Base class for XML handlers. More...

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

Inheritance diagram for XMLHandler:

Collaboration diagram for XMLHandler:

Classes
class	EndParsingSoftly
	Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file is needed). More...

Public Types
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
	XMLHandler (const std::string &filename, const std::string &version)
	Default constructor.

virtual	~XMLHandler ()
	Destructor.

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

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

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

void	warning (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Warning handler.

Protected Member Functions
General MetaInfo handling (for idXML, featureXML, consensusXML)
void	writeUserParam_ (const std::string &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes the content of MetaInfoInterface to the file.

std::string conversion
Int	asInt_ (const std::string &in) const
	Conversion of a std::string to an integer value.

Int	asInt_ (const char16_t *in) const
	Conversion of a Xerces string to an integer value.

UInt	asUInt_ (const std::string &in) const
	Conversion of a std::string to an unsigned integer value.

double	asDouble_ (const std::string &in) const
	Conversion of a std::string to a double value.

float	asFloat_ (const std::string &in) const
	Conversion of a std::string to a float value.

bool	asBool_ (const std::string &in) const
	Conversion of a string to a boolean value.

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

Native (Xerces-free) SAX callbacks
Subclasses override these. `qname` / `chars` are UTF-16 code units (as delivered by the parser); attributes are exposed through the Xerces-free XMLAttributes view. The Xerces SAX parser is bridged to these callbacks by the internal SAX2HandlerAdapter.
std::string	file_
	File name.

std::string	version_
	Schema version.

StringManager	sm_
	Helper class for string conversion.

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

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

virtual void	onStartElement (const char16_t *qname, const XMLAttributes &attributes)
	Parsing method for opening tags.

virtual void	onEndElement (const char16_t *qname)
	Parsing method for closing tags.

virtual void	onCharacters (const char16_t *chars, Size length)
	Parsing method for character data.

virtual void	writeTo (std::ostream &)
	Writes the contents to a stream.

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

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

DataValue	cvParamToValue (const ControlledVocabulary &cv, const std::string &parent_tag, const std::string &accession, const std::string &name, const std::string &value, const std::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.

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.

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

static std::string	writeXMLEscape (const std::string &to_escape)
	Escapes a string and returns the escaped string.

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

bool	equal_ (const char16_t a, const char16_t b) const
	Returns if two Xerces strings are equal.

controlled vocabulary handling methods
std::vector< std::vector< std::string > >	cv_terms_
	Array of CV term lists (one sublist denotes one term and it's children)

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

Accessing attributes
std::string	attributeAsString_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a String.

Int	attributeAsInt_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a Int.

double	attributeAsDouble_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a double.

DoubleList	attributeAsDoubleList_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a DoubleList.

IntList	attributeAsIntList_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to an IntList.

StringList	attributeAsStringList_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to an StringList.

bool	optionalAttributeAsString_ (std::string &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the String value if the attribute is present.

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

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

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

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

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

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

std::string	attributeAsString_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a String.

Int	attributeAsInt_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a Int.

double	attributeAsDouble_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a double.

DoubleList	attributeAsDoubleList_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a DoubleList.

IntList	attributeAsIntList_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a IntList.

StringList	attributeAsStringList_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a StringList.

bool	optionalAttributeAsString_ (std::string &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the String value if the attribute is present.

bool	optionalAttributeAsInt_ (Int &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the Int value if the attribute is present.

bool	optionalAttributeAsUInt_ (UInt &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the UInt value if the attribute is present.

bool	optionalAttributeAsDouble_ (double &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the double value if the attribute is present.

bool	optionalAttributeAsDoubleList_ (DoubleList &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present.

bool	optionalAttributeAsIntList_ (IntList &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the IntList value if the attribute is present.

bool	optionalAttributeAsStringList_ (StringList &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the StringList value if the attribute is present.

	XMLHandler ()
	Not implemented.

const std::string &	expectList_ (const std::string &str) const

Detailed Description

Base class for XML handlers.

