git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
in progress
[jalview.git] / forester / java / src / org / forester / archaeopteryx / ControlPanel.java
diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index d3b56e2..5509327 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -4,7 +4,7 @@
 //
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -14,7 +14,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -109,6 +109,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     private JComboBox            _show_sequence_relations;
     private JComboBox            _sequence_relation_type_box;
     private JCheckBox            _show_vector_data_cb;
+    private JCheckBox            _show_properties_cb;
     private JLabel               _click_to_label;
     private JLabel               _zoom_label;
     private JLabel               _domain_display_label;
@@ -172,6 +173,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     /**
      * Handle an action.
      */
+    @Override
     public void actionPerformed( final ActionEvent e ) {
         try {
             final TreePanel tp = getMainPanel().getCurrentTreePanel();
@@ -395,11 +397,6 @@ final class ControlPanel extends JPanel implements ActionListener {
                 addJCheckBox( _show_node_names, ch_panel );
                 add( ch_panel );
                 break;
-            case Configuration.show_tax_code:
-                _show_taxo_code = new JCheckBox( title );
-                addJCheckBox( _show_taxo_code, ch_panel );
-                add( ch_panel );
-                break;
             case Configuration.show_taxonomy_scientific_names:
                 _show_taxo_scientific_names = new JCheckBox( title );
                 addJCheckBox( _show_taxo_scientific_names, ch_panel );
@@ -410,6 +407,11 @@ final class ControlPanel extends JPanel implements ActionListener {
                 addJCheckBox( _show_taxo_common_names, ch_panel );
                 add( ch_panel );
                 break;
+            case Configuration.show_tax_code:
+                _show_taxo_code = new JCheckBox( title );
+                addJCheckBox( _show_taxo_code, ch_panel );
+                add( ch_panel );
+                break;
             case Configuration.show_taxonomy_images:
                 _show_taxo_images_cb = new JCheckBox( title );
                 addJCheckBox( _show_taxo_images_cb, ch_panel );
@@ -494,6 +496,11 @@ final class ControlPanel extends JPanel implements ActionListener {
                 addJCheckBox( _show_vector_data_cb, ch_panel );
                 add( ch_panel );
                 break;
+            case Configuration.show_properties:
+                _show_properties_cb = new JCheckBox( title );
+                addJCheckBox( _show_properties_cb, ch_panel );
+                add( ch_panel );
+                break;
             default:
                 throw new RuntimeException( "unknown checkbox: " + which );
         }
@@ -586,10 +593,10 @@ final class ControlPanel extends JPanel implements ActionListener {
         add( horizGrid );
         add( getSequenceRelationBox() );
         if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
-            addCheckbox( Configuration.show_relation_confidence, _configuration
-                    .getDisplayTitle( Configuration.show_relation_confidence ) );
-            setCheckbox( Configuration.show_relation_confidence, _configuration
-                    .doCheckOption( Configuration.show_relation_confidence ) );
+            addCheckbox( Configuration.show_relation_confidence,
+                         _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
+            setCheckbox( Configuration.show_relation_confidence,
+                         _configuration.doCheckOption( Configuration.show_relation_confidence ) );
         }
     }// addSequenceRelationBlock
 
@@ -644,6 +651,10 @@ final class ControlPanel extends JPanel implements ActionListener {
         return _color_branches_cb;
     }
 
+    public JCheckBox getColorAccSpeciesCb() {
+        return _color_acc_species;
+    }
+
     Configuration getConfiguration() {
         return _configuration;
     }
@@ -815,6 +826,10 @@ final class ControlPanel extends JPanel implements ActionListener {
         return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
     }
 
+    public boolean isShowProperties() {
+        return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
+    }
+
     boolean isShowGeneSymbols() {
         return ( ( _show_gene_symbols != null ) && _show_gene_symbols.isSelected() );
     }
@@ -827,10 +842,6 @@ final class ControlPanel extends JPanel implements ActionListener {
         return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
     }
 
-    boolean isShowProperty() {
-        return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
-    }
-
     boolean isShowSequenceAcc() {
         return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
     }
@@ -989,11 +1000,6 @@ final class ControlPanel extends JPanel implements ActionListener {
                     _show_node_names.setSelected( state );
                 }
                 break;
-            case Configuration.show_tax_code:
-                if ( _show_taxo_code != null ) {
-                    _show_taxo_code.setSelected( state );
-                }
-                break;
             case Configuration.show_taxonomy_scientific_names:
                 if ( _show_taxo_scientific_names != null ) {
                     _show_taxo_scientific_names.setSelected( state );
@@ -1004,6 +1010,11 @@ final class ControlPanel extends JPanel implements ActionListener {
                     _show_taxo_common_names.setSelected( state );
                 }
                 break;
+            case Configuration.show_tax_code:
