- //logger.finest("trying: " + connstr) ;
- URL dasUrl = new URL(connstr);
- //DAS_httpConnector dhtp = new DAS_httpConnector() ;
- logger.info("requesting sequence from " + connstr);
- InputStream dasInStream =open(dasUrl);
-
-
- SAXParserFactory spfactory =
- SAXParserFactory.newInstance();
-
- // never do this
- //String vali = System.getProperty("XMLVALIDATION");
- String vali = "false";
- boolean validate = false ;
- if ((vali != null) && ( vali.equals("true")) )
- validate = true ;
- spfactory.setValidating(validate);
-
- SAXParser saxParser = null ;
-
- try{
- saxParser =
- spfactory.newSAXParser();
- } catch (ParserConfigurationException e) {
- //e.printStackTrace();
- logger.log(Level.FINER,"Uncaught exception", e);
- }
-
- XMLReader xmlreader = saxParser.getXMLReader();
-
- try {
- xmlreader.setFeature("http://xml.org/sax/features/validation", validate);
- } catch (SAXException e) {
- logger.finer("Cannot set validation to " + validate);
- logger.log(Level.FINER,"Uncaught exception", e);
- }
-
- try {
- xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validate);
- } catch (SAXNotRecognizedException e){
- //e.printStackTrace();
- logger.finer("Cannot set load-external-dtd to" + validate);
- logger.log(Level.FINER,"Uncaught exception", e);
- //System.err.println("Cannot set load-external-dtd to" + validate);
- }
-
-
- //DAS_DNA_Handler cont_handle = new DAS_DNA_Handler() ;
- DAS_Sequence_Handler cont_handle = new DAS_Sequence_Handler() ;
- xmlreader.setContentHandler(cont_handle);
- xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
- InputSource insource = new InputSource() ;
- insource.setByteStream(dasInStream);
-
- xmlreader.parse(insource);
- String sequence = cont_handle.get_sequence();
- //logger.finest("Got sequence from DAS: " +sequence);
- logger.exiting(this.getClass().getName(), "retreiveSequence", sequence);
- return sequence ;
+ }
+
+ /**
+ * retrieve the Sequence from a DAS server.
+ *
+ * @param connstr -
+ * the DAS - request string. e.g.
+ * http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/sequence?segment=P00280
+ * @return the requested Sequence
+ * @throws Exception
+ */
+ public String retrieveSequence(String connstr) throws Exception
+ {
+
+ // logger.finest("trying: " + connstr) ;
+ URL dasUrl = new URL(connstr);
+ // DAS_httpConnector dhtp = new DAS_httpConnector() ;
+ logger.info("requesting sequence from " + connstr);
+ InputStream dasInStream = open(dasUrl);
+
+ SAXParserFactory spfactory = SAXParserFactory.newInstance();
+
+ // never do this
+ // String vali = System.getProperty("XMLVALIDATION");
+ String vali = "false";
+ boolean validate = false;
+ if ((vali != null) && (vali.equals("true")))
+ validate = true;
+ spfactory.setValidating(validate);
+
+ SAXParser saxParser = null;
+
+ try
+ {
+ saxParser = spfactory.newSAXParser();
+ } catch (ParserConfigurationException e)
+ {
+ // e.printStackTrace();
+ logger.log(Level.FINER, "Uncaught exception", e);