special domain coloring

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

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
index fbcc0bf..25ed68a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
@@ -21,22 +21,22 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx.tools;
 
 import java.net.UnknownHostException;
-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;
+import org.forester.ws.seqdb.SequenceDbWsTools;
 
-public class AncestralTaxonomyInferrer implements Runnable {
+public class AncestralTaxonomyInferrer extends RunnableProcess {
 
     private final Phylogeny            _phy;
     private final MainFrameApplication _mf;
@@ -48,18 +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();
-        SortedSet<String> not_found = null;
+        start( _mf, "ancestral taxonomy" );
         try {
-            not_found = AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
+            AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
         }
-        catch ( final IllegalArgumentException e ) {
-            _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
+        catch ( final AncestralTaxonomyInferenceException e ) {
+            end( _mf );
             JOptionPane.showMessageDialog( _mf,
                                            e.getMessage(),
                                            "Error during ancestral taxonomy inference",
@@ -67,7 +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",
@@ -75,67 +74,35 @@ 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 );
-        if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
-            int max = not_found.size();
-            boolean more = false;
-            if ( max > 20 ) {
-                more = true;
-                max = 20;
-            }
-            final StringBuffer sb = new StringBuffer();
-            sb.append( "Not all taxonomies could be resolved.\n" );
-            sb.append( "The result is incomplete, and, possibly, misleading.\n" );
-            if ( not_found.size() == 1 ) {
-                sb.append( "The following taxonomy was not found:\n" );
-            }
-            else {
-                sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
-            }
-            int i = 0;
-            for( final String string : not_found ) {
-                if ( i > 19 ) {
-                    break;
-                }
-                sb.append( string );
-                sb.append( "\n" );
-                ++i;
-            }
-            if ( more ) {
-                sb.append( "..." );
-            }
-            try {
-                JOptionPane.showMessageDialog( _mf,
-                                               sb.toString(),
-                                               "Ancestral Taxonomy Inference Completed",
-                                               JOptionPane.WARNING_MESSAGE );
-            }
-            catch ( final Exception e ) {
-                // Not important if this fails, do nothing. 
-            }
+        end( _mf );
+        try {
+            JOptionPane.showMessageDialog( _mf,
+                                           "Ancestral taxonomy inference successfully completed",
+                                           "Ancestral Taxonomy Inference Completed",
+                                           JOptionPane.INFORMATION_MESSAGE );
         }
-        else {
-            try {
-                JOptionPane.showMessageDialog( _mf,
-                                               "Ancestral taxonomy inference successfully completed",
-                                               "Ancestral Taxonomy Inference Completed",
-                                               JOptionPane.INFORMATION_MESSAGE );
-            }
-            catch ( final Exception e ) {
-                // Not important if this fails, do nothing.
-            }
+        catch ( final Exception e ) {
+            // Not important if this fails, do nothing.
         }
     }