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 1913555..9a7619b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -59,17 +59,18 @@ 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;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
 import org.forester.archaeopteryx.tools.GoAnnotation;
+import org.forester.archaeopteryx.tools.InferenceManager;
 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;
@@ -241,6 +242,7 @@ public final class MainFrameApplication extends MainFrame {
                                   final Configuration config,
                                   final String title,
                                   final File current_dir ) {
+        super();
         _configuration = config;
         if ( _configuration == null ) {
             throw new IllegalArgumentException( "configuration is null" );
@@ -677,13 +679,12 @@ public final class MainFrameApplication extends MainFrame {
     }
 
     void buildPhylogeneticInferenceMenu() {
+        final InferenceManager inference_manager = InferenceManager.getInstance();
         _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
-        _inference_menu
-                .add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
+        _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
         customizeJMenuItem( _inference_from_msa_item );
         _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
-        _inference_menu
-                .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
+        _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
         customizeJMenuItem( _inference_from_seqs_item );
         _inference_from_seqs_item.setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
         _jmenubar.add( _inference_menu );
@@ -953,9 +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" ) );
@@ -1515,9 +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();
             }
         }
@@ -1527,10 +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();
             }
         }