phylotastic hackathon at NESCENT 120607

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrameApplication.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index d6fe0f6..9a7619b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -59,6 +59,7 @@ import javax.swing.event.ChangeListener;
 import javax.swing.filechooser.FileFilter;
 import javax.swing.plaf.synth.SynthLookAndFeel;
 
+import org.forester.analysis.TaxonomyDataManager;
 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
@@ -70,7 +71,6 @@ import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
-import org.forester.archaeopteryx.tools.TaxonomyDataObtainer;
 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
 import org.forester.archaeopteryx.webservices.WebservicesManager;
 import org.forester.io.parsers.FastaParser;
@@ -954,9 +954,9 @@ public final class MainFrameApplication extends MainFrame {
         _obtain_detailed_taxonomic_information_deleting_jmi
                 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
         _tools_menu
-                .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information (from UniProt)" ) );
+                .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
         customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
-        _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
+        _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information" );
         _tools_menu.addSeparator();
         if ( !Constants.__RELEASE ) {
             _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
@@ -1516,9 +1516,9 @@ public final class MainFrameApplication extends MainFrame {
         if ( getCurrentTreePanel() != null ) {
             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
             if ( ( phy != null ) && !phy.isEmpty() ) {
-                final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+                final TaxonomyDataManager t = new TaxonomyDataManager( this,
                                                                          _mainpanel.getCurrentTreePanel(),
-                                                                         phy.copy() );
+                                                                         phy.copy(), false,true );
                 new Thread( t ).start();
             }
         }
@@ -1528,10 +1528,10 @@ public final class MainFrameApplication extends MainFrame {
         if ( getCurrentTreePanel() != null ) {
             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
             if ( ( phy != null ) && !phy.isEmpty() ) {
-                final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+                final TaxonomyDataManager t = new TaxonomyDataManager( this,
                                                                          _mainpanel.getCurrentTreePanel(),
                                                                          phy.copy(),
-                                                                         true );
+                                                                         true,true );
                 new Thread( t ).start();
             }
         }