+++ /dev/null
-/**
- * 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.io.*;
-import java.lang.reflect.*;
-import java.net.*;
-import java.util.*;
-import java.util.logging.*;
-import javax.xml.parsers.*;
-
-import org.xml.sax.*;
-
-/**
- * A class to perform a DAS features request
- *
- * @author Andreas Prlic Adapted for jalview use.
- * @author Andrew Waterhouse Updated to Das 1.53e feature spec.
- * @author Jim Procter
- */
-public class DAS_FeatureRetrieve
-{
- String version;
-
- 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;
- System.out.println("NO RESPONSE FROM " + url);
- 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();
- version = cont_handle.getVersion();
-
- comeBackLater = cont_handle.getComBackLater();
- } catch (Exception e)
- {
- System.out
- .println("Error parsing response from: " + url + "\n" + e);
- 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);
-
- int timeout = 10000;
- System
- .setProperty("sun.net.client.defaultConnectTimeout", timeout
- + "");
- System.setProperty("sun.net.client.defaultReadTimeout", timeout + "");
-
- // 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
-
- 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;
- }
-
- /**
- * Get the version string of the reference object. If it does not match the
- * version string that is obtained from the reference server there is a
- * version problem!
- *
- * @return version string. (e.g. a MD5 digest of the reference sequence)
- */
- public String getVersion()
- {
- return version;
- }
-
- public void setVersion(String version)
- {
- this.version = version;
- }
-
- /**
- * 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;
-
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff