*/
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 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;
-
-
-
+import org.xml.sax.*;
/**
* A class to perform a DAS features request
- *
- * @author Andreas Prlic
- *
+ *
+ * @author Andreas Prlic Adapted for jalview use.
+ * @author Andrew Waterhouse Updated to Das 1.53e feature spec.
+ * @author Jim Procter
*/
-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;
- 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 ;
+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;
+ }
- XMLReader xmlreader = saxParser.getXMLReader();
+ SAXParserFactory spfactory = SAXParserFactory.newInstance();
- //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);
- }
+ spfactory.setValidating(false);
- 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);
+ SAXParser saxParser = null;
- }
+ try
+ {
+ saxParser = spfactory.newSAXParser();
+ } catch (ParserConfigurationException e)
+ {
+ e.printStackTrace();
+ }
- 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);
+ String vali = System.getProperty("XMLVALIDATION");
- try {
- xmlreader.parse(insource);
- features = cont_handle.get_features();
- 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)
+ boolean validation = false;
+ if (vali != null)
+ {
+ if (vali.equals("true"))
{
- ex.printStackTrace();
- comeBackLater = -1;
+ 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 {
+ }
+
+ /**
+ * 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_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 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);
-
+ 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...
+ 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
+ try
{
- 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;
-
+ // 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