public Model convertFromOWL(InputStream in)
	{
		init(in);

		//cache the namespaces.
		namespaces = this.readNameSpaces();

		autodetectBiopaxLevel(); // this may update level, editorMap and factory!

		Model model = factory.createModel();

		model.getNameSpacePrefixMap().putAll(namespaces);

		model.setXmlBase(base);

		boolean fixingPEPS = model.getLevel() == BioPAXLevel.L2 && this.isFixReusedPEPs();
		if (fixingPEPS)
		{
			reusedPEPHelper = new ReusedPEPHelper(model);
		}

		createAndBind(model);

		if (fixingPEPS)
		{
			this.getReusedPEPHelper().copyPEPFields();
		}
		
		reset(in);

		return model;
	}
public Model convertFromOWL ( InputStream in ) { init ( in ) ; namespaces = this . readNameSpaces ( ) ; autodetectBiopaxLevel ( ) ; Model model = factory . createModel ( ) ; model . getNameSpacePrefixMap ( ) . putAll ( namespaces ) ; model . setXmlBase ( base ) ; boolean fixingPEPS = model . getLevel ( ) == BioPAXLevel . L2 && this . isFixReusedPEPs ( ) ; if ( fixingPEPS ) { reusedPEPHelper = new ReusedPEPHelper ( model ) ; } createAndBind ( model ) ; if ( fixingPEPS ) { this . getReusedPEPHelper ( ) . copyPEPFields ( ) ; } reset ( in ) ; return model ; }
Reads a BioPAX model from an OWL file input stream (<em>in</em>) and converts it to a model.
@param in inputStream from which the model will be read
@return an empty model in case of invalid input.