}
else if ( o == _search_case_senstive_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _search_whole_words_only_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _inverse_search_result_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _show_scale_cbmi ) {
updateOptions( getOptions() );
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 JCheckBox _show_annotation;
private JCheckBox _show_binary_character_counts;
private JCheckBox _show_binary_characters;
+ // Search
+ private JLabel _search_found_label_0;
+ private JButton _search_reset_button_0;
+ private JTextField _search_tf_0;
+ private JLabel _search_found_label_1;
+ private JButton _search_reset_button_1;
+ private JTextField _search_tf_1;
+
// Indices for the click-to options in the combo box
private int _show_data_item;
private JCheckBox _show_domain_architectures;
displayedPhylogenyMightHaveChanged( true );
}
else if ( e.getSource() == _show_domain_architectures ) {
- search();
+ search0();
+ search1();
displayedPhylogenyMightHaveChanged( true );
}
else if ( ( tp != null ) && ( tp.getPhylogeny() != null ) ) {
_mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThreshold();
displayedPhylogenyMightHaveChanged( true );
}
- else if ( e.getSource() == _search_tf ) {
- search();
+ else if ( e.getSource() == _search_tf_0 ) {
+ search0();
+ displayedPhylogenyMightHaveChanged( true );
+ }
+ else if ( e.getSource() == _search_tf_1 ) {
+ search1();
displayedPhylogenyMightHaveChanged( true );
}
else {
return getMainPanel().getOptions();
}
- JLabel getSearchFoundCountsLabel() {
- return _search_found_label;
+ JLabel getSearchFoundCountsLabel0() {
+ return _search_found_label_0;
+ }
+
+ JLabel getSearchFoundCountsLabel1() {
+ return _search_found_label_1;
}
- JButton getSearchResetButton() {
- return _search_reset_button;
+ JButton getSearchResetButton0() {
+ return _search_reset_button_0;
+ }
+
+ JButton getSearchResetButton1() {
+ return _search_reset_button_1;
}
- JTextField getSearchTextField() {
- return _search_tf;
+ JTextField getSearchTextField0() {
+ return _search_tf_0;
+ }
+
+ JTextField getSearchTextField1() {
+ return _search_tf_1;
}
List<String> getSingleClickToNames() {
getIsDrawPhylogramList().remove( index );
}
- void search() {
+ void search0() {
final MainPanel main_panel = getMainPanel();
final Phylogeny tree = main_panel.getCurrentPhylogeny();
if ( ( tree == null ) || tree.isEmpty() ) {
return;
}
- String query = getSearchTextField().getText();
+ String query = getSearchTextField0().getText();
if ( query != null ) {
query = query.trim();
}
+
+
+ if ( !ForesterUtil.isEmpty( query ) ) {
+ search0( main_panel, tree, query );
+ }
else {
- getSearchFoundCountsLabel().setVisible( false );
- getSearchResetButton().setEnabled( false );
- getSearchResetButton().setVisible( false );
- searchReset();
+ getSearchFoundCountsLabel0().setVisible( false );
+ getSearchResetButton0().setEnabled( false );
+ getSearchResetButton0().setVisible( false );
+ searchReset0();
+ }
+ }
+
+ void search1() {
+ final MainPanel main_panel = getMainPanel();
+ final Phylogeny tree = main_panel.getCurrentPhylogeny();
+ if ( ( tree == null ) || tree.isEmpty() ) {
+ return;
+ }
+ String query = getSearchTextField1().getText();
+ if ( query != null ) {
+ query = query.trim();
}
+
if ( !ForesterUtil.isEmpty( query ) ) {
- search( main_panel, tree, query );
+ search1( main_panel, tree, query );
}
else {
- getSearchFoundCountsLabel().setVisible( false );
- getSearchResetButton().setEnabled( false );
- getSearchResetButton().setVisible( false );
- searchReset();
+ getSearchFoundCountsLabel1().setVisible( false );
+ getSearchResetButton1().setEnabled( false );
+ getSearchResetButton1().setVisible( false );
+ searchReset1();
}
}
+
+
- void searchReset() {
+ void searchReset0() {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
+ }
+ }
+
+ void searchReset1() {
if ( getMainPanel().getCurrentTreePanel() != null ) {
- getMainPanel().getCurrentTreePanel().setFoundNodes( null );
+ getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
}
}
// }
}
- void setSearchFoundCountsOnLabel( final int counts ) {
- getSearchFoundCountsLabel().setText( "Found: " + counts );
+ void setSearchFoundCountsOnLabel0( final int counts ) {
+ getSearchFoundCountsLabel0().setText( "Found: " + counts );
+ }
+
+ void setSearchFoundCountsOnLabel1( final int counts ) {
+ getSearchFoundCountsLabel1().setText( "Found: " + counts );