Member Enumeration Documentation

◆ ActionMode

enum ActionMode

Action to set the current mode (for error messages)

Enumerator
LOAD	Loading a file.
STORE	Storing a file.

◆ LOADDETAIL

enum LOADDETAIL

Enumerator
LD_ALLDATA
LD_RAWCOUNTS
LD_COUNTS_WITHOPTIONS

Constructor & Destructor Documentation

◆ XMLHandler() [1/2]

XMLHandler	(	const std::string &	filename,
		const std::string &	version
	)

Default constructor.

◆ ~XMLHandler()

virtual ~XMLHandler ( )

virtual

Destructor.

◆ XMLHandler() [2/2]

XMLHandler ( )

private

Not implemented.

Member Function Documentation

◆ asBool_()

bool asBool_ ( const std::string & in ) const

inlineprotected

Conversion of a string to a boolean value.

'true', 'false', '1' and '0' are accepted.

For all other values a parse error is produced.

◆ asDateTime_()

DateTime asDateTime_ ( std::string date_string ) const

inlineprotected

Conversion of a xs:datetime string to a DateTime value.

References DateTime::set().

◆ asDouble_()

double asDouble_ ( const std::string & in ) const

inlineprotected

Conversion of a std::string to a double value.

◆ asFloat_()

float asFloat_ ( const std::string & in ) const

inlineprotected

Conversion of a std::string to a float value.

◆ asInt_() [1/2]

Int asInt_ ( const char16_t * in ) const

inlineprotected

Conversion of a Xerces string to an integer value.

References StringManager::parseInt().

◆ asInt_() [2/2]

Int asInt_ ( const std::string & in ) const

inlineprotected

Conversion of a std::string to an integer value.

◆ asUInt_()

UInt asUInt_ ( const std::string & in ) const

inlineprotected

Conversion of a std::string to an unsigned integer value.

◆ attributeAsDouble_() [1/2]

double attributeAsDouble_	(	const XMLAttributes &	a,
		const char *	name
	)		const

inlineprotected

Converts an attribute to a double.

References StringManager::convert(), and XMLAttributes::value().

◆ attributeAsDouble_() [2/2]

double attributeAsDouble_	(	const XMLAttributes &	a,
		const char16_t *	name
	)		const

inlineprotected

Converts an attribute to a double.

References StringManager::convert(), and XMLAttributes::value().

◆ attributeAsDoubleList_() [1/2]

DoubleList attributeAsDoubleList_	(	const XMLAttributes &	a,
		const char *	name
	)		const

protected

Converts an attribute to a DoubleList.

◆ attributeAsDoubleList_() [2/2]

DoubleList attributeAsDoubleList_	(	const XMLAttributes &	a,
		const char16_t *	name
	)		const

protected

Converts an attribute to a DoubleList.

◆ attributeAsInt_() [1/2]

Int attributeAsInt_	(	const XMLAttributes &	a,
		const char *	name
	)		const

inlineprotected

Converts an attribute to a Int.

References StringManager::parseInt(), and XMLAttributes::value().

◆ attributeAsInt_() [2/2]

Int attributeAsInt_	(	const XMLAttributes &	a,
		const char16_t *	name
	)		const

inlineprotected

Converts an attribute to a Int.

References StringManager::convert(), StringManager::parseInt(), and XMLAttributes::value().

◆ attributeAsIntList_() [1/2]

IntList attributeAsIntList_	(	const XMLAttributes &	a,
		const char *	name
	)		const

protected

Converts an attribute to an IntList.

◆ attributeAsIntList_() [2/2]

IntList attributeAsIntList_	(	const XMLAttributes &	a,
		const char16_t *	name
	)		const

protected

Converts an attribute to a IntList.

◆ attributeAsString_() [1/2]

std::string attributeAsString_	(	const XMLAttributes &	a,
		const char *	name
	)		const

inlineprotected

Converts an attribute to a String.

References StringManager::convert(), and XMLAttributes::value().

