/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
package jalview.ws;
/**
* @author not attributable
* @version 1.0
*/
+import java.util.*;
+
+import javax.swing.*;
+
import ext.vamsas.*;
-import java.util.Vector;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
-import javax.swing.JOptionPane;
public class Discoverer
extends Thread implements Runnable
public static java.util.Hashtable services = null; // vectors of services stored by abstractServiceType string
public static java.util.Vector serviceList = null; // flat list of services
- static private Vector getDiscoveryURLS() {
+ static private Vector getDiscoveryURLS()
+ {
Vector urls = new Vector();
String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
- try{
+ try
+ {
StringTokenizer st = new StringTokenizer(RootServiceURLs, ",");
while (st.hasMoreElements())
{
{
java.net.URL u = new java.net.URL(url = st.nextToken());
if (!urls.contains(u))
+ {
urls.add(u);
+ }
else
- jalview.bin.Cache.log.info("Ignoring duplicate url in DISCOVERY_URLS list");
+ {
+ jalview.bin.Cache.log.info(
+ "Ignoring duplicate url in DISCOVERY_URLS list");
+ }
}
catch (Exception ex)
{
jalview.bin.Cache.log.warn(
"Problem whilst trying to make a URL from '" +
- ( (url != null) ? url : "<null>")+"'");
- jalview.bin.Cache.log.warn("This was probably due to a malformed comma separated list"
- +" in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
- jalview.bin.Cache.log.debug("Exception was ",ex);
+ ( (url != null) ? url : "<null>") + "'");
+ jalview.bin.Cache.log.warn(
+ "This was probably due to a malformed comma separated list"
+ + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
+ jalview.bin.Cache.log.debug("Exception was ", ex);
}
}
- }catch(Exception ex)
- {jalview.bin.Cache.log.warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",ex);}
- if (urls.size()>0)
+ }
+ catch (Exception ex)
+ {
+ jalview.bin.Cache.log.warn(
+ "Error parsing comma separated list of urls in DISCOVERY_URLS.", ex);
+ }
+ if (urls.size() > 0)
+ {
return urls;
+ }
return null;
}
jalview.bin.Cache.log.debug("Setting default services");
services = new Hashtable();
// Muscle, Clustal and JPred.
- ServiceHandle[] defServices = {
+ ServiceHandle[] defServices =
+ {
new ServiceHandle(
"MsaWS",
"Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " +
"with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
"Muscle Multiple Protein Sequence Alignment"
-),
+ ),
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",
+ "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(
"Cuff J. A and Barton G.J (2000) Application of " +
"multiple sequence alignment profiles to improve protein secondary structure prediction, " +
"Proteins 40:502-511",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JNet Secondary Structure Prediction"
- )};
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
+ "JNet Secondary Structure Prediction"
+ )};
services = new Hashtable();
serviceList = new Vector();
buildServiceLists(defServices, serviceList, services);
}
}
+
// TODO: JBPNote : make this discover more services based on list of
// discovery service urls, break cyclic references to the same url and
// duplicate service entries (same endpoint *and* same interface)
jalview.bin.Cache.log.debug("Discovering services using " + location);
shs = locateWebService(location).getServices();
}
- catch (org.apache.axis.AxisFault f) {
+ 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)
+ 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 {
+ "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) {
+ catch (Exception e)
+ {
jalview.bin.Cache.log.warn("No Discovery service at " +
location);
jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
* @return boolean
*/
static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat,
- Hashtable sscat)
+ Hashtable sscat)
{
boolean seenNewDiscovery = false;
for (int i = 0, j = sh.length; i < j; i++)
if (!cat.contains(sh[i]))
{
jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() +
- " service called " +
- sh[i].getName() + " exists at " +
- sh[i].getEndpointURL() + "\n");
+ " service called " +
+ sh[i].getName() + " exists at " +
+ sh[i].getEndpointURL() + "\n");
if (!sscat.containsKey(sh[i].getAbstractName()))
{
sscat.put(sh[i].getAbstractName(), cat = new Vector());
Vector cat = new Vector();
ServiceHandle sh[] = null;
int s_url = 0;
- if (ServiceURLList==null)
+ if (ServiceURLList == null)
{
- jalview.bin.Cache.log.debug("No service endpoints to use for service discovery.");
+ jalview.bin.Cache.log.debug(
+ "No service endpoints to use for service discovery.");
return;
}
while (s_url < ServiceURLList.size())
{
buildServiceLists(sh, cat, sscat);
- } else {
+ }
+ else
+ {
jalview.bin.Cache.log.warn(
"No services at "
- +((java.net.URL) ServiceURLList.get(s_url))
- +" - check DISCOVERY_URLS property in .jalview_properties");
+ + ( (java.net.URL) ServiceURLList.get(s_url))
+ + " - check DISCOVERY_URLS property in .jalview_properties");
}
s_url++;
}
public void run()
{
final Discoverer discoverer = this;
- Thread discoverThread = new Thread() {
- public void run() {
+ Thread discoverThread = new Thread()
+ {
+ public void run()
+ {
discoverer.doDiscovery();
discoverer.discoverServices();
}
git://source.jalview.org / jalview.git / blobdiff