This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation. More...

#include <OpenMS/FORMAT/ConsensusXMLFile.h>

Inheritance diagram for ConsensusXMLFile:

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Collaboration diagram for ConsensusXMLFile:

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Public Member Functions
	ConsensusXMLFile ()
	Default constructor. More...

	~ConsensusXMLFile () override
	Destructor. More...

void	load (const String &filename, ConsensusMap &map)
	Loads a consensus map from file and calls updateRanges. More...

void	store (const String &filename, const ConsensusMap &consensus_map)
	Stores a consensus map to file. More...

PeakFileOptions &	getOptions ()
	Mutable access to the options for loading/storing. More...

const PeakFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing. More...

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

String	errorString ()
	Returns the last error description. 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)

Public Member Functions inherited from XMLFile
	XMLFile ()
	Default constructor. More...

	XMLFile (const String &schema_location, const String &version)
	Constructor that sets the schema location. More...

virtual	~XMLFile ()
	Destructor. More...

bool	isValid (const String &filename, std::ostream &os)
	Checks if a file validates against the XML schema. More...

const String &	getVersion () const
	return the version of the schema More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Protected Member Functions
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	writePeptideIdentification_ (const String &filename, std::ostream &os, const PeptideIdentification &id, const String &tag_name, UInt indentation_level)
	Writes a peptide identification to a stream (for assigned/unassigned peptide identifications) More...

void	addProteinGroups_ (MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::unordered_map< std::string, UInt > &accession_to_id, const String &runid, XMLHandler::ActionMode mode)

void	getProteinGroups_ (std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name)
	Read and store ProteinGroup data. 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)
	Conversion of a String to an integer value. More...

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

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

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

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

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

DateTime	asDateTime_ (String date_string)
	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 Member Functions inherited from XMLFile
void	parse_ (const String &filename, XMLHandler *handler)
	Parses the XML file given by `filename` using the handler given by `handler`. More...

void	parseBuffer_ (const std::string &buffer, XMLHandler *handler)
	Parses the in-memory buffer given by `buffer` using the handler given by `handler`. More...

void	save_ (const String &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by `handler` in the file given by `filename`. More...

void	enforceEncoding_ (const String &encoding)

Protected Attributes
PeakFileOptions	options_
	Options that can be set. More...

Temporary variables for parsing
ConsensusMap *	consensus_map_

ConsensusFeature	act_cons_element_

DPosition< 2 >	pos_

double	it_

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

ProteinIdentification	prot_id_
	Temporary protein ProteinIdentification. More...

PeptideIdentification	pep_id_
	Temporary peptide ProteinIdentification. More...

ProteinHit	prot_hit_
	Temporary protein hit. More...

PeptideHit	pep_hit_
	Temporary peptide hit. More...

std::vector< PeptideEvidence >	peptide_evidences_
	Temporary peptide evidences. More...

Map< String, String >	proteinid_to_accession_
	Map from protein id to accession. More...

std::unordered_map< std::string, UInt >	accession_to_id_
	Map from search identifier concatenated with protein accession to id. More...

Map< String, String >	identifier_id_
	Map from identification run identifier to file xs:id (for linking peptide identifications to the corresponding run) More...

Map< String, String >	id_identifier_
	Map from file xs:id to identification run identifier (for linking peptide identifications to the corresponding run) More...

ProteinIdentification::SearchParameters	search_param_
	Temporary search parameters file. More...

UInt	progress_

Protected Attributes inherited from XMLHandler
String	error_message_
	Error message of the last error. More...

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...

Protected Attributes inherited from XMLFile
String	schema_location_
	XML schema file location. More...

String	schema_version_
	Version string. More...

String	enforced_encoding_
	Encoding string that replaces the encoding (system dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

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...

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

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation.

This class can be used to load the content of a consensusXML file into a ConsensusMap or to save the content of an ConsensusMap object into an XML file.

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 ConsensusXMLFile::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

◆ ConsensusXMLFile()

ConsensusXMLFile ( )

Default constructor.

◆ ~ConsensusXMLFile()

~ConsensusXMLFile ( )

override

Destructor.

