X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Ftools%2FAncestralTaxonomyInferrer.java;h=55a740d0d532a782d2f864166517a037dc4a48fe;hb=755675533024c40e69c0b3a4f93e5f19d87cab79;hp=09e8804d44c88a56e86599e6b37e263f47a4936c;hpb=c4f9dc6343e1fee8846c893b968065d9d9178655;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
index 09e8804..55a740d 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
@@ -30,12 +30,13 @@ import java.net.UnknownHostException;
 import javax.swing.JOptionPane;
 
 import org.forester.analysis.AncestralTaxonomyInference;
+import org.forester.analysis.AncestralTaxonomyInferenceException;
 import org.forester.archaeopteryx.MainFrameApplication;
 import org.forester.archaeopteryx.TreePanel;
 import org.forester.phylogeny.Phylogeny;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.seqdb.SequenceDbWsTools;
 
-public class AncestralTaxonomyInferrer implements Runnable {
+public class AncestralTaxonomyInferrer extends RunnableProcess {
 
     private final Phylogeny            _phy;
     private final MainFrameApplication _mf;
@@ -47,17 +48,17 @@ public class AncestralTaxonomyInferrer implements Runnable {
         _treepanel = treepanel;
     }
 
-    private String getBaseUrl() {
-        return UniProtWsTools.BASE_URL;
+    public static String getBaseUrl() {
+        return SequenceDbWsTools.BASE_UNIPROT_URL;
     }
 
     private void inferTaxonomies() {
-        _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
+        start( _mf, "ancestral taxonomy" );
         try {
             AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
         }
         catch ( final AncestralTaxonomyInferenceException e ) {
-            _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
+            end( _mf );
             JOptionPane.showMessageDialog( _mf,
                                            e.getMessage(),
                                            "Error during ancestral taxonomy inference",
@@ -65,7 +66,7 @@ public class AncestralTaxonomyInferrer implements Runnable {
             return;
         }
         catch ( final UnknownHostException e ) {
-            _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
+            end( _mf );
             JOptionPane.showMessageDialog( _mf,
                                            "Could not connect to \"" + getBaseUrl() + "\"",
                                            "Network error during ancestral taxonomy inference",
@@ -73,19 +74,27 @@ public class AncestralTaxonomyInferrer implements Runnable {
             return;
         }
         catch ( final Exception e ) {
-            _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
+            end( _mf );
             e.printStackTrace();
             JOptionPane.showMessageDialog( _mf,
                                            e.toString(),
+                                           "Unexpected exception during ancestral taxonomy inference",
+                                           JOptionPane.ERROR_MESSAGE );
+            return;
+        }
+        catch ( final Error e ) {
+            end( _mf );
+            JOptionPane.showMessageDialog( _mf,
+                                           e.toString(),
                                            "Unexpected error during ancestral taxonomy inference",
                                            JOptionPane.ERROR_MESSAGE );
             return;
         }
-        _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
         _phy.setRerootable( false );
         _treepanel.setTree( _phy );
         _mf.showWhole();
         _treepanel.setEdited( true );
+        end( _mf );
         try {
             JOptionPane.showMessageDialog( _mf,
                                            "Ancestral taxonomy inference successfully completed",