}
void setShowEvents( final boolean show_events ) {
endClickToOptions();
// Zoom and quick edit buttons
addButtons();
- setupSearchTools();
+ setupSearchTools0();
+ setupSearchTools1();
}
void setUpControlsForDomainStrucures() {
addJButton( _incr_domain_structure_evalue_thr, d2_panel );
}
- void setupSearchTools() {
+ void setupSearchTools0() {
final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
- final JLabel search_label = new JLabel( "Search:" );
+ final JLabel search_label = new JLabel( "Search (A):" );
search_label.setFont( ControlPanel.jcb_bold_font );
if ( !getConfiguration().isUseNativeUI() ) {
search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
}
add( search_label );
search_label.setToolTipText( tip );
- _search_found_label = new JLabel();
- getSearchFoundCountsLabel().setVisible( false );
- _search_found_label.setFont( ControlPanel.jcb_bold_font );
+ _search_found_label_0 = new JLabel();
+ getSearchFoundCountsLabel0().setVisible( false );
+ _search_found_label_0.setFont( ControlPanel.jcb_bold_font );
if ( !getConfiguration().isUseNativeUI() ) {
- _search_found_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+ _search_found_label_0.setForeground( getConfiguration().getGuiCheckboxTextColor() );
}
- _search_tf = new JTextField( 3 );
- _search_tf.setToolTipText( tip );
- _search_tf.setEditable( true );
+ _search_tf_0 = new JTextField( 3 );
+ _search_tf_0.setToolTipText( tip );
+ _search_tf_0.setEditable( true );
if ( !getConfiguration().isUseNativeUI() ) {
- _search_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
- _search_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
- _search_tf.setBorder( null );
- }
- _search_reset_button = new JButton();
- getSearchResetButton().setText( "Reset" );
- getSearchResetButton().setEnabled( false );
- getSearchResetButton().setVisible( false );
+ _search_tf_0.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
+ _search_tf_0.setBackground( getConfiguration().getGuiCheckboxTextColor() );
+ _search_tf_0.setBorder( null );
+ }
+ _search_reset_button_0 = new JButton();
+ getSearchResetButton0().setText( "Reset" );
+ getSearchResetButton0().setEnabled( false );
+ getSearchResetButton0().setVisible( false );
final JPanel s_panel_1 = new JPanel( new BorderLayout() );
final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
s_panel_1.setBackground( getBackground() );
@Override
public void keyReleased( final KeyEvent key_event ) {
- search();
+ search0();
displayedPhylogenyMightHaveChanged( true );
}
};
@Override
public void actionPerformed( final ActionEvent e ) {
- searchReset();
- setSearchFoundCountsOnLabel( 0 );
- getSearchFoundCountsLabel().setVisible( false );
- getSearchTextField().setText( "" );
- getSearchResetButton().setEnabled( false );
- getSearchResetButton().setVisible( false );
+ searchReset0();
+ setSearchFoundCountsOnLabel0( 0 );
+ getSearchFoundCountsLabel0().setVisible( false );
+ getSearchTextField0().setText( "" );
+ getSearchResetButton0().setEnabled( false );
+ getSearchResetButton0().setVisible( false );
displayedPhylogenyMightHaveChanged( true );
}
};
- _search_reset_button.addActionListener( action_listener );
- _search_tf.addKeyListener( key_adapter );
- addJTextField( _search_tf, s_panel_1 );
- s_panel_2.add( _search_found_label );
- addJButton( _search_reset_button, s_panel_2 );
+ _search_reset_button_0.addActionListener( action_listener );
+ _search_tf_0.addKeyListener( key_adapter );
+ addJTextField( _search_tf_0, s_panel_1 );
+ s_panel_2.add( _search_found_label_0 );
+ addJButton( _search_reset_button_0, s_panel_2 );
}
+ void setupSearchTools1() {
+ final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
+ final JLabel search_label = new JLabel( "Search (B):" );
+ search_label.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+ }
+ add( search_label );
+ search_label.setToolTipText( tip );
+ _search_found_label_1 = new JLabel();
+ getSearchFoundCountsLabel1().setVisible( false );
+ _search_found_label_1.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _search_found_label_1.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+ }
+ _search_tf_1 = new JTextField( 3 );
+ _search_tf_1.setToolTipText( tip );
+ _search_tf_1.setEditable( true );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _search_tf_1.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
+ _search_tf_1.setBackground( getConfiguration().getGuiCheckboxTextColor() );
