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
{
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",
- MessageManager.getString("label.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",
- MessageManager.getString("label.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",
- MessageManager.getString("label.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,
- MessageManager.getString("label.set_proxy_settings"),
- MessageManager.getString("label.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++;