Used to load OMSSAXML files. More...

#include <OpenMS/FORMAT/OMSSAXMLFile.h>

Inheritance diagram for OMSSAXMLFile:

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

virtual	~OMSSAXMLFile ()
	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)
	Parsing method for closing tags. More...

void	startElement (const XMLCh const, const XMLCh const, const XMLCh *const qname, const xercesc::Attributes &attributes)
	Parsing method for opening tags. More...

void	characters (const XMLCh *const chars, const XMLSize_t)
	Parsing method for character data. More...

Protected Member Functions inherited from XMLHandler
bool	equal_ (const XMLCh a, const XMLCh b) const
	Returns if two Xerces strings are equal. More...

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...

char *	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...

char *	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...

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

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

virtual	~XMLHandler ()
	Destructor. More...

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

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...

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

String	errorString ()
	Returns the last error description. More...

void	fatalError (const xercesc::SAXParseException &exception)

void	error (const xercesc::SAXParseException &exception)

void	warning (const xercesc::SAXParseException &exception)

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	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...

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

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...

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

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...

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()

virtual ~OMSSAXMLFile ( )

virtual

Destructor.

◆ OMSSAXMLFile() [2/2]

OMSSAXMLFile ( const OMSSAXMLFile & rhs )

private

Member Function Documentation

◆ characters()

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

protectedvirtual

Parsing method for character data.

Reimplemented from XMLHandler.

◆ endElement()

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

protectedvirtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

◆ 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 *	uri,
		const XMLCh *	localname,
		const XMLCh *const	qname,
		const xercesc::Attributes &	attrs
	)

protectedvirtual

Parsing method for opening tags.

Reimplemented from XMLHandler.

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_

Map<UInt, std::vector<ResidueModification> > mods_map_

private

modifications mapping file from OMSSA mod num to UniMod accession

◆ mods_to_num_

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_