final class ControlPanel extends JPanel implements ActionListener {
- private static final String RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
+ final static Font jcb_bold_font = new Font( Configuration.getDefaultFontFamilyName(),
+ Font.BOLD,
+ 9 );
final static Font jcb_font = new Font( Configuration.getDefaultFontFamilyName(),
Font.PLAIN,
9 );
final static Font js_font = new Font( Configuration.getDefaultFontFamilyName(),
Font.PLAIN,
9 );
- final static Font jcb_bold_font = new Font( Configuration.getDefaultFontFamilyName(),
- Font.BOLD,
- 9 );
+ private static final String RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
private static final long serialVersionUID = -8463483932821545633L;
- private final MainPanel _mainpanel;
+ 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 _click_to_combobox;
+ private JLabel _click_to_label;
+ private List<String> _click_to_names;
+ private int _collapse_cb_item;
+ private JCheckBox _color_acc_species;
+ private JCheckBox _color_according_to_annotation;
+ private boolean _color_branches;
+ private JCheckBox _color_branches_cb;
+ private int _color_subtree_cb_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 JCheckBox _display_as_phylogram_cb;
// Tree checkboxes
private JCheckBox _display_internal_data;
- private JCheckBox _show_node_names;
- private JCheckBox _show_taxo_code;
- private JCheckBox _write_confidence;
- private JCheckBox _show_events;
- private JCheckBox _color_acc_species;
- private JCheckBox _color_branches_cb;
- private JCheckBox _width_branches;
- private JCheckBox _show_domain_architectures;
+ private JLabel _domain_display_label;
+ private JTextField _domain_structure_evalue_thr_tf;
+ private List<Boolean> _draw_phylogram;
+ 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 JButton _order;
+ private boolean _order_of_appearance;
+ private int _paste_subtree_item;
+ private int _reroot_cb_item;
+ private JButton _return_to_super_tree;
+ private JLabel _search_found_label;
+ private JButton _search_reset_button;
+ private JTextField _search_tf;
+ private int _select_nodes_item;
+ private Sequence _selected_query_seq;
+ private JCheckBox _seq_relation_confidence_switch;
+ private JComboBox _sequence_relation_type_box;
private JCheckBox _show_annotation;
- private JCheckBox _show_binary_characters;
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_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_gene_names;
private JCheckBox _show_sequence_acc;
- private JCheckBox _node_desc_popup_cb;
- private JCheckBox _dynamically_hide_data;
- private JCheckBox _show_taxo_scientific_names;
+ private JComboBox _show_sequence_relations;
+ private JCheckBox _show_taxo_code;
private JCheckBox _show_taxo_common_names;
private JCheckBox _show_taxo_images_cb;
- private JCheckBox _color_according_to_annotation;
- private JCheckBox _display_as_phylogram_cb;
- private JCheckBox _seq_relation_confidence_switch;
- private JComboBox _show_sequence_relations;
- private JComboBox _sequence_relation_type_box;
+ private JCheckBox _show_taxo_scientific_names;
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;
- private JComboBox _click_to_combobox;
- private Map<Integer, String> _all_click_to_names;
- private List<String> _click_to_names;
- // Indices for the click-to options in the combo box
- private int _show_data_item;
- private int _collapse_cb_item;
- private int _reroot_cb_item;
- private int _swap_cb_item;
- private int _subtree_cb_item;
- private int _color_subtree_cb_item;
- private int _open_seq_web_item;
+ private JButton _show_whole;
private int _sort_descendents_item;
- private int _open_tax_web_item;
- private int _cut_subtree_item;
- private int _copy_subtree_item;
- private int _delete_node_or_subtree_item;
- private int _paste_subtree_item;
- private int _add_new_node_item;
- private int _edit_node_data_item;
- private int _select_nodes_item;
- private int _get_ext_desc_data;
- private int _open_pdb_item;
- private int _blast_item;
+ private Map<String, Color> _species_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;
// zooming and quick tree manipulation buttons:
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 _show_whole;
- private JButton _order;
- private JButton _uncollapse_all;
- private JButton _zoom_in_domain_structure;
- private JButton _zoom_out_domain_structure;
- private JButton _decr_domain_structure_evalue_thr;
- private JButton _incr_domain_structure_evalue_thr;
- private JButton _return_to_super_tree;
- private JTextField _domain_structure_evalue_thr_tf;
- private JTextField _search_tf;
- private boolean _order_of_appearance;
- private boolean _color_branches;
- private NodeClickAction _action_when_node_clicked;
- private List<Boolean> _draw_phylogram;
- private Map<String, Color> _annotation_colors;
- private Map<String, Color> _species_colors;