+ _search_tf_1.setBorder( null );
+ }
+ _search_reset_button_1 = new JButton();
+ getSearchResetButton1().setText( "Reset" );
+ getSearchResetButton1().setEnabled( false );
+ getSearchResetButton1().setVisible( false );
+ final JPanel s_panel_1 = new JPanel( new BorderLayout() );
+ final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
+ s_panel_1.setBackground( getBackground() );
+ add( s_panel_1 );
+ s_panel_2.setBackground( getBackground() );
+ add( s_panel_2 );
+ final KeyAdapter key_adapter = new KeyAdapter() {
+
+ @Override
+ public void keyReleased( final KeyEvent key_event ) {
+ search1();
+ displayedPhylogenyMightHaveChanged( true );
+ }
+ };
+ final ActionListener action_listener = new ActionListener() {
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ searchReset1();
+ setSearchFoundCountsOnLabel1( 0 );
+ getSearchFoundCountsLabel1().setVisible( false );
+ getSearchTextField1().setText( "" );
+ getSearchResetButton1().setEnabled( false );
+ getSearchResetButton1().setVisible( false );
+ displayedPhylogenyMightHaveChanged( true );
+ }
+ };
+ _search_reset_button_1.addActionListener( action_listener );
+ _search_tf_1.addKeyListener( key_adapter );
+ addJTextField( _search_tf_1, s_panel_1 );
+ s_panel_2.add( _search_found_label_1 );
+ addJButton( _search_reset_button_1, s_panel_2 );
+ }
+
+
void showAnnotations() {
if ( _show_annotation != null ) {
_show_annotation.setSelected( true );
.getPhylogenyGraphicsType() );
}
getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
getSequenceRelationTypeBox().removeAllItems();
for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
return getIsDrawPhylogramList().get( index );
}
- private void search( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
- getSearchFoundCountsLabel().setVisible( true );
- getSearchResetButton().setEnabled( true );
- getSearchResetButton().setVisible( true );
+ private void search0( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
+ getSearchFoundCountsLabel0().setVisible( true );
+ getSearchResetButton0().setEnabled( true );
+ getSearchResetButton0().setVisible( true );
+ String[] queries = null;
+ List<PhylogenyNode> nodes = null;
+ if ( query_str.indexOf( ',' ) >= 0 ) {
+ queries = query_str.split( ",+" );
+ }
+ else {
+ queries = new String[ 1 ];
+ queries[ 0 ] = query_str.trim();
+ }
+ if ( ( queries != null ) && ( queries.length > 0 ) ) {
+ nodes = new ArrayList<PhylogenyNode>();
+ for( String query : queries ) {
+ if ( ForesterUtil.isEmpty( query ) ) {
+ continue;
+ }
+ query = query.trim();
+ if ( query.indexOf( '+' ) >= 0 ) {
+ nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ isShowDomainArchitectures() ) );
+ }
+ else {
+ nodes.addAll( PhylogenyMethods.searchData( query,
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ isShowDomainArchitectures() ) );
+ }
+ }
+ if ( getOptions().isInverseSearchResult() ) {
+ final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
+ all.removeAll( nodes );
+ nodes = all;
+ }
+ }
+ if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
+ main_panel.getCurrentTreePanel().setFoundNodes0( new HashSet<Long>() );
+ for( final PhylogenyNode node : nodes ) {
+ main_panel.getCurrentTreePanel().getFoundNodes0().add( node.getId() );
+ }
+ setSearchFoundCountsOnLabel0( nodes.size() );
+ }
+ else {
+ setSearchFoundCountsOnLabel0( 0 );
+ searchReset0();
+ }
+ }
+
+ private void search1( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
+ getSearchFoundCountsLabel1().setVisible( true );
+ getSearchResetButton1().setEnabled( true );
+ getSearchResetButton1().setVisible( true );
String[] queries = null;
List<PhylogenyNode> nodes = null;
if ( query_str.indexOf( ',' ) >= 0 ) {
}
}
if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
- main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Long>() );
+ main_panel.getCurrentTreePanel().setFoundNodes1( new HashSet<Long>() );
for( final PhylogenyNode node : nodes ) {
- main_panel.getCurrentTreePanel().getFoundNodes().add( node.getId() );
+ main_panel.getCurrentTreePanel().getFoundNodes1().add( node.getId() );
}
- setSearchFoundCountsOnLabel( nodes.size() );
+ setSearchFoundCountsOnLabel1( nodes.size() );
}
else {
- setSearchFoundCountsOnLabel( 0 );
- searchReset();
+ setSearchFoundCountsOnLabel1( 0 );
+ searchReset1();
}
}
}
