resetting Discoverer

[jalview.git] / src / jalview / ws / jws1 / Discoverer.java

diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index 4af342a..943305e 100644 (file)
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -20,7 +20,8 @@
  */
 package jalview.ws.jws1;
 
-import jalview.bin.Instance;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
 
@@ -35,18 +36,17 @@ import ext.vamsas.RegistryServiceSoapBindingStub;
 import ext.vamsas.ServiceHandle;
 import ext.vamsas.ServiceHandles;
 
-public class Discoverer implements Runnable
+public class Discoverer implements Runnable, ApplicationSingletonI
 {
 
-  private Discoverer()
+  public static Discoverer getInstance()
   {
-  };
+    return (Discoverer) ApplicationSingletonProvider.getInstance(Discoverer.class);
+  }
 
-  public static Discoverer getInstance()
+  private Discoverer()
   {
-    Instance j = Instance.getInstance();
-    return (j.discoverer == null ? j.discoverer = new Discoverer()
-            : j.discoverer);
+    // use getInstance()
   }
 
   private java.net.URL RootServiceURL = null;
@@ -208,32 +208,40 @@ public class Discoverer implements Runnable
         jalview.bin.Cache.log.debug("Setting default services");
         d.services = new Hashtable<>();
         // Muscle, Clustal and JPred.
-        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")),
-            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")),
-            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")),
-            new ServiceHandle("SecStrPred",
-                    "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",
-                    "JPred Secondary Structure Prediction") };
+        ServiceHandle[] defServices = new ServiceHandle[0];
+          try
+          {
+            // BH 2020.03.18 issue with applet branch Module problem.
+            defServices = new ServiceHandle[] { 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")),
+              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")),
+              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")),
+              new ServiceHandle("SecStrPred",
+                      "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",
+                      "JPred Secondary Structure Prediction") };
+          } catch (Throwable e)
+          {
+
+        }
         d.services = new Hashtable<>();
         d.serviceList = new Vector<>();
         buildServiceLists(defServices, d.serviceList, d.services);