-/**
- * BioJava development code
- *
- * This code may be freely distributed and modified under the
- * terms of the GNU Lesser General Public Licence. This should
- * be distributed with the code. If you do not have a copy,
- * see:
- *
- * http://www.gnu.org/copyleft/lesser.html
- *
- * Copyright for this code is held jointly by the individual
- * authors. These should be listed in @author doc comments.
- *
- * For more information on the BioJava project and its aims,
- * or to join the biojava-l mailing list, visit the home page
- * at:
- *
- * http://www.biojava.org/
- *
- * Created on 19.03.2004
- * @author Andreas Prlic
- *
- */
-package org.biojava.dasobert.das;
-
-
-import java.net.URL ;
-import java.io.InputStream ;
-import org.xml.sax.InputSource ;
-import org.xml.sax.XMLReader ;
-import javax.xml.parsers.* ;
-import org.xml.sax.* ;
-import java.util.ArrayList ;
-import java.util.List;
-import java.util.logging.* ;
-import java.net.HttpURLConnection ;
-import java.io.IOException;
-import java.net.ConnectException;
-import java.lang.reflect.Method;
-
-
-
-
-/**
- * A class to perform a DAS features request
- *
- * @author Andreas Prlic
- *
- */
-public class DAS_FeatureRetrieve {
-
- List features ;
- Logger logger ;
- int comeBackLater;
- URL url;
- /**
- * @param url the URL the features should be downloaded from
- *
- */
- public DAS_FeatureRetrieve(URL url) {
- super();
-
- logger = Logger.getLogger("org.biojava.spice");
- features = new ArrayList() ;
- comeBackLater = -1;
- this.url=url;
- reload();
- }
-
-
- /** contact the DAS-feature server again. Usually
- * it is not necessary to call this again, because the constructor already does, but
- * if comeBackLater > -1 this should be called again.
- *
- */
- public void reload(){
-
- try {
-
- InputStream dasInStream = null;
- try {
- dasInStream = open(url);
- } catch (Exception e ){
- comeBackLater = -1;
- logger.log(Level.FINE,"could not open connection to " + url,e);
- return ;
- }
-
-
- SAXParserFactory spfactory =
- SAXParserFactory.newInstance();
-
- spfactory.setValidating(false);
-
- SAXParser saxParser = null ;
-
- try{
- saxParser =
- spfactory.newSAXParser();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
-
-
-
- String vali = System.getProperty("XMLVALIDATION");
-
- boolean validation = false ;
- if ( vali != null )
- if ( vali.equals("true") )
- validation = true ;
-
-
- XMLReader xmlreader = saxParser.getXMLReader();
-
- //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
- try {
- xmlreader.setFeature("http://xml.org/sax/features/validation", validation);
- } catch (SAXException e) {
- logger.log(Level.FINE,"Cannot set validation " + validation);
- }
-
- try {
- xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validation);
- } catch (SAXNotRecognizedException e){
- e.printStackTrace();
- logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
-
- }
-
- DAS_Feature_Handler cont_handle = new DAS_Feature_Handler() ;
- cont_handle.setDASCommand(url.toString());
- xmlreader.setContentHandler(cont_handle);
- xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
- InputSource insource = new InputSource() ;
- insource.setByteStream(dasInStream);
-
- try {
- xmlreader.parse(insource);
- features = cont_handle.get_features();
- comeBackLater = cont_handle.getComBackLater();
- }
- catch ( Exception e){
- e.printStackTrace();
- logger.log(Level.FINE,"error while parsing response from "+ url);
- comeBackLater = -1;
- features = new ArrayList();
- }
- }
- catch (Exception ex) {
- ex.printStackTrace();
- comeBackLater = -1;
- }
- }
-
-
- /** open HttpURLConnection. Recommended way to open
- * HttpURLConnections, since this take care of setting timeouts
- * properly for java 1.4 and 1.5*/
- public static HttpURLConnection openHttpURLConnection(URL url)
- throws IOException, ConnectException {
- HttpURLConnection huc = null;
- huc = (HttpURLConnection) url.openConnection();
-
- String os_name = java.lang.System.getProperty("os.name");
- String os_version = java.lang.System.getProperty("os.version");
- String os_arch = java.lang.System.getProperty("os.arch");
- String VERSION = "1.0";
-
- String userAgent = "Jalview " + VERSION + "("+os_name+"; "+os_arch + " ; "+ os_version+")";
- //e.g. "Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.7.2) Gecko/20040803"
- huc.addRequestProperty("User-Agent", userAgent);
- //logger.finest("opening "+url);
-
-
- // use reflection to determine if get and set timeout methods for urlconnection are available
- // seems java 1.5 does not watch the System properties any longer...
- // and java 1.4 did not provide these...
- // for 1.4 see setSystemProperties
- int timeout = 15000;
- try {
- // try to use reflection to set timeout property
- Class urlconnectionClass = Class.forName("java.net.HttpURLConnection");
-
- Method setconnecttimeout = urlconnectionClass.getMethod (
- "setConnectTimeout", new Class [] {int.class}
- );
- setconnecttimeout.invoke(huc,new Object[] {new Integer(timeout)});
-
- Method setreadtimeout = urlconnectionClass.getMethod (
- "setReadTimeout", new Class[] {int.class}
- );
- setreadtimeout.invoke(huc,new Object[] {new Integer(timeout)});
- //System.out.println("successfully set java 1.5 timeout");
- } catch (Exception e) {
- //e.printStackTrace();
- // most likely it was a NoSuchMEthodException and we are running java 1.4.
- }
- return huc;
- }
-
-
- private InputStream open(URL url)
- throws java.io.IOException, java.net.ConnectException
- {
- InputStream inStream = null;
-
-
- HttpURLConnection huc = openHttpURLConnection(url);
-
- inStream = huc.getInputStream();
-
- return inStream;
-
- }
-
- /** returns a List of Features
- * @return a List of Maps containing the features*/
- public List get_features() {
-
- return features;
- }
-
- /** returns the comeBackLater value - if a server returned suchh -
- *
- * @return comeBackLater in seconds, or -1 if not provided by server
- */
- public int getComeBackLater(){
-
- return comeBackLater;
-
- }
-
-
-}