FeatureXMLHandler Class Reference

This class provides Input/Output functionality for feature maps. More...

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

Inheritance diagram for FeatureXMLHandler:

Collaboration diagram for FeatureXMLHandler:

Protected Attributes
temporary data structures to hold parsed data
Param	param_
ConvexHull2D::PointArrayType	current_chull_
DPosition< 2 >	hull_position_
UInt	dim_
	current dimension of the feature position, quality, or convex hull point
bool	in_description_
	for downward compatibility, all tags in the old description must be ignored
Int	subordinate_feature_level_
	level in Feature stack during parsing
MetaInfoInterface *	last_meta_
	Pointer to last read object as a MetaInfoInterface, or null.
ProteinIdentification	prot_id_
	Temporary protein ProteinIdentification.
PeptideIdentification	pep_id_
	Temporary peptide ProteinIdentification.
ProteinHit	prot_hit_
	Temporary protein hit.
PeptideHit	pep_hit_
	Temporary peptide hit.
std::map< std::string, std::string >	proteinid_to_accession_
	Map from protein id to accession.
std::map< std::string, Size >	accession_to_id_
	Map from search identifier concatenated with protein accession to id.
std::map< std::string, std::string >	identifier_id_
	Map from identification run identifier to file xs:id (for linking peptide identifications to the corresponding run)
std::map< std::string, std::string >	id_identifier_
	Map from file xs:id to identification run identifier (for linking peptide identifications to the corresponding run)
ProteinIdentification::SearchParameters	search_param_
	Temporary search parameters file.
Protected Attributes inherited from XMLHandler
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
std::vector< std::vector< std::string > >	cv_terms_
	Array of CV term lists (one sublist denotes one term and it's children)
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_

Constructors and Destructor
Int	disable_parsing_
Feature *	current_feature_
	points to the last open <feature> tag (possibly a subordinate feature)
FeatureMap *	map_
	Feature map pointer for writing.
const FeatureMap *	cmap_
	Feature map pointer for reading.
FeatureFileOptions	options_
	Options that can be set.
bool	size_only_
	only parse until "count" tag is reached (used in loadSize())
Size	expected_size_
	holds the putative size given in count
	FeatureXMLHandler (FeatureMap &map, const std::string &filename)
	Default constructor.
	FeatureXMLHandler (const FeatureMap &map, const std::string &filename)
	~FeatureXMLHandler () override
	Destructor.
void	writeTo (std::ostream &os) override
	Docu in base class XMLHandler::writeTo.
FeatureFileOptions &	getOptions ()
	Mutable access to the options for loading/storing.
const FeatureFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing.
void	setOptions (const FeatureFileOptions &)
	setter for options for loading/storing
void	setSizeOnly (const bool size_only)
Size	getSize () const
void	resetMembers_ ()
void	onEndElement (const char16_t *qname) override
	Parsing method for closing tags.
void	onStartElement (const char16_t *qname, const XMLAttributes &attributes) override
	Parsing method for opening tags.
void	onCharacters (const char16_t *chars, Size length) override
	Parsing method for character data.
void	writeFeature_ (const std::string &filename, std::ostream &os, const Feature &feat, const std::string &identifier_prefix, UInt64 identifier, UInt indentation_level)
	Writes a feature to a stream.
void	writePeptideIdentification_ (const std::string &filename, std::ostream &os, const PeptideIdentification &id, const std::string &tag_name, UInt indentation_level)
	Writes a peptide identification to a stream (for assigned/unassigned peptide identifications)
void	updateCurrentFeature_ (bool create)
	update the pointer to the current feature

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 Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Public Member Functions inherited from XMLHandler
	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.
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
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.
virtual	~ProgressLogger ()
	Destructor.
	ProgressLogger (const ProgressLogger &other)
	Copy constructor.
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!
LogType	getLogType () const
	Returns the type of progress log being used.
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.
void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.
void	setProgress (SignedSize value) const
	Sets the current progress.
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end)
Static Public Member Functions inherited from XMLHandler
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.
Protected Member Functions inherited from XMLHandler
void	writeUserParam_ (const std::string &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes the content of MetaInfoInterface to the file.
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.
bool	equal_ (const char16_t *a, const char16_t *b) const
	Returns if two Xerces strings are equal.
SignedSize	cvStringToEnum_ (const Size section, const std::string &term, const char *message, const SignedSize result_on_error=0)
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.
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class provides Input/Output functionality for feature maps.