+                if ( _show_taxo_code != null ) {
+                    _show_taxo_code.setSelected( state );
+                }
+                break;
             case Configuration.show_taxonomy_images:
                 if ( _show_taxo_images_cb != null ) {
                     _show_taxo_images_cb.setSelected( state );
@@ -1064,6 +1075,11 @@ final class ControlPanel extends JPanel implements ActionListener {
                     _show_vector_data_cb.setSelected( state );
                 }
                 break;
+            case Configuration.show_properties:
+                if ( _show_properties_cb != null ) {
+                    _show_properties_cb.setSelected( state );
+                }
+                break;
             case Configuration.show_sequence_acc:
                 if ( _show_sequence_acc != null ) {
                     _show_sequence_acc.setSelected( state );
@@ -1258,8 +1274,8 @@ final class ControlPanel extends JPanel implements ActionListener {
         int cb_index = 0;
         if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
             _show_data_item = cb_index;
-            addClickToOption( Configuration.display_node_data, _configuration
-                    .getClickToTitle( Configuration.display_node_data ) );
+            addClickToOption( Configuration.display_node_data,
+                              _configuration.getClickToTitle( Configuration.display_node_data ) );
             if ( default_option == Configuration.display_node_data ) {
                 selected_index = cb_index;
             }
@@ -1267,8 +1283,8 @@ final class ControlPanel extends JPanel implements ActionListener {
         }
         if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
             _collapse_cb_item = cb_index;
-            addClickToOption( Configuration.collapse_uncollapse, _configuration
-                    .getClickToTitle( Configuration.collapse_uncollapse ) );
+            addClickToOption( Configuration.collapse_uncollapse,
+                              _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
             if ( default_option == Configuration.collapse_uncollapse ) {
                 selected_index = cb_index;
             }
@@ -1333,8 +1349,8 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
             if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
                 _copy_subtree_item = cb_index;
-                addClickToOption( Configuration.copy_subtree, _configuration
-                        .getClickToTitle( Configuration.copy_subtree ) );
+                addClickToOption( Configuration.copy_subtree,
+                                  _configuration.getClickToTitle( Configuration.copy_subtree ) );
                 if ( default_option == Configuration.copy_subtree ) {
                     selected_index = cb_index;
                 }
@@ -1342,8 +1358,8 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
             if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
                 _paste_subtree_item = cb_index;
-                addClickToOption( Configuration.paste_subtree, _configuration
-                        .getClickToTitle( Configuration.paste_subtree ) );
+                addClickToOption( Configuration.paste_subtree,
+                                  _configuration.getClickToTitle( Configuration.paste_subtree ) );
                 if ( default_option == Configuration.paste_subtree ) {
                     selected_index = cb_index;
                 }
@@ -1351,8 +1367,8 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
             if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
                 _delete_node_or_subtree_item = cb_index;
-                addClickToOption( Configuration.delete_subtree_or_node, _configuration
-                        .getClickToTitle( Configuration.delete_subtree_or_node ) );
+                addClickToOption( Configuration.delete_subtree_or_node,
+                                  _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
                 if ( default_option == Configuration.delete_subtree_or_node ) {
                     selected_index = cb_index;
                 }
@@ -1360,8 +1376,8 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
             if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
                 _add_new_node_item = cb_index;
-                addClickToOption( Configuration.add_new_node, _configuration
-                        .getClickToTitle( Configuration.add_new_node ) );
+                addClickToOption( Configuration.add_new_node,
+                                  _configuration.getClickToTitle( Configuration.add_new_node ) );
                 if ( default_option == Configuration.add_new_node ) {
                     selected_index = cb_index;
                 }
@@ -1369,8 +1385,8 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
             if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
                 _edit_node_data_item = cb_index;
-                addClickToOption( Configuration.edit_node_data, _configuration
-                        .getClickToTitle( Configuration.edit_node_data ) );
+                addClickToOption( Configuration.edit_node_data,
+                                  _configuration.getClickToTitle( Configuration.edit_node_data ) );
                 if ( default_option == Configuration.edit_node_data ) {
                     selected_index = cb_index;
                 }
@@ -1452,38 +1468,38 @@ final class ControlPanel extends JPanel implements ActionListener {
 
     private void setupDisplayCheckboxes() {
         if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
-            addCheckbox( Configuration.display_as_phylogram, _configuration
-                    .getDisplayTitle( Configuration.display_as_phylogram ) );
