import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.ForesterUtil;
-
-final class ControlPanel extends JPanel implements ActionListener {
+public final class ControlPanel extends JPanel implements ActionListener {
enum NodeClickAction {
ADD_NEW_NODE,
UNCOLLAPSE_ALL,
ORDER_SUBTREE;
}
- final static Font jcb_bold_font = new Font( Configuration
+ final static Font jcb_bold_font = new Font( Configuration
.getDefaultFontFamilyName(), Font.BOLD, Configuration.getGuiFontSize() );
- final static Font jcb_font = new Font( Configuration
- .getDefaultFontFamilyName(), Font.PLAIN, Configuration.getGuiFontSize());
- final static Font js_font = new Font( Configuration
+ final static Font jcb_font = new Font( Configuration
+ .getDefaultFontFamilyName(), Font.PLAIN, Configuration.getGuiFontSize() );
+ final static Font js_font = new Font( Configuration
.getDefaultFontFamilyName(), Font.PLAIN, Configuration.getGuiFontSize() );
- private static final String RETURN_TO_SUPER_TREE_TEXT = "R";
- private static final String SEARCH_TIP_TEXT = "Enter text to search for. Use ',' for logical OR and '+' for logical AND (not used in this manner for regular expression searches).";
- private static final long serialVersionUID = -8463483932821545633L;
- private NodeClickAction _action_when_node_clicked;
- private int _add_new_node_item;
- private Map<Integer, String> _all_click_to_names;
- private Map<String, Color> _annotation_colors;
- private int _blast_item;
- private JComboBox<String> _click_to_combobox;
- private JLabel _click_to_label;
- private List<String> _click_to_names;
- private int _collapse_cb_item;
- private int _uncollapse_all_cb_item;
- private int _order_subtree_cb_item;
- private JCheckBox _color_acc_species;
- private JCheckBox _color_acc_sequence;
- private JCheckBox _color_according_to_annotation;
- private boolean _color_branches;
- private JCheckBox _use_visual_styles_cb;
- private int _color_subtree_cb_item;
- private int _change_node_font_item;
+ private static final String RETURN_TO_SUPER_TREE_TEXT = "R";
+ private static final String SEARCH_TIP_TEXT = "Enter text to search for. Use ',' for logical OR and '+' for logical AND (not used in this manner for regular expression searches).";
+ private static final long serialVersionUID = -8463483932821545633L;
+ private NodeClickAction _action_when_node_clicked;
+ private int _add_new_node_item;
+ private Map<Integer, String> _all_click_to_names;
+ private Map<String, Color> _annotation_colors;
+ private int _blast_item;
+ private JComboBox<String> _click_to_combobox;
+ private JLabel _click_to_label;
+ private List<String> _click_to_names;
+ private int _collapse_cb_item;
+ private int _uncollapse_all_cb_item;
+ private int _order_subtree_cb_item;
+ private JCheckBox _color_acc_species;
+ private JCheckBox _color_acc_sequence;
+ private JCheckBox _color_according_to_annotation;
+ private boolean _color_branches;
+ private JCheckBox _use_visual_styles_cb;
+ private int _color_subtree_cb_item;
+ private int _change_node_font_item;
// The settings from the conf file
- private final Configuration _configuration;
- private int _copy_subtree_item;
- private int _cut_subtree_item;
- private JButton _decr_domain_structure_evalue_thr;
- private int _delete_node_or_subtree_item;
- private JRadioButton _display_as_unaligned_phylogram_rb;
- private JRadioButton _display_as_aligned_phylogram_rb;
- private JRadioButton _display_as_cladogram_rb;
- private ButtonGroup _display_as_buttongroup;
+ private final Configuration _configuration;
+ private int _copy_subtree_item;
+ private int _cut_subtree_item;
+ private JButton _decr_domain_structure_evalue_thr;
+ private int _delete_node_or_subtree_item;
+ private JRadioButton _display_as_unaligned_phylogram_rb;
+ private JRadioButton _display_as_aligned_phylogram_rb;
+ private JRadioButton _display_as_cladogram_rb;
+ private ButtonGroup _display_as_buttongroup;
// Tree checkboxes
- private JCheckBox _display_internal_data;
- private JLabel _domain_display_label;
- private JTextField _domain_structure_evalue_thr_tf;
- private JTextField _depth_collapse_depth_tf;
- private JTextField _rank_collapse_depth_tf;
- private List<Options.PHYLOGENY_DISPLAY_TYPE> _tree_display_types;
- private JCheckBox _dynamically_hide_data;
- private int _edit_node_data_item;
- private int _get_ext_desc_data;
- private JButton _incr_domain_structure_evalue_thr;