◆ attributeAsString_() [2/2]

std::string attributeAsString_	(	const XMLAttributes &	a,
		const char16_t *	name
	)		const

inlineprotected

Converts an attribute to a String.

References StringManager::convert(), and XMLAttributes::value().

◆ attributeAsStringList_() [1/2]

StringList attributeAsStringList_	(	const XMLAttributes &	a,
		const char *	name
	)		const

protected

Converts an attribute to an StringList.

◆ attributeAsStringList_() [2/2]

StringList attributeAsStringList_	(	const XMLAttributes &	a,
		const char16_t *	name
	)		const

protected

Converts an attribute to a StringList.

◆ checkUniqueIdentifiers_()

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

throws a ParseError if protIDs are not unique, i.e. PeptideIDs will be randomly assigned (bad!) Should be called before writing any ProtIDs to file

◆ cvParamToValue() [1/2]

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.

Parameters

[in]	cv	A CV, usually the PSI-MS CV, see ControlledVocabulary::getPSIMSCV()
[in]	raw_term	Represenation of the raw data (i.e. all strings) from a <cvParam ...> without the conversion to a specific value type

Returns: DataValue::EMPTY if a conversion error occured (e.g. if value could not be converted to an integer for an accession which requires an integer) or the DataValue upon success

◆ cvParamToValue() [2/2]

DataValue cvParamToValue	(	const ControlledVocabulary &	cv,
		const std::string &	parent_tag,
		const std::string &	accession,
		const std::string &	name,
		const std::string &	value,
		const std::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.

Parameters

[in]	cv	A CV, usually the PSI-MS CV, see ControlledVocabulary::getPSIMSCV()
[in]	parent_tag	The tag which encloses the <cvParam>
[in]	accession	The accession from the 'accession' attribute of the <cvParam>
[in]	name	The name from the 'name' attribute of the <cvParam>
[in]	value	The value from the 'value' attribute of the <cvParam>
[in]	unit_accession	The unit_accession from the 'unitAccession' attribute of the <cvParam>

Returns: DataValue::EMPTY if a conversion error occured (e.g. if value could not be converted to an integer for an accession which requires an integer) or the DataValue upon success

◆ cvStringToEnum_()

SignedSize cvStringToEnum_	(	const Size	section,
		const std::string &	term,
		const char *	message,
		const SignedSize	result_on_error = `0`
	)

protected

Converts term to the index of the term in the cv_terms_ entry section If the term is not found, result_on_error is returned (0 by default)

◆ equal_()

bool equal_	(	const char16_t *	a,
		const char16_t *	b
	)		const

inlineprotected

Returns if two Xerces strings are equal.

◆ error()

void error	(	ActionMode	mode,
		const std::string &	msg,
		UInt	line = `0`,
		UInt	column = `0`
	)		const

Error handler for recoverable errors.

Referenced by SAX2HandlerAdapter::error().

◆ expectList_()

const std::string & expectList_ ( const std::string & str ) const

inlineprivate

◆ fatalError()

void fatalError	(	ActionMode	mode,
		const std::string &	msg,
		UInt	line = `0`,
		UInt	column = `0`
	)		const

Fatal error handler. Throws a ParseError exception.

Referenced by SAX2HandlerAdapter::fatalError().

◆ fromXSDString()

static DataValue fromXSDString	(	const std::string &	type,
		const std::string &	value
	)

inlinestatic

Convert an XSD type (e.g. 'xsd:double') to a DataValue.

Not all conversions are supported yet, due to DataValue using an Int64 as the largest possible integer. Thus, if the value contains a large UInt64, conversion will fail. Value ranges are currently also not checked, only for XSD types which happen to match the internal representation.

Parameters

[out]	type	An XSD type. If the type is not supported, the returned type will be a string
[in]	value	The value in sting format, e.g. "123.34"

Returns: The Datavalue with the respective type (double, int or string)

Exceptions

Exception::ConversionError if the value does not fit into the internal representation or (for few types) exceeds the XSD specs.

