- * Title: - *
- * - *- * Description: - *
- * - *- * Copyright: Copyright (c) 2004 - *
- * - *- * Company: Dundee University - *
- * - * @author not attributable - * @version 1.0 - */ - -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 extends Thread implements Runnable +public class Discoverer implements Runnable { ext.vamsas.IRegistry registry; // the root registry service. @@ -173,8 +162,7 @@ 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) @@ -204,35 +192,37 @@ 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") }; + "JPred Secondary Structure Prediction") }; services = new Hashtable(); serviceList = new Vector(); buildServiceLists(defServices, serviceList, services); @@ -264,12 +254,11 @@ 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); + JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, + MessageManager.getString("label.set_proxy_settings"), + MessageManager + .getString("label.proxy_authorization_failed"), + JvOptionPane.WARNING_MESSAGE); } } else @@ -373,7 +362,7 @@ 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++; @@ -387,17 +376,19 @@ public class Discoverer extends Thread implements Runnable // Vector oldServicelist = serviceList; services = sscat; serviceList = cat; - firePropertyChange("services", oldServices, services); + changeSupport.firePropertyChange("services", oldServices, services); } /** * 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();