in progress

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

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 71e58a5..fb37c4f 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -608,12 +608,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             }
         } );
         if ( getConfiguration().isUseTabbedDisplay() ) {
-            AptxUtil.printAppletMessage( NAME, "using tabbed display" );
-            AptxUtil.addPhylogeniesToTabs( phys,
-                                           new File( phys_url.getFile() ).getName(),
-                                           phys_url.toString(),
-                                           getConfiguration(),
-                                           getMainPanel() );
+            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();
+            }
         }
         else {
             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
@@ -623,28 +629,34 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             }
             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 );
+        try {
+            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 );
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.printErrorMessage( NAME, e.toString() );
+            e.printStackTrace();
+        }
     }
 
     public void showTextFrame( final String s, final String title ) {
@@ -724,16 +736,16 @@ 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 ),