X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Ftools%2FTaxonomyDataObtainer.java;h=a6d814b1500c8114024061ea1a2b488d65270ffd;hb=d772adf9d23c4cdbf84b2af9d23e2e7ebedfcf3a;hp=952d3fa11265bfb4a2735c5c0c51c27c9d4d8dbc;hpb=93b3ffddb203151c92200b3498d5559cc4de7d18;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java b/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java
index 952d3fa..a6d814b 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java
@@ -33,12 +33,13 @@ import java.util.SortedSet;
 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;
 
-public class TaxonomyDataObtainer implements Runnable {
+public class TaxonomyDataObtainer extends RunnableProcess {
 
     private final Phylogeny            _phy;
     private final MainFrameApplication _mf;
@@ -48,7 +49,7 @@ public class TaxonomyDataObtainer implements Runnable {
     public TaxonomyDataObtainer( final MainFrameApplication mf,
                                  final TreePanel treepanel,
                                  final Phylogeny phy,
-                                 boolean delete ) {
+                                 final boolean delete ) {
         _phy = phy;
         _mf = mf;
         _treepanel = treepanel;
@@ -67,13 +68,12 @@ public class TaxonomyDataObtainer implements Runnable {
     }
 
     private void execute() {
-        _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
+        start( _mf, "taxonomy data" );
         SortedSet<String> not_found = null;
         try {
             not_found = AncestralTaxonomyInference.obtainDetailedTaxonomicInformation( _phy, _delete );
         }
         catch ( final UnknownHostException e ) {
-            _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
             JOptionPane.showMessageDialog( _mf,
                                            "Could not connect to \"" + getBaseUrl() + "\"",
                                            "Network error during taxonomic information gathering",
@@ -81,7 +81,14 @@ public class TaxonomyDataObtainer implements Runnable {
             return;
         }
         catch ( final IOException e ) {
-            _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
+            e.printStackTrace();
+            JOptionPane.showMessageDialog( _mf,
+                                           e.toString(),
+                                           "Failed to obtain taxonomic information",
+                                           JOptionPane.ERROR_MESSAGE );
+            return;
+        }
+        catch ( final AncestralTaxonomyInferenceException e ) {
             e.printStackTrace();
             JOptionPane.showMessageDialog( _mf,
                                            e.toString(),
@@ -90,7 +97,19 @@ public class TaxonomyDataObtainer implements Runnable {
             return;
         }
         finally {
-            _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
+            end( _mf );
+        }
+        if ( _phy == null || _phy.isEmpty() ) {
+            try {
+                JOptionPane.showMessageDialog( _mf,
+                                               "None of the external node taxonomies could be resolved",
+                                               "Taxonomy Tool Failed",
+                                               JOptionPane.WARNING_MESSAGE );
+            }
+            catch ( final Exception e ) {
+                // Not important if this fails, do nothing. 
+            }
+            return;
         }
         _treepanel.setTree( _phy );
         _mf.showWhole();