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 String &filename, const String &version)
	Default constructor. More...

	~XMLHandler () override
	Destructor. More...

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

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

String conversion
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...

Reimplemented XERCES-C error handlers
These methods forward the error message to our own error handlers below.
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...

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

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

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...

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

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

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

Accessing attributes
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...

	XMLHandler ()
	Not implemented. More...

const String &	expectList_ (const 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 String &	filename,
		const String &	version
	)

Default constructor.

◆ ~XMLHandler()

~XMLHandler ( )

override

Destructor.

◆ XMLHandler() [2/2]

XMLHandler ( )

private

Not implemented.

Member Function Documentation

◆ asBool_()

bool asBool_ ( const 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_ ( String date_string ) const

inlineprotected

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

References DateTime::set(), String::substr(), and String::trim().

◆ asDouble_()

double asDouble_ ( const String & in ) const

inlineprotected

Conversion of a String to a double value.

References String::toDouble().

◆ asFloat_()

float asFloat_ ( const String & in ) const

inlineprotected

Conversion of a String to a float value.

References String::toFloat().

◆ asInt_() [1/2]

Int asInt_ ( const String & in ) const

inlineprotected

Conversion of a String to an integer value.

References String::toInt().

◆ asInt_() [2/2]

Int asInt_ ( const XMLCh * in ) const

inlineprotected

Conversion of a Xerces string to an integer value.

◆ asUInt_()

UInt asUInt_ ( const String & in ) const

inlineprotected

Conversion of a String to an unsigned integer value.

References String::toInt().

◆ attributeAsDouble_() [1/2]

double attributeAsDouble_	(	const xercesc::Attributes &	a,
		const char *	name
	)		const

inlineprotected

Converts an attribute to a double.

References StringManager::convert(), StringManager::convertPtr(), and String::toDouble().

◆ attributeAsDouble_() [2/2]

double attributeAsDouble_	(	const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

Converts an attribute to a double.

References StringManager::convert().

◆ attributeAsDoubleList_() [1/2]

DoubleList attributeAsDoubleList_	(	const xercesc::Attributes &	a,
		const char *	name
	)		const

inlineprotected

Converts an attribute to a DoubleList.

References String::substr().

◆ attributeAsDoubleList_() [2/2]

DoubleList attributeAsDoubleList_	(	const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

Converts an attribute to a DoubleList.

References String::substr().

◆ attributeAsInt_() [1/2]

Int attributeAsInt_	(	const xercesc::Attributes &	a,
		const char *	name
	)		const

inlineprotected

Converts an attribute to a Int.

References StringManager::convertPtr().

◆ attributeAsInt_() [2/2]

Int attributeAsInt_	(	const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

Converts an attribute to a Int.

References StringManager::convert().

◆ attributeAsIntList_() [1/2]

IntList attributeAsIntList_	(	const xercesc::Attributes &	a,
		const char *	name
	)		const

inlineprotected

Converts an attribute to an IntList.

References String::substr().

◆ attributeAsIntList_() [2/2]

IntList attributeAsIntList_	(	const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

Converts an attribute to a IntList.

References String::substr().

◆ attributeAsString_() [1/2]

String attributeAsString_	(	const xercesc::Attributes &	a,
		const char *	name
	)		const

inlineprotected

Converts an attribute to a String.

References StringManager::convert(), and StringManager::convertPtr().

◆ attributeAsString_() [2/2]

String attributeAsString_	(	const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

Converts an attribute to a String.

References StringManager::convert().

◆ attributeAsStringList_() [1/2]

StringList attributeAsStringList_	(	const xercesc::Attributes &	a,
		const char *	name
	)		const

inlineprotected

Converts an attribute to an StringList.

References String::hasSubstring(), and String::substr().

◆ attributeAsStringList_() [2/2]

StringList attributeAsStringList_	(	const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

Converts an attribute to a StringList.

References String::hasSubstring(), and String::substr().

◆ characters()

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

override

Parsing method for character data.

◆ 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

◆ cvStringToEnum_()

SignedSize cvStringToEnum_	(	const Size	section,
		const 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)

◆ endElement()

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

override

Parsing method for closing tags.

◆ equal_()

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

inlineprotected

Returns if two Xerces strings are equal.

◆ error() [1/2]

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

Error handler for recoverable errors.

◆ error() [2/2]

void error ( const xercesc::SAXParseException & exception )

override

◆ expectList_()

const String& expectList_ ( const String & str ) const

inlineprivate

References String::hasPrefix(), and String::hasSuffix().

◆ fatalError() [1/2]

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

Fatal error handler. Throws a ParseError exception.

