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;
_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",
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",
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.
}
}