inprogress

[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 1060a32..8f65e7b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -66,7 +66,6 @@ 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;
@@ -466,9 +465,6 @@ public final class MainFrameApplication extends MainFrame {
                 }
                 executeLineageInference();
             }
-            else if ( o == _function_analysis ) {
-                executeFunctionAnalysis();
-            }
             else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
                 if ( isSubtreeDisplayed() ) {
                     return;
@@ -912,6 +908,7 @@ public final class MainFrameApplication extends MainFrame {
         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
         }
+        _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
@@ -984,6 +981,7 @@ public final class MainFrameApplication extends MainFrame {
         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
+        customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
@@ -1085,6 +1083,9 @@ public final class MainFrameApplication extends MainFrame {
         customizeJMenuItem( _move_node_names_to_seq_names_jmi );
         _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
         _tools_menu.addSeparator();
+        _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
+        customizeJMenuItem( _obtain_seq_information_jmi );
+        _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
         _tools_menu
                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
         customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
@@ -1095,17 +1096,7 @@ public final class MainFrameApplication extends MainFrame {
         customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
         _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_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
-        customizeJMenuItem( _obtain_seq_information_jmi );
-        _obtain_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" ) );
-            customizeJMenuItem( _function_analysis );
-            _function_analysis
-                    .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
-            _tools_menu.addSeparator();
-        }
         _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
         customizeJMenuItem( _read_values_jmi );
         _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
@@ -1131,16 +1122,6 @@ public final class MainFrameApplication extends MainFrame {
         exit();
     }
 
-    void executeFunctionAnalysis() {
-        if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
-            return;
-        }
-        final GoAnnotation a = new GoAnnotation( this,
-                                                 _mainpanel.getCurrentTreePanel(),
-                                                 _mainpanel.getCurrentPhylogeny() );
-        new Thread( a ).start();
-    }
-
     void executeLineageInference() {
         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
             return;
@@ -1492,6 +1473,9 @@ public final class MainFrameApplication extends MainFrame {
                         nodes = phy.getNodesViaSequenceSymbol( seq_name );
                     }
                     if ( nodes.isEmpty() ) {
+                        nodes = phy.getNodesViaGeneName( seq_name );
+                    }
+                    if ( nodes.isEmpty() ) {
                         nodes = phy.getNodes( seq_name );
                     }
                     if ( nodes.size() > 1 ) {