/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
+import jalview.bin.Cache;
+import jalview.gui.Desktop;
+import jalview.util.MessageManager;
-import java.util.*;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import javax.swing.*;
+import javax.swing.JOptionPane;
-import ext.vamsas.*;
+import ext.vamsas.IRegistry;
+import ext.vamsas.IRegistryServiceLocator;
+import ext.vamsas.RegistryServiceSoapBindingStub;
+import ext.vamsas.ServiceHandle;
+import ext.vamsas.ServiceHandles;
public class Discoverer implements Runnable
{
// timeout
} catch (Exception ex)
{
- jalview.bin.Cache.log
+ Cache.log
.error("Serious! Service location failed\nfor URL :" + WsURL
+ "\n", ex);
static private Vector getDiscoveryURLS()
{
Vector urls = new Vector();
- String RootServiceURLs = jalview.bin.Cache
+ String RootServiceURLs = Cache
.getDefault("DISCOVERY_URLS",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
}
else
{
- jalview.bin.Cache.log
+ Cache.log
.info("Ignoring duplicate url in DISCOVERY_URLS list");
}
} catch (Exception ex)
{
- jalview.bin.Cache.log
+ Cache.log
.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- jalview.bin.Cache.log
+ 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);
+ Cache.log.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log
+ Cache.log
.warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",
ex);
}
*/
static public void doDiscovery()
{
- jalview.bin.Cache.log
+ Cache.log
.debug("(Re)-Initialising the discovery URL list.");
try
{
- reallyDiscoverServices = jalview.bin.Cache.getDefault(
+ reallyDiscoverServices = Cache.getDefault(
"DISCOVERY_START", false);
if (reallyDiscoverServices)
{
}
else
{
- jalview.bin.Cache.log.debug("Setting default services");
+ Cache.log.debug("Setting default services");
services = new Hashtable();
// Muscle, Clustal and JPred.
ServiceHandle[] defServices =
"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"),
+ MessageManager.getString("label.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",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
- "MAFFT Multiple Sequence Alignment"),
+ MessageManager.getString("label.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",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
- "ClustalW Multiple Sequence Alignment"),
+ MessageManager.getString("label.clustalw_multiple_sequence_alignment")),
new ServiceHandle(
"SecStrPred",
- "Cole C., Barber J. D., Barton G.J (2008) "
- + "The Jpred 3 secondary structure prediction server "
- + "Nucleic Acids Research, 36 W197-W201",
+ "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
+ + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)"
+ + "\ndoi://10.1093/nar/gkv332",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
"JNet Secondary Structure Prediction") };
services = new Hashtable();
ServiceHandles shs = null;
try
{
- jalview.bin.Cache.log.debug("Discovering services using " + location);
+ Cache.log.debug("Discovering services using " + location);
shs = locateWebService(location).getServices();
} 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 (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);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.set_proxy_settings"), MessageManager
+ .getString("label.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);
+ Cache.log.warn("No Discovery service at " + location);
+ 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);
+ Cache.log.warn("No Discovery service at " + location);
+ Cache.log.debug("Discovery Service General Exception", e);
}
if ((shs != null) && shs.getServices().length > 0)
{
{
if (!cat.contains(sh[i]))
{
- jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
+ Cache.log.debug("A " + sh[i].getAbstractName()
+ " service called " + sh[i].getName() + " exists at "
+ sh[i].getEndpointURL() + "\n");
if (!sscat.containsKey(sh[i].getAbstractName()))
disc_serv = new java.net.URL(sh[i].getEndpointURL());
if (!ServiceURLList.contains(disc_serv))
{
- jalview.bin.Cache.log
+ Cache.log
.debug("Adding new discovery service at "
+ disc_serv);
ServiceURLList.add(disc_serv);
}
} catch (Exception e)
{
- jalview.bin.Cache.log.debug(
+ Cache.log.debug(
"Ignoring bad discovery service URL "
+ sh[i].getEndpointURL(), e);
}
int s_url = 0;
if (ServiceURLList == null)
{
- jalview.bin.Cache.log
+ Cache.log
.debug("No service endpoints to use for service discovery.");
return;
}
}
else
{
- jalview.bin.Cache.log
+ Cache.log
.warn("No services at "
- + ((java.net.URL) ServiceURLList.get(s_url))
+ + (ServiceURLList.get(s_url))
+ " - check DISCOVERY_URLS property in .jalview_properties");
}
s_url++;
git://source.jalview.org / jalview.git / blobdiff