◆ getLoadDetail()

virtual LOADDETAIL getLoadDetail ( ) const

virtual

handler which support partial loading, implement this method

Reimplemented in MzMLHandler, and MzXMLHandler.

◆ onCharacters()

virtual void onCharacters	(	const char16_t *	chars,
		Size	length
	)

virtual

Parsing method for character data.

Reimplemented in ConsensusXMLHandler, FeatureXMLHandler, MzDataHandler, MzIdentMLHandler, MzMLHandler, MzXMLHandler, ToolDescriptionHandler, TraMLHandler, UniProtXMLHandler, QcMLFile, CVMappingFile, MascotXMLHandler, PTMXMLHandler, UnimodXMLHandler, OMSSAXMLFile, SemanticValidator, and XTandemXMLFile.

Referenced by SAX2HandlerAdapter::characters().

◆ onEndElement()

virtual void onEndElement ( const char16_t * qname )

virtual

Parsing method for closing tags.

Reimplemented in CVMappingFile, ConsensusXMLHandler, FeatureXMLHandler, ImzMLHandler, MascotXMLHandler, MzDataHandler, MzIdentMLHandler, MzMLHandler, MzXMLHandler, ParamXMLHandler, PTMXMLHandler, ToolDescriptionHandler, TraMLHandler, UnimodXMLHandler, UniProtXMLHandler, XQuestResultXMLHandler, IdXMLFile, OMSSAXMLFile, PepXMLFile, PepXMLFileMascot, ProtXMLFile, QcMLFile, SemanticValidator, and XTandemXMLFile.

Referenced by SAX2HandlerAdapter::endElement().

◆ onStartElement()

virtual void onStartElement	(	const char16_t *	qname,
		const XMLAttributes &	attributes
	)

virtual

Parsing method for opening tags.

Reimplemented in CVMappingFile, IdXMLFile, OMSSAXMLFile, PepXMLFile, PepXMLFileMascot, ProtXMLFile, QcMLFile, TransformationXMLFile, XTandemXMLFile, ConsensusXMLHandler, FeatureXMLHandler, MascotXMLHandler, MzDataHandler, MzIdentMLHandler, MzMLHandler, MzXMLHandler, ParamXMLHandler, PTMXMLHandler, ToolDescriptionHandler, TraMLHandler, UnimodXMLHandler, XQuestResultXMLHandler, MzMLValidator, SemanticValidator, ImzMLHandler, and UniProtXMLHandler.

Referenced by SAX2HandlerAdapter::startElement().

◆ optionalAttributeAsDouble_() [1/2]

bool optionalAttributeAsDouble_	(	double &	value,
		const XMLAttributes &	a,
		const char *	name
	)		const

inlineprotected

Assigns the attribute content to the double value if the attribute is present.

Returns: if the attribute was present

References StringManager::convert(), and XMLAttributes::value().

◆ optionalAttributeAsDouble_() [2/2]

bool optionalAttributeAsDouble_	(	double &	value,
		const XMLAttributes &	a,
		const char16_t *	name
	)		const

inlineprotected

Assigns the attribute content to the double value if the attribute is present.

References StringManager::convert(), and XMLAttributes::value().

◆ optionalAttributeAsDoubleList_() [1/2]

bool optionalAttributeAsDoubleList_	(	DoubleList &	value,
		const XMLAttributes &	a,
		const char *	name
	)		const

inlineprotected

Assigns the attribute content to the DoubleList value if the attribute is present.

Returns: if the attribute was present

References XMLAttributes::value().

◆ optionalAttributeAsDoubleList_() [2/2]

bool optionalAttributeAsDoubleList_	(	DoubleList &	value,
		const XMLAttributes &	a,
		const char16_t *	name
	)		const

inlineprotected

Assigns the attribute content to the DoubleList value if the attribute is present.

Returns: if the attribute was present

References XMLAttributes::value().

◆ optionalAttributeAsInt_() [1/2]

bool optionalAttributeAsInt_	(	Int &	value,
		const XMLAttributes &	a,
		const char *	name
	)		const

inlineprotected

Assigns the attribute content to the Int value if the attribute is present.

