X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws1%2FDiscoverer.java;h=ba4054e27164a9bea8166ec8d8350ef9fb3f373b;hb=c70905eb5589c7622a2c7cf8a008ba0863b5c010;hp=900d2e7444905926f3af7fa7284eda2d875cbad0;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index 900d2e7..ba4054e 100644
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -1,28 +1,37 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
-import java.util.*;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
-import javax.swing.*;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
-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
{
@@ -183,35 +192,37 @@ public class Discoverer implements Runnable
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") };
+ "JPred Secondary Structure Prediction") };
services = new Hashtable();
serviceList = new Vector();
buildServiceLists(defServices, serviceList, services);
@@ -243,12 +254,11 @@ public class Discoverer implements Runnable
{
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);
+ JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
+ MessageManager.getString("label.set_proxy_settings"),
+ MessageManager
+ .getString("label.proxy_authorization_failed"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
else
@@ -352,7 +362,7 @@ public class Discoverer implements Runnable
{
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++;
@@ -372,11 +382,13 @@ public class Discoverer implements Runnable
/**
* creates a new thread to call discoverServices()
*/
+ @Override
public void run()
{
final Discoverer discoverer = this;
Thread discoverThread = new Thread()
{
+ @Override
public void run()
{
discoverer.doDiscovery();