- private JButton _search_reset_button;
- private JLabel _search_found_label;
- private Sequence _selected_query_seq;
ControlPanel( final MainPanel ap, final Configuration configuration ) {
init();
}
else if ( e.getSource() == _show_domain_architectures ) {
search();
- displayedPhylogenyMightHaveChanged( false );
+ displayedPhylogenyMightHaveChanged( true );
}
else if ( ( tp != null ) && ( tp.getPhylogeny() != null ) ) {
if ( e.getSource() == getDisplayAsPhylogramCb() ) {
_return_to_super_tree.setEnabled( true );
}
- void showAnnotations() {
- if ( _show_annotation != null ) {
- _show_annotation.setSelected( true );
- }
- if ( _color_according_to_annotation != null ) {
- _color_according_to_annotation.setSelected( true );
- }
- if ( _color_acc_species != null ) {
- _color_acc_species.setSelected( false );
- }
- _mainpanel.getCurrentTreePanel().repaint();
- }
-
/**
* Add zoom and quick edit buttons. (Last modified 8/9/04)
*/
return getMainPanel().getOptions();
}
+ JLabel getSearchFoundCountsLabel() {
+ return _search_found_label;
+ }
+
+ JButton getSearchResetButton() {
+ return _search_reset_button;
+ }
+
JTextField getSearchTextField() {
return _search_tf;
}
return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
}
- boolean isShowSeqNames() {
- return ( ( _show_seq_names != null ) && _show_seq_names.isSelected() );
- }
-
- boolean isShowSeqSymbols() {
- return ( ( _show_seq_symbols != null ) && _show_seq_symbols.isSelected() );
+ boolean isShowGeneNames() {
+ return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
}
boolean isShowInternalData() {
return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
}
- boolean isShowSequenceAcc() {
- return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
+ boolean isShowSeqNames() {
+ return ( ( _show_seq_names != null ) && _show_seq_names.isSelected() );
}
- boolean isShowGeneNames() {
- return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
+ boolean isShowSeqSymbols() {
+ return ( ( _show_seq_symbols != null ) && _show_seq_symbols.isSelected() );
+ }
+
+ boolean isShowSequenceAcc() {
+ return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
}
boolean isShowSequenceRelationConfidence() {
}
}
+ void searchReset() {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().setFoundNodes( null );
+ }
+ }
+
void setActionWhenNodeClicked( final NodeClickAction action ) {
_action_when_node_clicked = action;
}
// }
}
+ void setSearchFoundCountsOnLabel( final int counts ) {
+ getSearchFoundCountsLabel().setText( "Found: " + counts );
+ }
+
void setShowEvents( final boolean show_events ) {
if ( getShowEventsCb() == null ) {
_show_events = new JCheckBox( "" );
addJButton( _search_reset_button, s_panel_2 );
}
+ void showAnnotations() {
+ if ( _show_annotation != null ) {
+ _show_annotation.setSelected( true );
+ }
+ if ( _color_according_to_annotation != null ) {
+ _color_according_to_annotation.setSelected( true );
+ }
+ if ( _color_acc_species != null ) {
+ _color_acc_species.setSelected( false );
+ }
+ _mainpanel.getCurrentTreePanel().repaint();
+ }
+
/**
* Fit entire tree into window.
*/
}
getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
getSequenceRelationTypeBox().removeAllItems();
for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
.getRelevantSequenceRelationTypes() ) {
_sequence_relation_type_box.addItem( type );
}
+ getMainPanel().getCurrentTreePanel().repaint();
//setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
// according to GUILHEM the line above can be removed.
}
return _draw_phylogram;
}
- JLabel getSearchFoundCountsLabel() {
- return _search_found_label;
- }
-
- JButton getSearchResetButton() {
- return _search_reset_button;
- }
-
private void init() {
_draw_phylogram = new ArrayList<Boolean>();
setSpeciesColors( new HashMap<String, Color>() );
}
}
- void searchReset() {
- if ( getMainPanel().getCurrentTreePanel() != null ) {
- getMainPanel().getCurrentTreePanel().setFoundNodes( null );
- }
- }
-
private void setDrawPhylogram( final int index, final boolean b ) {
getIsDrawPhylogramList().set( index, b );
}
- void setSearchFoundCountsOnLabel( final int counts ) {
- getSearchFoundCountsLabel().setText( "Found: " + counts );
- }
-
private void setupClickToOptions() {
final int default_option = _configuration.getDefaultDisplayClicktoOption();
int selected_index = 0;
}
enum NodeClickAction {
- SHOW_DATA,
+ ADD_NEW_NODE,
+ BLAST,
COLLAPSE,
- REROOT,
- SUBTREE,
- SWAP,
COLOR_SUBTREE,
- OPEN_TAX_WEB,
- OPEN_SEQ_WEB,
- CUT_SUBTREE,
COPY_SUBTREE,
+ CUT_SUBTREE,
DELETE_NODE_OR_SUBTREE,
- PASTE_SUBTREE,
- ADD_NEW_NODE,
EDIT_NODE_DATA,
+ GET_EXT_DESC_DATA,
+ OPEN_PDB_WEB,
+ OPEN_SEQ_WEB,
+ OPEN_TAX_WEB,
+ PASTE_SUBTREE,
+ REROOT,
SELECT_NODES,
+ SHOW_DATA,
SORT_DESCENDENTS,
- GET_EXT_DESC_DATA,
- BLAST,
- OPEN_PDB_WEB;
+ SUBTREE,
+ SWAP;
}
}
git://source.jalview.org / jalview.git / commitdiff