Used to load OMSSAXML files. More...

#include <OpenMS/FORMAT/OMSSAXMLFile.h>

Inheritance diagram for OMSSAXMLFile:

Collaboration diagram for OMSSAXMLFile:

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

	~OMSSAXMLFile () override
	Destructor. More...

void	load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true, bool load_empty_hits=true)
	loads data from a OMSSAXML file More...

void	setModificationDefinitionsSet (const ModificationDefinitionsSet &rhs)
	sets the valid modifications More...

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...

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) override

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...

	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...

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

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)

	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...

Private Member Functions
	OMSSAXMLFile (const OMSSAXMLFile &rhs)

OMSSAXMLFile &	operator= (const OMSSAXMLFile &rhs)

void	readMappingFile_ ()
	reads the mapping file needed for modifications More...

Private Attributes
std::vector< PeptideIdentification > *	peptide_identifications_
	the identifications (storing the peptide hits) More...

ProteinHit	actual_protein_hit_

PeptideHit	actual_peptide_hit_

PeptideEvidence	actual_peptide_evidence_

std::vector< PeptideEvidence >	actual_peptide_evidences_

PeptideIdentification	actual_peptide_id_

ProteinIdentification	actual_protein_id_

String	tag_

UInt	actual_mod_site_
	site of the actual modification (simple position in the peptide) More...

String	actual_mod_type_
	type of the modification More...

std::vector< std::pair< UInt, String > >	modifications_
	modifications of the peptide defined by site and type More...

bool	load_proteins_
	should protein hits be read from the file? More...

bool	load_empty_hits_
	should empty peptide identifications be loaded or skipped? More...

std::map< UInt, std::vector< const ResidueModification * > >	mods_map_
	modifications mapping file from OMSSA mod num to UniMod accession More...

std::map< String, UInt >	mods_to_num_
	modification mapping reverse, from the modification to the mod_num More...

ModificationDefinitionsSet	mod_def_set_
	modification definitions set of the search, needed to annotate fixed modifications More...

Additional Inherited Members
Protected 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 }

Static Protected 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 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...

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...

Detailed Description

Used to load OMSSAXML files.

This class is used to load documents that implement the schema of OMSSAXML files.

Constructor & Destructor Documentation

◆ OMSSAXMLFile() [1/2]

OMSSAXMLFile ( )

Default constructor.

◆ ~OMSSAXMLFile()

~OMSSAXMLFile ( )

override

Destructor.

◆ OMSSAXMLFile() [2/2]

OMSSAXMLFile ( const OMSSAXMLFile & rhs )

private

Member Function Documentation

◆ characters()

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

overrideprotected

◆ endElement()

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

overrideprotected

◆ operator=()

OMSSAXMLFile& operator= ( const OMSSAXMLFile & rhs )

private

◆ readMappingFile_()

void readMappingFile_ ( )

private

reads the mapping file needed for modifications

◆ setModificationDefinitionsSet()

void setModificationDefinitionsSet ( const ModificationDefinitionsSet & rhs )

sets the valid modifications

◆ startElement()

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

overrideprotected

Member Data Documentation

◆ actual_mod_site_

UInt actual_mod_site_

private

site of the actual modification (simple position in the peptide)

◆ actual_mod_type_

String actual_mod_type_

private

type of the modification

◆ actual_peptide_evidence_

PeptideEvidence actual_peptide_evidence_

private

◆ actual_peptide_evidences_

std::vector<PeptideEvidence> actual_peptide_evidences_

private

◆ actual_peptide_hit_

PeptideHit actual_peptide_hit_

private

◆ actual_peptide_id_

PeptideIdentification actual_peptide_id_

private

◆ actual_protein_hit_

ProteinHit actual_protein_hit_

private

◆ actual_protein_id_

ProteinIdentification actual_protein_id_

private

◆ load_empty_hits_

bool load_empty_hits_

private

should empty peptide identifications be loaded or skipped?

◆ load_proteins_

bool load_proteins_

private

should protein hits be read from the file?

◆ mod_def_set_

ModificationDefinitionsSet mod_def_set_

private

modification definitions set of the search, needed to annotate fixed modifications

◆ modifications_

std::vector<std::pair<UInt, String> > modifications_

private

modifications of the peptide defined by site and type

◆ mods_map_

std::map<UInt, std::vector<const ResidueModification*> > mods_map_

private

modifications mapping file from OMSSA mod num to UniMod accession

◆ mods_to_num_

std::map<String, UInt> mods_to_num_

private

modification mapping reverse, from the modification to the mod_num

◆ peptide_identifications_

std::vector<PeptideIdentification>* peptide_identifications_

private

the identifications (storing the peptide hits)

◆ tag_

String tag_

private

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ OMSSAXMLFile() [1/2]

◆ ~OMSSAXMLFile()

◆ OMSSAXMLFile() [2/2]

Member Function Documentation

◆ characters()

◆ endElement()

◆ operator=()

◆ readMappingFile_()

◆ setModificationDefinitionsSet()

◆ startElement()

Member Data Documentation

◆ actual_mod_site_

◆ actual_mod_type_

◆ actual_peptide_evidence_

◆ actual_peptide_evidences_

◆ actual_peptide_hit_

◆ actual_peptide_id_

◆ actual_protein_hit_

◆ actual_protein_id_

◆ load_empty_hits_

◆ load_proteins_

◆ mod_def_set_

◆ modifications_

◆ mods_map_

◆ mods_to_num_

◆ peptide_identifications_

◆ tag_