X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FDiscoverer.java;h=4643119d3e629d97796bca707397455a6f09310d;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=90581dc8e05208d76c567ddf1f7d3eb7381a6d67;hpb=add30afdc46a14e61ccf55881fa91b9ca9abfe80;p=jalview.git
diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index 90581dc..4643119 100644
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -1,50 +1,40 @@
/*
- * 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 ($$Version-Rel$$)
+ * 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
- * Title: - *
- * - *- * Description: - *
- * - *- * Copyright: Copyright (c) 2004 - *
- * - *- * Company: Dundee University - *
- * - * @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. @@ -173,8 +163,7 @@ public class Discoverer extends Thread implements Runnable } 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) @@ -204,33 +193,35 @@ public class Discoverer extends Thread 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") }; services = new Hashtable(); @@ -264,12 +255,11 @@ public class Discoverer extends Thread 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); + JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, + MessageManager.getString("label.set_proxy_settings"), + MessageManager + .getString("label.proxy_authorization_failed"), + JOptionPane.WARNING_MESSAGE); } } else @@ -373,7 +363,7 @@ public class Discoverer extends Thread 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++; @@ -387,7 +377,7 @@ public class Discoverer extends Thread implements Runnable // Vector oldServicelist = serviceList; services = sscat; serviceList = cat; - firePropertyChange("services", oldServices, services); + changeSupport.firePropertyChange("services", oldServices, services); } /**