/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.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 extends Thread implements Runnable
+public class Discoverer implements Runnable
{
ext.vamsas.IRegistry registry; // the root registry service.
} catch (Exception ex)
{
jalview.bin.Cache.log
- .warn(
- "Error parsing comma separated list of urls in DISCOVERY_URLS.",
+ .warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",
ex);
}
if (urls.size() > 0)
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"),
+ 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();
{
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);
+ JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
+ MessageManager.getString("label.set_proxy_settings"),
+ MessageManager
+ .getString("label.proxy_authorization_failed"),
+ JOptionPane.WARNING_MESSAGE);
}
}
else
{
jalview.bin.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++;
// Vector oldServicelist = serviceList;
services = sscat;
serviceList = cat;
- firePropertyChange("services", oldServices, services);
+ changeSupport.firePropertyChange("services", oldServices, services);
}
/**
git://source.jalview.org / jalview.git / blobdiff