else if ( o == _search_case_senstive_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _search_whole_words_only_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _inverse_search_result_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _show_scale_cbmi ) {
updateOptions( getOptions() );
private void annotateSequences() {
if ( getCurrentTreePanel() != null ) {
- final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
+ final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();
if ( ( nodes == null ) || nodes.isEmpty() ) {
JOptionPane
.showMessageDialog( this,
new Color( 255, 255, 255 ), // branch_color
new Color( 255, 255, 255 ), // box_color
new Color( 255, 255, 0 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_color
+ new Color( 0, 255, 0 ), // found_color 0
+ new Color( 255, 0, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 1 + 2
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
new Color( 255, 255, 255 ), // branch_color
new Color( 255, 255, 255 ), // box_color
new Color( 255, 255, 0 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_color
+ new Color( 0, 255, 0 ), // found_color 0
+ new Color( 255, 0, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 1 + 2
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
new Color( 0, 0, 0 ), // branch_color
new Color( 0, 0, 0 ), // box_color
new Color( 0, 0, 0 ), // collapesed_fill_color
- new Color( 255, 0, 0 ), // found_color
+ new Color( 255, 0, 0 ), // found_color 0
+ new Color( 0, 255, 0 ), // found_color 1
+ new Color( 0, 0, 255 ), // found_color 1 + 2
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
new Color( 240, 240, 240 ), // branch_color
new Color( 140, 140, 140 ), // box_color
new Color( 140, 140, 140 ), // collapesed_fill_color
- new Color( 255, 0, 0 ), // found_color
+ new Color( 255, 0, 0 ), // found_color 0
+ new Color( 0, 255, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 1 + 2
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
new Color( 0, 155, 0 ), // branch_color
new Color( 0, 255, 0 ), // box_color
new Color( 0, 255, 0 ), // collapesed_fill_color
- new Color( 255, 255, 255 ), // found_color
+ new Color( 255, 0, 0 ), // found_color 0
+ new Color( 0, 255, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 1 + 2
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
new Color( 0, 20, 200 ), // branch_color
new Color( 0, 20, 200 ), // box_color
new Color( 255, 255, 0 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_color
+ new Color( 0, 255, 0 ), // found_color 0
+ new Color( 255, 0, 0 ), // found_color 1
+ new Color( 0, 0, 255 ), // found_color 0 + 1
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
new Color( 0, 255, 255 ), // branch_color
new Color( 0, 255, 255 ), // box_color
new Color( 255, 255, 0 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_color
+ new Color( 0, 255, 0 ), // found_color 0
+ new Color( 0, 0, 255 ), // found_color 1
+ new Color( 0, 255, 255 ), // found_color 0 + 1
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
new Color( 255, 200, 0 ), // branch_color
new Color( 255, 200, 0 ), // box_color
new Color( 255, 255, 255 ), // collapesed_fill_color
- new Color( 255, 255, 255 ), // found_color
+ new Color( 255, 255, 0 ), // found_color 0
+ new Color( 0, 255, 255 ), // found_color 1
+ new Color( 255, 255, 255 ), // found_color 0 + 1
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
new Color( 255, 0, 0 ), // box_color
new Color( 0, 0, 0 ), // collapesed_fill_color
new Color( 0, 255, 0 ), // found_color
+ new Color( 255, 0, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 1 + 2
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
new Color( 0, 191, 255 ), // branch_color
new Color( 0, 191, 255 ), // box_color
new Color( 255, 255, 255 ), // collapesed_fill_color
- new Color( 255, 0, 0 ), // found_color
+ new Color( 255, 0, 0 ), // found_color 0
+ new Color( 0, 255, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 0 + 1
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
new Color( 77, 77, 255 ), // branch_length_color
new Color( 234, 173, 234 ), // branch_color
new Color( 77, 77, 255 ), // box_color
- new Color( 77, 77, 255 ), // collapesed_fill_color
- new Color( 243, 243, 21 ), // found_color
+ new Color( 77, 77, 255 ), // collapsed_fill_color
+ new Color( 243, 243, 21 ), // found_color 0
+ new Color( 255,20, 147 ), // found_color 1
+ new Color( 255, 255, 255 ), // found_color 1 + 2
new Color( 255, 0, 0 ), // duplication_box_color
new Color( 0, 255, 0 ), // speciation_box_color