Returns: if the attribute was present

References StringManager::parseInt(), and XMLAttributes::value().

◆ optionalAttributeAsInt_() [2/2]

bool optionalAttributeAsInt_	(	Int &	value,
		const XMLAttributes &	a,
		const char16_t *	name
	)		const

inlineprotected

Assigns the attribute content to the Int value if the attribute is present.

References StringManager::parseInt(), and XMLAttributes::value().

◆ optionalAttributeAsIntList_() [1/2]

bool optionalAttributeAsIntList_	(	IntList &	value,
		const XMLAttributes &	a,
		const char *	name
	)		const

inlineprotected

Assigns the attribute content to the IntList value if the attribute is present.

Returns: if the attribute was present

References XMLAttributes::value().

◆ optionalAttributeAsIntList_() [2/2]

bool optionalAttributeAsIntList_	(	IntList &	value,
		const XMLAttributes &	a,
		const char16_t *	name
	)		const

inlineprotected

Assigns the attribute content to the IntList value if the attribute is present.

Returns: if the attribute was present

References XMLAttributes::value().

◆ optionalAttributeAsString_() [1/2]

bool optionalAttributeAsString_	(	std::string &	value,
		const XMLAttributes &	a,
		const char *	name
	)		const

inlineprotected

Assigns the attribute content to the String value if the attribute is present.

Returns: if the attribute was present

References StringManager::convert(), and XMLAttributes::value().

◆ optionalAttributeAsString_() [2/2]

bool optionalAttributeAsString_	(	std::string &	value,
		const XMLAttributes &	a,
		const char16_t *	name
	)		const

inlineprotected

Assigns the attribute content to the String value if the attribute is present.

References StringManager::convert(), and XMLAttributes::value().

◆ optionalAttributeAsStringList_() [1/2]

bool optionalAttributeAsStringList_	(	StringList &	value,
		const XMLAttributes &	a,
		const char *	name
	)		const

inlineprotected

Assigns the attribute content to the StringList value if the attribute is present.

Returns: if the attribute was present

References XMLAttributes::value().

◆ optionalAttributeAsStringList_() [2/2]

bool optionalAttributeAsStringList_	(	StringList &	value,
		const XMLAttributes &	a,
		const char16_t *	name
	)		const

inlineprotected

Assigns the attribute content to the StringList value if the attribute is present.

Returns: if the attribute was present

References XMLAttributes::value().

◆ optionalAttributeAsUInt_() [1/2]

bool optionalAttributeAsUInt_	(	UInt &	value,
		const XMLAttributes &	a,
		const char *	name
	)		const

inlineprotected

Assigns the attribute content to the UInt value if the attribute is present.

Returns: if the attribute was present

References StringManager::parseInt(), and XMLAttributes::value().

◆ optionalAttributeAsUInt_() [2/2]

bool optionalAttributeAsUInt_	(	UInt &	value,
		const XMLAttributes &	a,
		const char16_t *	name
	)		const

inlineprotected

Assigns the attribute content to the UInt value if the attribute is present.

References StringManager::parseInt(), and XMLAttributes::value().

◆ reset()

void reset ( )

Release internal memory used for parsing (call.

◆ setLoadDetail()

virtual void setLoadDetail ( const LOADDETAIL d )

virtual

handler which support partial loading, implement this method

Reimplemented in MzMLHandler, and MzXMLHandler.

◆ warning()

void warning	(	ActionMode	mode,
		const std::string &	msg,
		UInt	line = `0`,
		UInt	column = `0`
	)		const

Warning handler.

Referenced by SAX2HandlerAdapter::warning().

◆ writeTo()

virtual void writeTo ( std::ostream & )

virtual

Writes the contents to a stream.

Reimplemented in ConsensusXMLHandler, FeatureXMLHandler, MzDataHandler, MzIdentMLHandler, MzMLHandler, MzXMLHandler, PTMXMLHandler, ToolDescriptionHandler, TraMLHandler, and XQuestResultXMLHandler.

