_() [1/3]

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

inlineprotected

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"/>

◆ writeCVS_() [2/3]

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

inlineprotected

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"/>

◆ writeCVS_() [3/3]

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

inlineprotected

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=""/>

◆ writeTo()

void writeTo ( std::ostream & os )

overridevirtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

◆ writeUserParam_()

void writeUserParam_	(	std::ostream &	os,
		const MetaInfoInterface &	meta,
		UInt	indent = `4`
	)

inlineprotected

Writing the MetaInfo as UserParam to the file.

Member Data Documentation

◆ cexp_

const MapType* cexp_

protected

map pointer for writing

◆ data_processing_

boost::shared_ptr< DataProcessing > data_processing_

protected

◆ data_to_decode_

std::vector<String> data_to_decode_

protected

encoded data which is read and has to be decoded

◆ data_to_encode_

std::vector<float> data_to_encode_

protected

floating point numbers which have to be encoded and written

◆ decoded_double_list_

std::vector<std::vector<double> > decoded_double_list_

protected

◆ decoded_list_

std::vector<std::vector<float> > decoded_list_

protected

◆ endians_

std::vector<String> endians_

protected

◆ exp_

MapType* exp_

protected

map pointer for reading

◆ logger_

const ProgressLogger& logger_

protected

Progress logger.

◆ meta_id_descs_

std::vector<std::pair<String, MetaInfoDescription> > meta_id_descs_

protected

An array of pairs MetaInfodescriptions and their ids.

◆ options_

PeakFileOptions options_

protected

Options that can be set for loading/storing.

◆ peak_count_

UInt peak_count_

protected

The number of peaks in the current spectrum (according to the length attribute – which should not be trusted)

◆ precisions_

std::vector<String> precisions_

protected

◆ skip_spectrum_

bool skip_spectrum_

protected

Flag that indicates whether this spectrum should be skipped (due to options)

◆ spec_

SpectrumType spec_

protected

The current spectrum.

Constructors and destructor

temporary datastructures to hold parsed data

cvParam and userParam handling methods (for mzData and featureXML)

Additional Inherited Members

Member Typedef Documentation

◆ PeakType

◆ SpectrumType

Constructor & Destructor Documentation

◆ MzDataHandler() [1/2]

◆ MzDataHandler() [2/2]

◆ ~MzDataHandler()

Member Function Documentation

◆ characters()

◆ cvParam_()

◆ endElement()

◆ fillData_()

◆ init_()

◆ setOptions()

◆ startElement()

◆ writeBinary_()

◆ writeCVS_() [1/3]

◆ writeCVS_() [2/3]

◆ writeCVS_() [3/3]

◆ writeTo()

◆ writeUserParam_()

Member Data Documentation

◆ cexp_

◆ data_processing_

◆ data_to_decode_

◆ data_to_encode_

◆ decoded_double_list_

◆ decoded_list_

◆ endians_

◆ exp_

◆ logger_

◆ meta_id_descs_

◆ options_

◆ peak_count_

◆ precisions_

◆ skip_spectrum_

◆ spec_