A documented schema for this format can be found at https://github.com/OpenMS/OpenMS/tree/develop/share/OpenMS/SCHEMAS

Todo:

Take care that unique ids are assigned properly by TOPP tools before calling FeatureXMLFile::store(). There will be a message on OPENMS_LOG_INFO but we will make no attempt to fix the problem in this class. (all developers)

Constructor & Destructor Documentation

FeatureXMLHandler() [1/2]

FeatureXMLHandler	(	FeatureMap &	map,
		const std::string &	filename
	)

Default constructor.

FeatureXMLHandler() [2/2]

FeatureXMLHandler	(	const FeatureMap &	map,
		const std::string &	filename
	)

~FeatureXMLHandler()

~FeatureXMLHandler ( )

override

Destructor.

Member Function Documentation

getOptions() [1/2]

FeatureFileOptions & getOptions

(

)

Mutable access to the options for loading/storing.

getOptions() [2/2]

const FeatureFileOptions & getOptions

(

)

const

Non-mutable access to the options for loading/storing.

getSize()

Size getSize ( ) const

inline

onCharacters()

void onCharacters ( const char16_t *  chars, Size  length  )

overrideprotectedvirtual

Parsing method for character data.

Reimplemented from XMLHandler.

onEndElement()

void onEndElement ( const char16_t *  qname )

overrideprotectedvirtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

onStartElement()

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

overrideprotectedvirtual

Parsing method for opening tags.

Reimplemented from XMLHandler.

resetMembers_()

void resetMembers_ ( )

protected

setOptions()

void setOptions

(

const FeatureFileOptions &

)

setter for options for loading/storing

setSizeOnly()

void setSizeOnly ( const bool  size_only )

inline

updateCurrentFeature_()

void updateCurrentFeature_ ( bool  create )

protected

update the pointer to the current feature

Parameters

[in]

create

If true, a new (empty) Feature is added at the appropriate subordinate_feature_level_

writeFeature_()

void writeFeature_ ( const std::string &  filename, std::ostream &  os, const Feature &  feat, const std::string &  identifier_prefix, UInt64  identifier, UInt  indentation_level  )

protected

Writes a feature to a stream.

writePeptideIdentification_()

void writePeptideIdentification_ ( const std::string &  filename, std::ostream &  os, const PeptideIdentification &  id, const std::string &  tag_name, UInt  indentation_level  )

protected

Writes a peptide identification to a stream (for assigned/unassigned peptide identifications)

writeTo()

void writeTo ( std::ostream &  os )

overridevirtual

Docu in base class XMLHandler::writeTo.

Reimplemented from XMLHandler.

Member Data Documentation

accession_to_id_

std::map<std::string, Size> accession_to_id_

protected

Map from search identifier concatenated with protein accession to id.

cmap_

const FeatureMap* cmap_

protected

Feature map pointer for reading.

current_chull_

ConvexHull2D::PointArrayType current_chull_

protected

current_feature_

Feature* current_feature_

protected

points to the last open <feature> tag (possibly a subordinate feature)

dim_

UInt dim_

protected

current dimension of the feature position, quality, or convex hull point

disable_parsing_

Int disable_parsing_

protected

allows for early return in parsing functions when certain sections should be ignored <=0 - parsing ON >0 - this number of tags have been entered that forbid parsing and need to be exited before parsing continues

expected_size_

Size expected_size_

protected

holds the putative size given in count

hull_position_

DPosition<2> hull_position_

protected

id_identifier_

std::map<std::string, std::string> id_identifier_

protected

Map from file xs:id to identification run identifier (for linking peptide identifications to the corresponding run)

identifier_id_

std::map<std::string, std::string> identifier_id_

protected

Map from identification run identifier to file xs:id (for linking peptide identifications to the corresponding run)

in_description_

bool in_description_

protected

for downward compatibility, all tags in the old description must be ignored

last_meta_

MetaInfoInterface* last_meta_

protected

Pointer to last read object as a MetaInfoInterface, or null.

map_

FeatureMap* map_

protected

Feature map pointer for writing.

options_

FeatureFileOptions options_

protected

Options that can be set.

param_

Param param_

protected

pep_hit_

PeptideHit pep_hit_

protected

Temporary peptide hit.

pep_id_

PeptideIdentification pep_id_

protected

Temporary peptide ProteinIdentification.

prot_hit_

ProteinHit prot_hit_

protected

Temporary protein hit.

prot_id_

ProteinIdentification prot_id_

protected

Temporary protein ProteinIdentification.

proteinid_to_accession_

std::map<std::string, std::string> proteinid_to_accession_

protected

Map from protein id to accession.

search_param_

ProteinIdentification::SearchParameters search_param_

protected

Temporary search parameters file.

size_only_

bool size_only_

protected

only parse until "count" tag is reached (used in loadSize())

subordinate_feature_level_

Int subordinate_feature_level_

protected

level in Feature stack during parsing