-            setCheckbox( Configuration.display_as_phylogram, _configuration
-                    .doCheckOption( Configuration.display_as_phylogram ) );
+            addCheckbox( Configuration.display_as_phylogram,
+                         _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
+            setCheckbox( Configuration.display_as_phylogram,
+                         _configuration.doCheckOption( Configuration.display_as_phylogram ) );
         }
         if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
-            addCheckbox( Configuration.dynamically_hide_data, _configuration
-                    .getDisplayTitle( Configuration.dynamically_hide_data ) );
-            setCheckbox( Configuration.dynamically_hide_data, _configuration
-                    .doCheckOption( Configuration.dynamically_hide_data ) );
+            addCheckbox( Configuration.dynamically_hide_data,
+                         _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
+            setCheckbox( Configuration.dynamically_hide_data,
+                         _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
         }
         if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
             addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
             setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
         }
         if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
-            addCheckbox( Configuration.display_internal_data, _configuration
-                    .getDisplayTitle( Configuration.display_internal_data ) );
-            setCheckbox( Configuration.display_internal_data, _configuration
-                    .doCheckOption( Configuration.display_internal_data ) );
+            addCheckbox( Configuration.display_internal_data,
+                         _configuration.getDisplayTitle( Configuration.display_internal_data ) );
+            setCheckbox( Configuration.display_internal_data,
+                         _configuration.doCheckOption( Configuration.display_internal_data ) );
         }
         if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
-            addCheckbox( Configuration.color_according_to_species, _configuration
-                    .getDisplayTitle( Configuration.color_according_to_species ) );
-            setCheckbox( Configuration.color_according_to_species, _configuration
-                    .doCheckOption( Configuration.color_according_to_species ) );
+            addCheckbox( Configuration.color_according_to_species,
+                         _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
+            setCheckbox( Configuration.color_according_to_species,
+                         _configuration.doCheckOption( Configuration.color_according_to_species ) );
         }
         if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
-            addCheckbox( Configuration.color_according_to_annotation, _configuration
-                    .getDisplayTitle( Configuration.color_according_to_annotation ) );
-            setCheckbox( Configuration.color_according_to_annotation, _configuration
-                    .doCheckOption( Configuration.color_according_to_annotation ) );
+            addCheckbox( Configuration.color_according_to_annotation,
+                         _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
+            setCheckbox( Configuration.color_according_to_annotation,
+                         _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
         }
         if ( _configuration.doDisplayOption( Configuration.color_branches ) ) {
             addCheckbox( Configuration.color_branches, _configuration.getDisplayTitle( Configuration.color_branches ) );
@@ -1508,76 +1524,80 @@ final class ControlPanel extends JPanel implements ActionListener {
             setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
-            addCheckbox( Configuration.show_taxonomy_scientific_names, _configuration
-                    .getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
-            setCheckbox( Configuration.show_taxonomy_scientific_names, _configuration
-                    .doCheckOption( Configuration.show_taxonomy_scientific_names ) );
+            addCheckbox( Configuration.show_taxonomy_scientific_names,
+                         _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
+            setCheckbox( Configuration.show_taxonomy_scientific_names,
+                         _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
-            addCheckbox( Configuration.show_taxonomy_common_names, _configuration
-                    .getDisplayTitle( Configuration.show_taxonomy_common_names ) );
-            setCheckbox( Configuration.show_taxonomy_common_names, _configuration
-                    .doCheckOption( Configuration.show_taxonomy_common_names ) );
+            addCheckbox( Configuration.show_taxonomy_common_names,
+                         _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
+            setCheckbox( Configuration.show_taxonomy_common_names,
+                         _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
-            addCheckbox( Configuration.show_taxonomy_images, _configuration
-                    .getDisplayTitle( Configuration.show_taxonomy_images ) );
-            setCheckbox( Configuration.show_taxonomy_images, _configuration
-                    .doCheckOption( Configuration.show_taxonomy_images ) );
+            addCheckbox( Configuration.show_taxonomy_images,
+                         _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
+            setCheckbox( Configuration.show_taxonomy_images,
+                         _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_gene_symbols ) ) {
