/*
* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
import java.util.Vector;
import java.util.Hashtable;
import java.util.StringTokenizer;
+import javax.swing.JOptionPane;
public class Discoverer
extends Thread implements Runnable
return urls;
return null;
}
- static
- {
+ /**
+ * fetch new services or reset to hardwired defaults depending on preferences.
+ */
+ static public void doDiscovery()
+ {
+ jalview.bin.Cache.log.debug("(Re)-Initialising the discovery URL list.");
try
{
reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false);
),
new ServiceHandle(
"MsaWS",
+ "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "+
+ "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""+
+ " Nucleic Acids Research, 33 511-518",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
+ "MAFFT Multiple Sequence Alignment"),
+ new ServiceHandle(
+ "MsaWS",
"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" +
" sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." +
" Nucleic Acids Research, 22 4673-4680",
jalview.bin.Cache.log.debug("Discovering services using " + location);
shs = locateWebService(location).getServices();
}
- catch (Exception e)
- {
- jalview.bin.Cache.log.debug("No Discovery service at " +
- location);
- jalview.bin.Cache.log.debug(e);
-
+ catch (org.apache.axis.AxisFault f) {
+ // JBPNote - should do this a better way!
+ if (f.getFaultReason().indexOf("(407)")>-1) {
+ if (jalview.gui.Desktop.desktop!=null)
+ JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, "Please set up your proxy settings in the 'Connections' tab of the Preferences window",
+ "Proxy Authorization Failed",
+ JOptionPane.WARNING_MESSAGE);
+ } else {
+ jalview.bin.Cache.log.warn("No Discovery service at " +
+ location);
+ jalview.bin.Cache.log.debug("Axis Fault", f);
+ }
+ }
+ catch (Exception e) {
+ jalview.bin.Cache.log.warn("No Discovery service at " +
+ location);
+ jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
}
if ( (shs != null) && shs.getServices().length > 0)
{
firePropertyChange("services", oldServices, services);
}
+ /**
+ * creates a new thread to call discoverServices()
+ */
public void run()
{
- discoverServices();
+ final Discoverer discoverer = this;
+ Thread discoverThread = new Thread() {
+ public void run() {
+ discoverer.doDiscovery();
+ discoverer.discoverServices();
+ }
+ };
+ discoverThread.start();
}
}