- private final MainPanel _mainpanel;
- private JCheckBox _node_desc_popup_cb;
- private int _open_pdb_item;
- private int _open_seq_web_item;
- private int _open_tax_web_item;
- private int _color_node_font_item;
- private JButton _order;
- private int _paste_subtree_item;
- private int _reroot_cb_item;
- private JButton _return_to_super_tree;
+ private JCheckBox _display_internal_data;
+ private JCheckBox _display_external_data;
+ private JLabel _domain_display_label;
+ private JTextField _domain_structure_evalue_thr_tf;
+ private JTextField _depth_collapse_depth_tf;
+ private JTextField _rank_collapse_depth_tf;
+ private List<Options.PHYLOGENY_DISPLAY_TYPE> _tree_display_types;
+ private JCheckBox _dynamically_hide_data;
+ private int _edit_node_data_item;
+ private int _get_ext_desc_data;
+ private JButton _incr_domain_structure_evalue_thr;
+ private final MainPanel _mainpanel;
+ private JCheckBox _node_desc_popup_cb;
+ private int _open_pdb_item;
+ private int _open_seq_web_item;
+ private int _open_tax_web_item;
+ private int _color_node_font_item;
+ private JButton _order;
+ private int _paste_subtree_item;
+ private int _reroot_cb_item;
+ private JButton _return_to_super_tree;
// Search
- private JLabel _search_found_label_0;
- private JLabel _search_found_label_1;
- private JButton _search_reset_button_0;
- private JButton _search_reset_button_1;
- private JTextField _search_tf_0;
- private JTextField _search_tf_1;
- private int _select_nodes_item;
- private Sequence _selected_query_seq;
- private JCheckBox _seq_relation_confidence_switch;
- private JComboBox<SEQUENCE_RELATION_TYPE> _sequence_relation_type_box;
- private JCheckBox _show_annotation;
- private JCheckBox _show_binary_character_counts;
- private JCheckBox _show_binary_characters;
+ private JLabel _search_found_label_0;
+ private JLabel _search_found_label_1;
+ private JButton _search_reset_button_0;
+ private JButton _search_reset_button_1;
+ private JTextField _search_tf_0;
+ private JTextField _search_tf_1;
+ private int _select_nodes_item;
+ private Sequence _selected_query_seq;
+ private JCheckBox _seq_relation_confidence_switch;
+ private JComboBox<SEQUENCE_RELATION_TYPE> _sequence_relation_type_box;
+ private JCheckBox _show_annotation;
+ private JCheckBox _show_binary_character_counts;
+ private JCheckBox _show_binary_characters;
// Indices for the click-to options in the combo box
- private int _show_data_item;
- private JCheckBox _show_domain_architectures;
- private JCheckBox _show_mol_seqs;
- private JCheckBox _write_branch_length_values;
- private JCheckBox _show_events;
- private JCheckBox _show_gene_names;
- private JCheckBox _show_node_names;
- private JCheckBox _show_properties_cb;
- private JCheckBox _show_seq_names;
- private JCheckBox _show_seq_symbols;
- private JCheckBox _show_sequence_acc;
- private JComboBox<String> _show_sequence_relations;
- private JCheckBox _show_taxo_code;
- private JCheckBox _show_taxo_rank;
- private JCheckBox _show_taxo_common_names;
- private JCheckBox _show_taxo_images_cb;
- private JCheckBox _show_taxo_scientific_names;
- private JCheckBox _show_vector_data_cb;
- private JButton _show_whole;
- private int _sort_descendents_item;
- private Map<String, Color> _species_colors;
- private Map<String, Color> _sequence_colors;
- private int _subtree_cb_item;
- private int _swap_cb_item;
- private JButton _uncollapse_all;
- private JCheckBox _width_branches;
- private JCheckBox _write_confidence;
- private JButton _zoom_in_domain_structure;
- private JButton _zoom_in_x;
- private JButton _zoom_in_y;
- private JLabel _zoom_label;
- private JButton _zoom_out_domain_structure;
- private JButton _zoom_out_x;
- private JButton _zoom_out_y;
- private JButton _decr_depth_collapse_level;
- private JButton _incr_depth_collapse_level;
- private JLabel _depth_collapse_label;
- private JButton _decr_rank_collapse_level;
- private JButton _incr_rank_collapse_level;
- private JLabel _rank_collapse_label;
-
+ private int _show_data_item;
+ private JCheckBox _show_domain_architectures;
+ private JCheckBox _show_mol_seqs;
+ private JCheckBox _write_branch_length_values;
+ private JCheckBox _show_events;
+ private JCheckBox _show_gene_names;
+ private JCheckBox _show_node_names;
+ private JCheckBox _show_properties_cb;
+ private JCheckBox _show_seq_names;
+ private JCheckBox _show_seq_symbols;
+ private JCheckBox _show_sequence_acc;
