X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=251a43c8670a3142df13fd3f25269ad70c111486;hb=4cc856b8c526a8b82bef79901739d9330206921a;hp=95f546c03018d5a57de89d7f3d9d5078130828a9;hpb=bf4f34e0511813622f68e54ffb783e4e6d92bfa4;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 95f546c..251a43c 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -117,7 +117,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
     private JCheckBoxMenuItem           _show_overview_cbmi;
     private JMenuItem                   _choose_minimal_confidence_mi;
-    private JCheckBoxMenuItem           _show_branch_length_values_cbmi;
     private JMenuItem                   _collapse_species_specific_subtrees;
     private JMenuItem                   _overview_placment_mi;
     private ButtonGroup                 _radio_group_1;
@@ -132,10 +131,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JMenuItem                   _gsdi_item;
     private JMenuItem                   _gsdir_item;
     private Phylogeny                   _species_tree;
-    
-    private JCheckBoxMenuItem _right_line_up_domains_cbmi;
-    private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
-    
+    private JCheckBoxMenuItem           _right_line_up_domains_cbmi;
+    private JCheckBoxMenuItem           _line_up_renderable_data_cbmi;
 
     @Override
     public void actionPerformed( final ActionEvent e ) {
@@ -265,9 +262,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         else if ( o == _show_scale_cbmi ) {
             updateOptions( getOptions() );
         }
-        else if ( o == _show_branch_length_values_cbmi ) {
-            updateOptions( getOptions() );
-        }
         else if ( o == _show_confidence_stddev_cbmi ) {
             updateOptions( getOptions() );
         }
@@ -353,9 +347,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         else if ( o == _color_by_taxonomic_group_cbmi ) {
             updateOptions( getOptions() );
         }
-       
-        
-        
         else if ( o == _line_up_renderable_data_cbmi ) {
             if ( !_line_up_renderable_data_cbmi.isSelected() ) {
                 _right_line_up_domains_cbmi.setSelected( false );
@@ -368,7 +359,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             }
             updateOptions( getOptions() );
         }
-        
         repaint();
     }
 