-            addCheckbox( Configuration.show_gene_symbols, _configuration
-                    .getDisplayTitle( Configuration.show_gene_symbols ) );
-            setCheckbox( Configuration.show_gene_symbols, _configuration
-                    .doCheckOption( Configuration.show_gene_symbols ) );
+            addCheckbox( Configuration.show_gene_symbols,
+                         _configuration.getDisplayTitle( Configuration.show_gene_symbols ) );
+            setCheckbox( Configuration.show_gene_symbols,
+                         _configuration.doCheckOption( Configuration.show_gene_symbols ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
             addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
             setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
-            addCheckbox( Configuration.show_sequence_acc, _configuration
-                    .getDisplayTitle( Configuration.show_sequence_acc ) );
-            setCheckbox( Configuration.show_sequence_acc, _configuration
-                    .doCheckOption( Configuration.show_sequence_acc ) );
+            addCheckbox( Configuration.show_sequence_acc,
+                         _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
+            setCheckbox( Configuration.show_sequence_acc,
+                         _configuration.doCheckOption( Configuration.show_sequence_acc ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
             addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
             setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
-            addCheckbox( Configuration.show_binary_characters, _configuration
-                    .getDisplayTitle( Configuration.show_binary_characters ) );
-            setCheckbox( Configuration.show_binary_characters, _configuration
-                    .doCheckOption( Configuration.show_binary_characters ) );
+            addCheckbox( Configuration.show_binary_characters,
+                         _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
+            setCheckbox( Configuration.show_binary_characters,
+                         _configuration.doCheckOption( Configuration.show_binary_characters ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
-            addCheckbox( Configuration.show_binary_character_counts, _configuration
-                    .getDisplayTitle( Configuration.show_binary_character_counts ) );
-            setCheckbox( Configuration.show_binary_character_counts, _configuration
-                    .doCheckOption( Configuration.show_binary_character_counts ) );
+            addCheckbox( Configuration.show_binary_character_counts,
+                         _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
+            setCheckbox( Configuration.show_binary_character_counts,
+                         _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
-            addCheckbox( Configuration.show_domain_architectures, _configuration
-                    .getDisplayTitle( Configuration.show_domain_architectures ) );
-            setCheckbox( Configuration.show_domain_architectures, _configuration
-                    .doCheckOption( Configuration.show_domain_architectures ) );
+            addCheckbox( Configuration.show_domain_architectures,
+                         _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
+            setCheckbox( Configuration.show_domain_architectures,
+                         _configuration.doCheckOption( Configuration.show_domain_architectures ) );
         }
         if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
-            addCheckbox( Configuration.write_confidence_values, _configuration
-                    .getDisplayTitle( Configuration.write_confidence_values ) );
-            setCheckbox( Configuration.write_confidence_values, _configuration
-                    .doCheckOption( Configuration.write_confidence_values ) );
+            addCheckbox( Configuration.write_confidence_values,
+                         _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
+            setCheckbox( Configuration.write_confidence_values,
+                         _configuration.doCheckOption( Configuration.write_confidence_values ) );
         }
         if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
             addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
             setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
-            addCheckbox( Configuration.show_vector_data, _configuration
-                    .getDisplayTitle( Configuration.show_vector_data ) );
+            addCheckbox( Configuration.show_vector_data,
+                         _configuration.getDisplayTitle( Configuration.show_vector_data ) );
             setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
         }
+        if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
+            addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
+            setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
+        }
     }
 
     void setupSearchTools() {
@@ -1694,8 +1714,9 @@ final class ControlPanel extends JPanel implements ActionListener {
         for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
             if ( tree_panel != null ) {
                 tree_panel.validate();
-                tree_panel.setParametersForPainting( _mainpanel.getSizeOfViewport().width, _mainpanel
-                        .getSizeOfViewport().height, true );
+                tree_panel.setParametersForPainting( _mainpanel.getSizeOfViewport().width,
+                                                     _mainpanel.getSizeOfViewport().height,
+                                                     true );
                 tree_panel.resetPreferredSize();
                 tree_panel.repaint();
             }