◆ writeUserParam_()

void writeUserParam_	(	const std::string &	tag_name,
		std::ostream &	os,
		const MetaInfoInterface &	meta,
		UInt	indent
	)		const

protected

Writes the content of MetaInfoInterface to the file.

◆ writeXMLEscape()

static std::string writeXMLEscape ( const std::string & to_escape )

inlinestatic

Escapes a string and returns the escaped string.

Some characters must be escaped which are allowed in user params. E.g. > and & are not in XML and need to be escaped. Parsing those escaped strings from file again is automatically done by Xerces. Escaped characters are: & < > " '

Member Data Documentation

◆ cv_terms_

std::vector<std::vector<std::string> > cv_terms_

protected

Array of CV term lists (one sublist denotes one term and it's children)

◆ file_

std::string file_

protected

File name.

◆ load_detail_

LOADDETAIL load_detail_

protected

parse only until total number of scans and chroms have been determined from attributes

◆ open_tags_

std::vector<std::string> open_tags_

protected

Stack of open XML tags.

This member is used only in those XML parsers that need this information.

◆ sm_

StringManager sm_

protected

Helper class for string conversion.

◆ version_

std::string version_

protected

Schema version.

Classes

Public Types

Public Member Functions

Protected Member Functions

Native (Xerces-free) SAX callbacks

controlled vocabulary handling methods

Accessing attributes

Detailed Description

Member Enumeration Documentation

◆ ActionMode

◆ LOADDETAIL

Constructor & Destructor Documentation

◆ XMLHandler() [1/2]

◆ ~XMLHandler()

◆ XMLHandler() [2/2]

Member Function Documentation

◆ asBool_()

◆ asDateTime_()

◆ asDouble_()

◆ asFloat_()

◆ asInt_() [1/2]

◆ asInt_() [2/2]

◆ asUInt_()

◆ attributeAsDouble_() [1/2]

◆ attributeAsDouble_() [2/2]

◆ attributeAsDoubleList_() [1/2]

◆ attributeAsDoubleList_() [2/2]

◆ attributeAsInt_() [1/2]

◆ attributeAsInt_() [2/2]

◆ attributeAsIntList_() [1/2]

◆ attributeAsIntList_() [2/2]

◆ attributeAsString_() [1/2]

◆ attributeAsString_() [2/2]

◆ attributeAsStringList_() [1/2]

◆ attributeAsStringList_() [2/2]

◆ checkUniqueIdentifiers_()

◆ cvParamToValue() [1/2]

◆ cvParamToValue() [2/2]

◆ cvStringToEnum_()

◆ equal_()

◆ error()

◆ expectList_()

◆ fatalError()

◆ fromXSDString()

◆ getLoadDetail()

◆ onCharacters()

◆ onEndElement()

◆ onStartElement()

◆ optionalAttributeAsDouble_() [1/2]

◆ optionalAttributeAsDouble_() [2/2]

◆ optionalAttributeAsDoubleList_() [1/2]

◆ optionalAttributeAsDoubleList_() [2/2]

◆ optionalAttributeAsInt_() [1/2]

◆ optionalAttributeAsInt_() [2/2]

◆ optionalAttributeAsIntList_() [1/2]

◆ optionalAttributeAsIntList_() [2/2]

◆ optionalAttributeAsString_() [1/2]

◆ optionalAttributeAsString_() [2/2]

◆ optionalAttributeAsStringList_() [1/2]

◆ optionalAttributeAsStringList_() [2/2]

◆ optionalAttributeAsUInt_() [1/2]

◆ optionalAttributeAsUInt_() [2/2]

◆ reset()

◆ setLoadDetail()

◆ warning()

◆ writeTo()

◆ writeUserParam_()

◆ writeXMLEscape()

Member Data Documentation

◆ cv_terms_

◆ file_

◆ load_detail_

◆ open_tags_

◆ sm_

◆ version_