(no commit message)

[jalview.git] / forester / java / src / org / forester / archaeopteryx / tools / TaxonomyDataObtainer.java

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java b/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java
index 3101295..a6d814b 100644 (file)
--- 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;
@@ -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();