@@ -576,81 +566,89 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             }
         }
         //
-        setVisible( false );
-        setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
-        _jmenubar = new JMenuBar();
-        if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
-            if ( !getConfiguration().isUseNativeUI() ) {
-                _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+        try {
+            setVisible( false );
+            setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
+            _jmenubar = new JMenuBar();
+            if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
+                if ( !getConfiguration().isUseNativeUI() ) {
+                    _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+                }
+                if ( getSpeciesTree() != null ) {
+                    buildAnalysisMenu();
+                }
+                buildToolsMenu();
+                buildViewMenu();
+                buildFontSizeMenu();
+                buildOptionsMenu();
+                buildTypeMenu();
+                buildHelpMenu();
+                setJMenuBar( _jmenubar );
             }
-            if ( getSpeciesTree() != null ) {
-                buildAnalysisMenu();
+            final Container contentpane = getContentPane();
+            contentpane.setLayout( new BorderLayout() );
+            contentpane.add( getMainPanel(), BorderLayout.CENTER );
+            addComponentListener( new ComponentAdapter() {
+
+                @Override
+                public void componentResized( final ComponentEvent e ) {
+                    if ( getMainPanel().getCurrentTreePanel() != null ) {
+                        getMainPanel().getCurrentTreePanel()
+                                .calcParametersForPainting( getMainPanel().getCurrentTreePanel().getWidth(),
+                                                            getMainPanel().getCurrentTreePanel().getHeight(),
+                                                            getOptions().isAllowFontSizeChange() );
+                    }
+                }
+            } );
+            if ( getConfiguration().isUseTabbedDisplay() ) {
+                try {
+                    AptxUtil.printAppletMessage( NAME, "using tabbed display" );
+                    AptxUtil.addPhylogeniesToTabs( phys,
+                                                   new File( phys_url.getFile() ).getName(),
+                                                   phys_url.toString(),
+                                                   getConfiguration(),
+                                                   getMainPanel() );
+                }
+                catch ( final Exception e ) {
+                    ForesterUtil.printErrorMessage( NAME, e.toString() );
+                    e.printStackTrace();
+                }
             }
-            buildToolsMenu();
-            buildViewMenu();
-            buildFontSizeMenu();
-            buildOptionsMenu();
-            buildTypeMenu();
-            buildHelpMenu();
-            setJMenuBar( _jmenubar );
-        }
-        final Container contentpane = getContentPane();
-        contentpane.setLayout( new BorderLayout() );
-        contentpane.add( getMainPanel(), BorderLayout.CENTER );
-        addComponentListener( new ComponentAdapter() {
-
-            @Override
-            public void componentResized( final ComponentEvent e ) {
-                if ( getMainPanel().getCurrentTreePanel() != null ) {
-                    getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
-                                                                                            .getCurrentTreePanel()
-                                                                                            .getWidth(),
-                                                                                    getMainPanel()
-                                                                                            .getCurrentTreePanel()
-                                                                                            .getHeight(),
-                                                                                    getOptions()
-                                                                                            .isAllowFontSizeChange() );
+            else {
+                AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
+                if ( getSpeciesTree() != null ) {
+                    AptxUtil.printAppletMessage( NAME,
+                                                 "Warning: gsdi (gene duplication inference) only available tabbed display" );
                 }
+                AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
             }
-        } );
-        if ( getConfiguration().isUseTabbedDisplay() ) {
-            AptxUtil.printAppletMessage( NAME, "using tabbed display" );
-            AptxUtil.addPhylogeniesToTabs( phys,
-                                           new File( phys_url.getFile() ).getName(),
-                                           phys_url.toString(),
-                                           getConfiguration(),
-                                           getMainPanel() );
-        }
-        else {
-            AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
-            if ( getSpeciesTree() != null ) {
-                AptxUtil.printAppletMessage( NAME,
-                                             "Warning: gsdi (gene duplication inference) only available tabbed display" );
+            validate();
+            setName( NAME );
+            getMainPanel().getControlPanel().showWholeAll();
+            getMainPanel().getControlPanel().showWhole();
+            /* GUILHEM_BEG */
+            getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
+            for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
+                    .getRelevantSequenceRelationTypes() ) {
+                getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
+            }
+            final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
+            if ( default_relation != null ) {
+                getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
             }
-            AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
-        }
-        validate();
-        setName( NAME );
-        getMainPanel().getControlPanel().showWholeAll();
-        getMainPanel().getControlPanel().showWhole();
-        /* GUILHEM_BEG */
-        getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
-        for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
-                .getRelevantSequenceRelationTypes() ) {
-            getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
-        }
-        final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
-        if ( default_relation != null ) {
-            getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
-        }
-        final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
-        if ( default_sequence != null ) {
-            getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
-        }
-        /* GUILHEM_END */
-        System.gc();
-        AptxUtil.printAppletMessage( NAME, "successfully initialized" );
-        setVisible( true );
+            final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
+            if ( default_sequence != null ) {
+                getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
+            }
+            /* GUILHEM_END */
+            System.gc();
+            AptxUtil.printAppletMessage( NAME, "successfully initialized" );
+            setVisible( true );
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.printErrorMessage( NAME, e.toString() );
+            e.printStackTrace();
+        }
     }
 
     public void showTextFrame( final String s, final String title ) {
@@ -730,16 +728,16 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
-                MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
-                                                                     _show_scale_cbmi,
-                                                                     _show_branch_length_values_cbmi,
-                                                                     _non_lined_up_cladograms_rbmi,
-                                                                     _uniform_cladograms_rbmi,
-                                                                     _ext_node_dependent_cladogram_rbmi,
-                                                                     _label_direction_cbmi );
                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
+                try {
+                    getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
+                    getMainPanel().getControlPanel().setVisibilityOfX();
+                }
+                catch ( final Exception ignore ) {
+                    // do nothing, not important.
+                }
             }
         } );
         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
@@ -757,8 +755,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
         _options_jmenu
-                .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
-        _options_jmenu
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
         _options_jmenu
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
@@ -823,11 +819,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
-        customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+        customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
+        customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
         _jmenubar.add( _options_jmenu );
     }
 
@@ -1102,8 +1099,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         return _options;
     }
 
-   
-
     void initializeTypeMenu( final Options options ) {
         setTypeMenuToAllUnselected();
         try {
@@ -1338,9 +1333,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
                 && _show_confidence_stddev_cbmi.isSelected() );
-        if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
-            options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
-        }
         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
                 && _search_whole_words_only_cbmi.isSelected() );
         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
@@ -1372,17 +1364,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
         }
-        
-       
         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
         }
-        
-        
         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
         }
-        
     }
 
     void updateTypeCheckboxes( final Options options, final Object o ) {
@@ -1474,7 +1461,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         }
     }
 
-    private MainPanel getMainPanel() {
+    MainPanel getMainPanel() {
         return _mainpanel;
     }