+ private JComboBox<String> _show_sequence_relations;
+ private JCheckBox _show_taxo_code;
+ private JCheckBox _show_taxo_rank;
+ private JCheckBox _show_taxo_common_names;
+ private JCheckBox _show_taxo_images_cb;
+ private JCheckBox _show_taxo_scientific_names;
+ private JCheckBox _show_vector_data_cb;
+ private JButton _show_whole;
+ private int _sort_descendents_item;
+ private Map<String, Color> _species_colors;
+ private Map<String, Color> _sequence_colors;
+ private int _subtree_cb_item;
+ private int _swap_cb_item;
+ private JButton _uncollapse_all;
+ private JCheckBox _width_branches;
+ private JCheckBox _write_confidence;
+ private JButton _zoom_in_domain_structure;
+ private JButton _zoom_in_x;
+ private JButton _zoom_in_y;
+ private JLabel _zoom_label;
+ private JButton _zoom_out_domain_structure;
+ private JButton _zoom_out_x;
+ private JButton _zoom_out_y;
+ private JButton _decr_depth_collapse_level;
+ private JButton _incr_depth_collapse_level;
+ private JLabel _depth_collapse_label;
+ private JButton _decr_rank_collapse_level;
+ private JButton _incr_rank_collapse_level;
+ private JLabel _rank_collapse_label;
+
ControlPanel( final MainPanel ap, final Configuration configuration ) {
init();
_mainpanel = ap;
return _tree_display_types;
}
- final private MainFrame getMainFrame() {
+ final private MainFrame getMainFrame() {
return getMainPanel().getMainFrame();
}
}
private void setupDisplayCheckboxes() {
-
if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
addCheckbox( Configuration.dynamically_hide_data,
_configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
setCheckbox( Configuration.display_internal_data,
_configuration.doCheckOption( Configuration.display_internal_data ) );
}
+ if ( _configuration.doDisplayOption( Configuration.display_external_data ) ) {
+ addCheckbox( Configuration.display_external_data,
+ _configuration.getDisplayTitle( Configuration.display_external_data ) );
+ setCheckbox( Configuration.display_external_data,
+ _configuration.doCheckOption( Configuration.display_external_data ) );
+ }
if ( _configuration.doDisplayOption( Configuration.color_according_to_sequence ) ) {
addCheckbox( Configuration.color_according_to_sequence,
_configuration.getDisplayTitle( Configuration.color_according_to_sequence ) );
addJCheckBox( _display_internal_data, ch_panel );
add( ch_panel );
break;
+ case Configuration.display_external_data:
+ _display_external_data = new JCheckBox( title );
+ _display_external_data.setToolTipText( "To allow or disallow display of external labels" );
+ addJCheckBox( _display_external_data, ch_panel );
+ add( ch_panel );
+ break;
case Configuration.color_according_to_species:
_color_acc_species = new JCheckBox( title );
_color_acc_species.setToolTipText( "To colorize node labels as a function of taxonomy" );
boolean isDrawPhylogram() {
final Options.PHYLOGENY_DISPLAY_TYPE t = getTreeDisplayType( getMainPanel().getCurrentTabIndex() );
- return ((t == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM) ||( t == Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM));
+ return ( ( t == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM )
+ || ( t == Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM ) );
}
boolean isDynamicallyHideData() {
return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() );
}
+ boolean isShowExternalData() {
+ return ( ( _display_external_data == null ) || _display_external_data.isSelected() );
+ }
+
boolean isShowNodeNames() {
return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
}
}
void phylogenyAdded( final Configuration configuration ) {
- if (configuration.isDrawAsPhylogram()) {
- getTreeDisplayTypes().add( Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM);
+ if ( configuration.isDrawAsPhylogram() ) {
+ getTreeDisplayTypes().add( Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM );
}
else {
- getTreeDisplayTypes().add( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM);
+ getTreeDisplayTypes().add( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM );
}
}
_display_internal_data.setSelected( state );
}
break;
+ case Configuration.display_external_data:
+ if ( _display_external_data != null ) {
+ _display_external_data.setSelected( state );
+ }
+ break;
case Configuration.color_according_to_species:
if ( _color_acc_species != null ) {
_color_acc_species.setSelected( state );
