public void convert ( EntrySet entrySet , OutputStream outputStream , boolean forceInteractionToComplex ) { // check args if ( entrySet == null || outputStream == null ) { throw new IllegalArgumentException ( "convert: one or more null arguments." ) ; } if ( entrySet . getLevel ( ) != 2 ) { throw new IllegalArgumentException ( "convert: only PSI-MI Level 2.5 is supported." ) ; } //create a new empty BioPAX Model final Model model = BioPAXLevel . L3 . getDefaultFactory ( ) . createModel ( ) ; model . setXmlBase ( xmlBase ) ; // convert all psimi entries EntryMapper entryMapper = new EntryMapper ( model , forceInteractionToComplex ) ; for ( Entry entry : entrySet . getEntries ( ) ) { entryMapper . run ( entry ) ; } //try to release some RAM earlier entrySet . getEntries ( ) . clear ( ) ; entrySet = null ; // write BioPAX RDF/XML ( new SimpleIOHandler ( ) ) . convertToOWL ( model , outputStream ) ; }
Converts the PSI interactions from the EntrySet and places into BioPAX output stream . Stream will be closed by the converter .