Member Function Documentation

◆ addProteinGroups_()

void addProteinGroups_	(	MetaInfoInterface &	meta,
		const std::vector< ProteinIdentification::ProteinGroup > &	groups,
		const String &	group_name,
		const std::unordered_map< std::string, UInt > &	accession_to_id,
		const String &	runid,
		XMLHandler::ActionMode	mode
	)

protected

Add data from ProteinGroups to a MetaInfoInterface Since it can be used during load and store, it needs to take a param for the current mode (LOAD/STORE) to throw appropriate warnings/errors

◆ characters()

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

overrideprotected

◆ endElement()

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

overrideprotected

◆ getOptions() [1/2]

PeakFileOptions& getOptions ( )

Mutable access to the options for loading/storing.

◆ getOptions() [2/2]

const PeakFileOptions& getOptions ( ) const

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

◆ getProteinGroups_()

void getProteinGroups_	(	std::vector< ProteinIdentification::ProteinGroup > &	groups,
		const String &	group_name
	)

protected

Read and store ProteinGroup data.

◆ load()

void load	(	const String &	filename,
		ConsensusMap &	map
	)

Loads a consensus map from file and calls updateRanges.

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing
Exception::MissingInformation	is thrown if source files are missing/duplicated or map-IDs are referencing non-existing maps

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::fileChanged_(), and TOPPGNPSExport::main_().

◆ startElement()

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

overrideprotected

◆ store()

void store	(	const String &	filename,
		const ConsensusMap &	consensus_map
	)

Stores a consensus map to file.

Exceptions

Exception::UnableToCreateFile	is thrown if the file name is not writable
Exception::IllegalArgument	is thrown if the consensus map is not valid
Exception::MissingInformation	is thrown if source files are missing/duplicated or map-IDs are referencing non-existing maps

Referenced by TOPPViewBase::runTOPPTool_().

◆ writePeptideIdentification_()

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

protected

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

Member Data Documentation

◆ accession_to_id_

std::unordered_map<std::string, UInt> accession_to_id_

protected

Map from search identifier concatenated with protein accession to id.

◆ act_cons_element_

ConsensusFeature act_cons_element_

protected

◆ consensus_map_

ConsensusMap* consensus_map_

protected

◆ id_identifier_

Map<String, String> id_identifier_

protected

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

◆ identifier_id_

Map<String, String> identifier_id_

protected

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

◆ it_

double it_

protected

◆ last_meta_

MetaInfoInterface* last_meta_

protected

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

◆ options_

PeakFileOptions options_

protected

Options that can be set.

◆ pep_hit_

PeptideHit pep_hit_

protected

Temporary peptide hit.

◆ pep_id_

PeptideIdentification pep_id_

protected

Temporary peptide ProteinIdentification.

◆ peptide_evidences_

std::vector<PeptideEvidence> peptide_evidences_

protected

Temporary peptide evidences.

◆ pos_

DPosition<2> pos_

protected

◆ progress_

UInt progress_

protected

◆ prot_hit_

ProteinHit prot_hit_

protected

Temporary protein hit.

◆ prot_id_

ProteinIdentification prot_id_

protected

Temporary protein ProteinIdentification.

◆ proteinid_to_accession_

Map<String, String> proteinid_to_accession_

protected

Map from protein id to accession.

◆ search_param_

ProteinIdentification::SearchParameters search_param_

protected

Temporary search parameters file.

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ConsensusXMLFile()

◆ ~ConsensusXMLFile()

Member Function Documentation

◆ addProteinGroups_()

◆ characters()

◆ endElement()

◆ getOptions() [1/2]

◆ getOptions() [2/2]

◆ getProteinGroups_()

◆ load()

◆ startElement()

◆ store()

◆ writePeptideIdentification_()

Member Data Documentation

◆ accession_to_id_

◆ act_cons_element_

◆ consensus_map_

◆ id_identifier_

◆ identifier_id_

◆ it_

◆ last_meta_

◆ options_

◆ pep_hit_

◆ pep_id_

◆ peptide_evidences_

◆ pos_

◆ progress_

◆ prot_hit_

◆ prot_id_

◆ proteinid_to_accession_

◆ search_param_