Used to load Mascot PepXML files. More...

#include <OpenMS/FORMAT/PepXMLFileMascot.h>

Inheritance diagram for PepXMLFileMascot:

Public Member Functions
	PepXMLFileMascot ()
	Constructor. More...

void	load (const String &filename, std::map< String, std::vector< AASequence > > &peptides)
	Loads peptide sequences with modifications out of a PepXML file. 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
virtual void	endElement (const XMLCh const, const XMLCh const, const XMLCh *const qname)
	Parsing method for closing tags. More...

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

void	matchModification_ (double mass, String &modification_description)

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

Protected Attributes
members for loading data
String	actual_title_
	Pointer to fill in protein identifications. More...

String	actual_sequence_
	The sequence of the actual peptide hit. More...

std::vector< std::pair< String, UInt > >	actual_modifications_
	The modifications of the actual peptide hit (position is 1-based) More...

std::map< String, std::vector< AASequence > > *	peptides_
	The peptides together with the spectrum title. More...

std::vector< AASequence >	actual_aa_sequences_
	stores the actual peptide sequences More...

std::vector< String >	fixed_modifications_
	stores the fixed residue modifications More...

std::vector< std::pair< String, double > >	variable_modifications_
	stores the variable residue modifications 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...

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...

Detailed Description

Used to load Mascot PepXML files.

A schema for this format can be found at http://www.matrixscience.com/xmlns/schema/pepXML_v18/pepXML_v18.xsd.

Constructor & Destructor Documentation

◆ PepXMLFileMascot()

PepXMLFileMascot ( )

Constructor.

Member Function Documentation

◆ endElement()

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

protectedvirtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

◆ load()

void load	(	const String &	filename,
		std::map< String, std::vector< AASequence > > &	peptides
	)

Loads peptide sequences with modifications out of a PepXML file.

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing

◆ matchModification_()

void matchModification_	(	double	mass,
		String &	modification_description
	)

protected

◆ startElement()

virtual 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_aa_sequences_

std::vector<AASequence> actual_aa_sequences_

protected

stores the actual peptide sequences

◆ actual_modifications_

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

protected

The modifications of the actual peptide hit (position is 1-based)

◆ actual_sequence_

String actual_sequence_

protected

The sequence of the actual peptide hit.

◆ actual_title_

String actual_title_

protected

Pointer to fill in protein identifications.

The title of the actual spectrum

◆ fixed_modifications_

std::vector<String> fixed_modifications_

protected

stores the fixed residue modifications

◆ peptides_

std::map<String, std::vector<AASequence> >* peptides_

protected

The peptides together with the spectrum title.

◆ variable_modifications_

std::vector<std::pair<String, double> > variable_modifications_

protected

stores the variable residue modifications

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PepXMLFileMascot()

Member Function Documentation

◆ endElement()

◆ load()

◆ matchModification_()

◆ startElement()

Member Data Documentation

◆ actual_aa_sequences_

◆ actual_modifications_

◆ actual_sequence_

◆ actual_title_

◆ fixed_modifications_

◆ peptides_

◆ variable_modifications_