_click_to_combobox.setSelectedIndex( action );
}
- void setColorBranches( final boolean color_branches ) {
+ public void setColorBranches( final boolean color_branches ) {
_color_branches = color_branches;
}
void setTreeDisplayType( final Options.PHYLOGENY_DISPLAY_TYPE t ) {
- switch (t) {
+ switch ( t ) {
case UNALIGNED_PHYLOGRAM:
getDisplayAsUnalignedPhylogramRb().setSelected( true );
break;
case ALIGNED_PHYLOGRAM:
getDisplayAsAlignedPhylogramRb().setSelected( true );
break;
- case CLADOGRAM:
+ case CLADOGRAM:
getDisplayAsCladogramRb().setSelected( true );
break;
}
- setTreeDisplayType( getMainPanel().getCurrentTabIndex(), t );
+ setTreeDisplayType( getMainPanel().getCurrentTabIndex(), t );
}
void setDrawPhylogramEnabled( final boolean b ) {
- if ( getDisplayAsAlignedPhylogramRb() != null &&
- getDisplayAsUnalignedPhylogramRb() != null &&
- getDisplayAsCladogramRb() != null
- ) {
-
- getDisplayAsAlignedPhylogramRb().setEnabled( b );
- getDisplayAsUnalignedPhylogramRb().setEnabled( b );
- getDisplayAsCladogramRb().setEnabled( b );
- }
+ if ( getDisplayAsAlignedPhylogramRb() != null && getDisplayAsUnalignedPhylogramRb() != null
+ && getDisplayAsCladogramRb() != null ) {
+ getDisplayAsAlignedPhylogramRb().setEnabled( b );
+ getDisplayAsUnalignedPhylogramRb().setEnabled( b );
+ getDisplayAsCladogramRb().setEnabled( b );
+ }
}
void setDynamicHidingIsOn( final boolean is_on ) {
}
void setupControls() {
-
setupTreeDisplayTypeOptions();
setupDisplayCheckboxes();
/* GUILHEM_BEG */
setupJRadioButton( getDisplayAsUnalignedPhylogramRb() );
setupJRadioButton( getDisplayAsAlignedPhylogramRb() );
setupJRadioButton( getDisplayAsCladogramRb() );
- final JPanel p = new JPanel(new GridLayout( 1, 3, 0, 0 ));
+ final JPanel p = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
p.setFont( ControlPanel.jcb_font );
if ( !_configuration.isUseNativeUI() ) {
p.setBackground( getConfiguration().getGuiBackgroundColor() );
p.setForeground( getConfiguration().getGuiCheckboxTextColor() );
}
- p.add( _display_as_unaligned_phylogram_rb );
+ p.add( _display_as_unaligned_phylogram_rb );
p.add( _display_as_aligned_phylogram_rb );
p.add( _display_as_cladogram_rb );
add( p );
}
-
-
+
void setUpControlsForDomainStrucures() {
_domain_display_label = new JLabel( "Domain Architectures:" );
add( customizeLabel( _domain_display_label, getConfiguration() ) );
/**
* Fit entire tree into window.
*/
- void showWhole() {
+ public void showWhole() {
if ( ( _mainpanel.getCurrentScrollPane() == null )
|| _mainpanel.getCurrentTreePanel().getPhylogeny().isEmpty() ) {
return;
if ( getCurrentTreePanel().isPhyHasBranchLengths()
&& ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
setDrawPhylogramEnabled( true );
-
- setTreeDisplayType( getTreeDisplayType( getMainPanel().getCurrentTabIndex() ) );
+ setTreeDisplayType( getTreeDisplayType( getMainPanel().getCurrentTabIndex() ) );
}
else {
setDrawPhylogramEnabled( false );
setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM );
}
-
- getMainPanel().getMainFrame()
- .setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel().getPhylogenyGraphicsType() );
-
+ getMainPanel().getMainFrame()
+ .setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel().getPhylogenyGraphicsType() );
getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
getMainPanel().getCurrentTreePanel().updateButtonToUncollapseAll();
getMainPanel().getControlPanel().search0();
private final boolean isDrawPhylogram( int currentTabIndex ) {
Options.PHYLOGENY_DISPLAY_TYPE t = getTreeDisplayType( currentTabIndex );
- return ((t==Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM)|(t==Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM));
-
+ return ( ( t == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM )
+ | ( t == Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM ) );
}
final void zoomOutY( final float factor ) {
}
public Options.PHYLOGENY_DISPLAY_TYPE getTreeDisplayType() {
- if (_display_as_unaligned_phylogram_rb.isSelected() ) {
+ if ( _display_as_unaligned_phylogram_rb.isSelected() ) {
return Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM;
}
- else if (_display_as_aligned_phylogram_rb.isSelected() ) {
+ else if ( _display_as_aligned_phylogram_rb.isSelected() ) {
return Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM;
}
return Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM;
git://source.jalview.org / jalview.git / blobdiff