Class BiopaxLevel2Handler

Overrides: xml.sax.handler.ContentHandler.__init__

Receive notification of the beginning of a document.

The SAX parser will invoke this method only once, before any other methods in this interface or in DTDHandler (except for setDocumentLocator).

Overrides: xml.sax.handler.ContentHandler.startDocument

(inherited documentation)

Receive notification of the end of a document.

The SAX parser will invoke this method only once, and it will be the last method invoked during the parse. The parser shall not invoke this method until it has either abandoned parsing (because of an unrecoverable error) or reached the end of input.

Overrides: xml.sax.handler.ContentHandler.endDocument

(inherited documentation)

Signals the start of an element in non-namespace mode.

The name parameter contains the raw XML 1.0 name of the element type as a string and the attrs parameter holds an instance of the Attributes class containing the attributes of the element.

Overrides: xml.sax.handler.ContentHandler.startElement

(inherited documentation)

Signals the end of an element in non-namespace mode.

The name parameter contains the name of the element type, just as with the startElement event.

Overrides: xml.sax.handler.ContentHandler.endElement

(inherited documentation)

Receive notification of character data.

The Parser will call this method to report each chunk of character data. SAX parsers may return all contiguous character data in a single chunk, or they may split it into several chunks; however, all of the characters in any single event must come from the same external entity so that the Locator provides useful information.

Overrides: xml.sax.handler.ContentHandler.characters

(inherited documentation)

datatype_operations

Value:

{"uniprot": _identity, "ncbi_taxonomy": _identity, "tigr": _identity, "reactome": _identity, "chebi": _identity, "go": _identity, "pubchem c ompound": _identity, "glycan": _identity, "compound": _identity, "entr ez": _entrez_funct}

biopax_objects_dict

Value:

{'bp:biochemicalreaction': <class 'biana.BianaParser.biopaxLevel2Parse r.BiopaxBiochemicalReaction'>, 'bp:biosource': <class 'biana.BianaParser.biopaxLevel2Parser.BiopaxBi oSource'>, 'bp:catalysis': <class 'biana.BianaParser.biopaxLevel2Parser.BiopaxCa talysis'>, 'bp:complex': <class 'biana.BianaParser.biopaxLevel2Parser.BiopaxComp lex'>, ...