UnimodXMLFile Class Reference

Used to load XML files from unimod.org files. More...

#include <OpenMS/FORMAT/UnimodXMLFile.h>

Inheritance diagram for UnimodXMLFile:

Public Member Functions
	UnimodXMLFile ()
	Default constructor.
	~UnimodXMLFile () override
	Destructor.
void	load (const std::string &filename, std::vector< ResidueModification * > &modifications)
	loads data from unimod.xml file
Public Member Functions inherited from XMLFile
	XMLFile ()
	Construct an XMLFile without schema info; schema_location_ remains unset, so isValid cannot be used until derived-class logic initializes schema_location_ before calling isValid.
	XMLFile (const std::string &schema_location, const std::string &version)
	Construct with a schema location for later isValid calls.
virtual	~XMLFile ()
	Virtual destructor — defaulted; allows safe deletion through a base-class pointer.
bool	isValid (const std::string &filename, std::ostream &os)
	Check if filename validates against the bound XML schema.
const std::string &	getVersion () const
	Return the schema version string passed to the parameterised constructor; empty for default-constructed instances.

Private Member Functions
bool	loadInSlices_ (const std::string &file, std::vector< ResidueModification * > &modifications)
	Parses a large UniMod file in slices on several threads; false if it did not (the caller parses it as a whole)
	UnimodXMLFile (const UnimodXMLFile &rhs)
	Not implemented.
UnimodXMLFile &	operator= (const UnimodXMLFile &rhs)
	Not implemented.

Additional Inherited Members
Protected Member Functions inherited from XMLFile
void	parse_ (const std::string &filename, XMLHandler *handler, bool namespace_aware=false)
	Parse the XML file at filename through handler.
void	parseBuffer_ (const std::string &buffer, XMLHandler *handler, bool namespace_aware=false)
	Parse an in-memory XML buffer through handler.
void	save_ (const std::string &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by handler in the file given by filename.
void	enforceEncoding_ (const std::string &encoding)
	Set or clear the XML-encoding override applied to subsequent parse_ / parseBuffer_ calls.
Protected Attributes inherited from XMLFile
std::string	schema_location_
	Path of the XML schema for validation; empty when the default constructor was used (isValid then throws NotImplemented).
std::string	schema_version_
	Schema version string returned by getVersion.
std::string	enforced_encoding_
	Optional XML encoding override applied to the InputSource in parse_ and parseBuffer_; empty disables the override. Used as a workaround for XTandem output XML which carries an encoding the parser otherwise stumbles on.

Detailed Description

Used to load XML files from unimod.org files.

Constructor & Destructor Documentation

UnimodXMLFile() [1/2]

UnimodXMLFile

(

)

Default constructor.

~UnimodXMLFile()

~UnimodXMLFile ( )

override

Destructor.

UnimodXMLFile() [2/2]

UnimodXMLFile ( const UnimodXMLFile &  rhs )

private

Not implemented.

Member Function Documentation

loadInSlices_()

bool loadInSlices_ ( const std::string &  file, std::vector< ResidueModification * > &  modifications  )

private

Parses a large UniMod file in slices on several threads; false if it did not (the caller parses it as a whole)

The <umod:modifications> section of file is cut at end tags of <umod:mod> elements into a few slices; each is parsed with its own handler as the file with the other slices left out, and the modifications are appended to modifications in the order of the file. Only for a regular file whose text the handler provably reads the same way in slices: an XML declaration and comments before the root element only, no comments, CDATA sections, processing instructions or document type declaration after that, nothing the handler acts on outside the section, and in it complete <umod:mod> elements with specificities, neutral losses, deltas and elements nested as in unimod.xml and positions the handler knows. A file that is not like that, any error in a slice (whose messages are not written) or any failure (e.g. memory) leaves modifications unchanged and returns false, so that the result, messages and errors are those of the whole file.

operator=()

UnimodXMLFile & operator= ( const UnimodXMLFile &  rhs )

private

Not implemented.