Hi - I have been using the following snippet of code to read files from xembl that are in AGAVE format. Features seem to be added to the constructed sequence object ok but annotations seem to go missing.
Do I need to add some sort of listener somewhere? I'm a bit concerned about using the SeqIOAdapter as a SeqIOListener as it doesn't do anything, however there doesn't seem to be an appropriate implementation to use. Any advice? final AGAVEHandler handler = new AGAVEHandler(); SeqIOListener siol = new SeqIOAdapter(); handler.setFeatureListener(siol); SAX2StAXAdaptor adaptor = new SAX2StAXAdaptor(handler); XMLReader xmlReader = new SAXParser(); FileReader fr = new FileReader(args[0]); InputSource is = new InputSource(fr); xmlReader.setContentHandler(adaptor); xmlReader.parse(is); Mark Schreiber Bioinformatics AgResearch Invermay PO Box 50034 Mosgiel New Zealand PH: +64 3 489 9175 FAX: +64 3 489 3739 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l