◆ fatalError() [2/2]

void fatalError ( const xercesc::SAXParseException & exception )

override

◆ fromXSDString()

static DataValue fromXSDString	(	const String &	type,
		const 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

type	An XSD type. If the type is not supported, the returned type will be a string
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.

References String::toDouble(), String::toInt32(), and String::toInt64().

◆ getLoadDetail()

virtual LOADDETAIL getLoadDetail ( ) const

virtual

handler which support partial loading, implement this method

Reimplemented in MzXMLHandler, and MzMLHandler.

◆ optionalAttributeAsDouble_() [1/2]

bool optionalAttributeAsDouble_	(	double &	value,
		const xercesc::Attributes &	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(), StringManager::convertPtr(), and String::toDouble().

◆ optionalAttributeAsDouble_() [2/2]

bool optionalAttributeAsDouble_	(	double &	value,
		const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

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

References StringManager::convert().

◆ optionalAttributeAsDoubleList_() [1/2]

bool optionalAttributeAsDoubleList_	(	DoubleList &	value,
		const xercesc::Attributes &	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 StringManager::convertPtr().

◆ optionalAttributeAsDoubleList_() [2/2]

bool optionalAttributeAsDoubleList_	(	DoubleList &	value,
		const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

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

Returns: if the attribute was present

◆ optionalAttributeAsInt_() [1/2]

bool optionalAttributeAsInt_	(	Int &	value,
		const xercesc::Attributes &	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::convertPtr().

◆ optionalAttributeAsInt_() [2/2]

bool optionalAttributeAsInt_	(	Int &	value,
		const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

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

◆ optionalAttributeAsIntList_() [1/2]

bool optionalAttributeAsIntList_	(	IntList &	value,
		const xercesc::Attributes &	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 StringManager::convertPtr().

◆ optionalAttributeAsIntList_() [2/2]

bool optionalAttributeAsIntList_	(	IntList &	value,
		const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

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

Returns: if the attribute was present

◆ optionalAttributeAsString_() [1/2]

bool optionalAttributeAsString_	(	String &	value,
		const xercesc::Attributes &	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 StringManager::convertPtr().

◆ optionalAttributeAsString_() [2/2]

bool optionalAttributeAsString_	(	String &	value,
		const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

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

References StringManager::convert().

◆ optionalAttributeAsStringList_() [1/2]

bool optionalAttributeAsStringList_	(	StringList &	value,
		const xercesc::Attributes &	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 StringManager::convertPtr().

◆ optionalAttributeAsStringList_() [2/2]

bool optionalAttributeAsStringList_	(	StringList &	value,
		const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

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

Returns: if the attribute was present

◆ optionalAttributeAsUInt_() [1/2]

bool optionalAttributeAsUInt_	(	UInt &	value,
		const xercesc::Attributes &	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::convertPtr().

◆ optionalAttributeAsUInt_() [2/2]

bool optionalAttributeAsUInt_	(	UInt &	value,
		const xercesc::Attributes &	a,
		const XMLCh *	name
	)		const

inlineprotected

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

◆ 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 MzXMLHandler, and MzMLHandler.

◆ startElement()

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

override

Parsing method for opening tags.

◆ warning() [1/2]

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

Warning handler.

◆ warning() [2/2]

void warning ( const xercesc::SAXParseException & exception )

override

◆ writeTo()

virtual void writeTo ( std::ostream & )

virtual

Writes the contents to a stream.

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

◆ writeUserParam_()

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

protected

Writes the content of MetaInfoInterface to the file.

◆ writeXMLEscape()

static String writeXMLEscape ( const 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: & < > " '

References String::has(), and String::substitute().

Member Data Documentation

◆ cv_terms_

std::vector<std::vector<String> > cv_terms_

protected

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

◆ file_

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<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_

String version_

protected

Schema version.

Classes

Public Types

Public Member Functions

Protected Member Functions

Reimplemented XERCES-C error handlers

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]

◆ characters()

◆ checkUniqueIdentifiers_()

◆ cvStringToEnum_()

◆ endElement()

◆ equal_()

◆ error() [1/2]

◆ error() [2/2]

◆ expectList_()

◆ fatalError() [1/2]

◆ fatalError() [2/2]

◆ fromXSDString()

◆ getLoadDetail()

◆ 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()

◆ startElement()

◆ warning() [1/2]

◆ warning() [2/2]

◆ writeTo()

◆ writeUserParam_()

◆ writeXMLEscape()

Member Data Documentation

◆ cv_terms_

◆ file_

◆ load_detail_

◆ open_tags_

◆ sm_

◆ version_