new Color( 255, 255, 0 ), // duplication_speciation_color
private Color dup_box_color;
private Color spec_box_color;
private Color collapse_fill_color;
- private Color found_color;
+ private Color found_color_0;
+ private Color found_color_1;
+ private Color found_color_0_and_1;
private Color duplication_or_specation_color;
private Color domains_color;
private Color binary_domain_combinations_color;
return duplication_or_specation_color;
}
- Color getFoundColor() {
- return found_color;
+ Color getFoundColor0() {
+ return found_color_0;
+ }
+
+ Color getFoundColor1() {
+ return found_color_1;
+ }
+
+ Color getFoundColor0and1() {
+ return found_color_0_and_1;
}
Color getGainedCharactersColor() {
branch_color = _color_schemes[ scheme ][ 6 ];
box_color = _color_schemes[ scheme ][ 7 ];
collapse_fill_color = _color_schemes[ scheme ][ 8 ];
- found_color = _color_schemes[ scheme ][ 9 ];
- dup_box_color = _color_schemes[ scheme ][ 10 ];
- spec_box_color = _color_schemes[ scheme ][ 11 ];
- duplication_or_specation_color = _color_schemes[ scheme ][ 12 ];
- domains_color = _color_schemes[ scheme ][ 13 ];
- binary_domain_combinations_color = _color_schemes[ scheme ][ 14 ];
- annotation_color = _color_schemes[ scheme ][ 15 ];
- ov_color = _color_schemes[ scheme ][ 16 ];
+ found_color_0 = _color_schemes[ scheme ][ 9 ];
+
+ found_color_1 = _color_schemes[ scheme ][ 10 ];
+
+ found_color_0_and_1 = _color_schemes[ scheme ][11 ];
+
+
+ dup_box_color = _color_schemes[ scheme ][ 12 ];
+ spec_box_color = _color_schemes[ scheme ][ 13 ];
+ duplication_or_specation_color = _color_schemes[ scheme ][ 14 ];
+ domains_color = _color_schemes[ scheme ][ 15 ];
+ binary_domain_combinations_color = _color_schemes[ scheme ][ 16 ];
+ annotation_color = _color_schemes[ scheme ][ 17 ];
+ ov_color = _color_schemes[ scheme ][ 18 ];
}
void setCurrentColorScheme( final int color_scheme ) {
private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
private int _subtree_index = 0;
private MainPanel _main_panel = null;
- private Set<Long> _found_nodes = null;
+ private Set<Long> _found_nodes_0 = null;
+ private Set<Long> _found_nodes_1 = null;
+
private PhylogenyNode _highlight_node = null;
private JPopupMenu _node_popup_menu = null;
private JMenuItem _node_popup_menu_items[] = null;
return _domain_structure_e_value_thr_exp;
}
- final Set<Long> getFoundNodes() {
- return _found_nodes;
+ final Set<Long> getFoundNodes0() {
+ return _found_nodes_0;
+ }
+
+ final Set<Long> getFoundNodes1() {
+ return _found_nodes_1;
}
final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
// Check if shift key is down
if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
// Yes, so add to _found_nodes
- if ( getFoundNodes() == null ) {
- setFoundNodes( new HashSet<Long>() );
+ if ( getFoundNodes0() == null ) {
+ setFoundNodes0( new HashSet<Long>() );
}
- getFoundNodes().add( node.getId() );
+ getFoundNodes0().add( node.getId() );
// Check if control key is down
}
else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
root_x + ( Math.cos( angle ) * parent_radius ),
root_y + ( Math.sin( angle ) * parent_radius ),
g );
- paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c )
- || isInCurrentExternalNodes( c ) );
+ paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file );
if ( c.isExternal() ) {
- final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c );
+ final boolean is_in_found_nodes = isInFoundNodes0( c ) || isInFoundNodes1( c ) || isInCurrentExternalNodes( c );
if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
&& ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
return;
root_x + ( Math.cos( angle ) * parent_radius ),
root_y + ( Math.sin( angle ) * parent_radius ),
g );
- if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ if ( ( isInFoundNodes0( c ) && !isInFoundNodes1( c ) ) || isInCurrentExternalNodes( c ) ) {
+ g.setColor( getTreeColorSet().getFoundColor0() );
+ drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
+ }
+ else if ( ( isInFoundNodes1( c ) && !isInFoundNodes0( c ) ) ) {
+ g.setColor( getTreeColorSet().getFoundColor1() );
+ drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
+ }
+ else if ( isInFoundNodes0( c ) && isInFoundNodes1( c ) ) {
+ g.setColor( getTreeColorSet().getFoundColor0and1() );
drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
}
}
}
}
paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
- paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
+ paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file );
+ }
+
+ private boolean isInFoundNodes( PhylogenyNode n ) {
+ return isInFoundNodes0( n ) || isInFoundNodes1( n );
}
final void paintCircularLite( final Phylogeny phy,
}
final void selectNode( final PhylogenyNode node ) {
- if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
- getFoundNodes().remove( node.getId() );
- getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
- if ( getFoundNodes().size() < 1 ) {
- getControlPanel().searchReset();
+ if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) {
+ getFoundNodes0().remove( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
+ if ( getFoundNodes0().size() < 1 ) {
+ getControlPanel().searchReset0();
}
}
else {
- getControlPanel().getSearchFoundCountsLabel().setVisible( true );
- getControlPanel().getSearchResetButton().setEnabled( true );
- getControlPanel().getSearchResetButton().setVisible( true );
- if ( getFoundNodes() == null ) {
- setFoundNodes( new HashSet<Long>() );
+ getControlPanel().getSearchFoundCountsLabel0().setVisible( true );
+ getControlPanel().getSearchResetButton0().setEnabled( true );
+ getControlPanel().getSearchResetButton0().setVisible( true );
+ if ( getFoundNodes0() == null ) {
+ setFoundNodes0( new HashSet<Long>() );
}
- getFoundNodes().add( node.getId() );
- getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
+ getFoundNodes0().add( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
}
}
_current_external_nodes_data_buffer = sb;
}
- final void setFoundNodes( final Set<Long> found_nodes ) {
- _found_nodes = found_nodes;
+ final void setFoundNodes0( final Set<Long> found_nodes ) {
+ _found_nodes_0 = found_nodes;
+ }
+
+ final void setFoundNodes1( final Set<Long> found_nodes ) {
+ _found_nodes_1 = found_nodes;
}
final void setInOvRect( final boolean in_ov_rect ) {
&& ( getCopiedAndPastedNodes() != null )
&& !to_pdf
&& !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getTreeColorSet().getFoundColor0() );
}
else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
_color_chooser.setPreviewPanel( new JPanel() );
SubtreeColorizationActionListener al;
- if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
- final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodes0AsListOfPhylogenyNodes();
al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
}
else {
dialog.setVisible( true );
}
- private List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
+ private List<PhylogenyNode> getFoundNodes0AsListOfPhylogenyNodes() {
final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
- for( final Long id : getFoundNodes() ) {
+ for( final Long id : getFoundNodes0() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ return additional_nodes;
+ }
+
+ private List<PhylogenyNode> getFoundNodes1AsListOfPhylogenyNodes() {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ for( final Long id : getFoundNodes1() ) {
additional_nodes.add( _phylogeny.getNode( id ) );
}
return additional_nodes;
return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
}
- final private boolean isInFoundNodes( final PhylogenyNode node ) {
- return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
+ final private boolean isInFoundNodes0( final PhylogenyNode node ) {
+ return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) );
+ }
+
+ final private boolean isInFoundNodes1( final PhylogenyNode node ) {
+ return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) );
}
final private boolean isInOv() {
}
}
if ( node.isExternal() ) {
- paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
- || isInCurrentExternalNodes( node ) );
+ paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file );
}
}
c = Color.BLACK;
}
else if ( is_in_found_nodes ) {
- c = getTreeColorSet().getFoundColor();
+ c = getColorForFoundNode( node );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
c = getTaxonomyBasedColor( node );
}
}
- final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
+ private final Color getColorForFoundNode( final PhylogenyNode n ) {
+ if ( isInCurrentExternalNodes( n ) ) {
+ return getTreeColorSet().getFoundColor0();
+ }
+ else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor0() ;
+ }
+ else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor1() ;
+ }
+ else {
+ return getTreeColorSet().getFoundColor0and1() ;
+ }
+ }
+
+
+ final private void paintFoundNode( final PhylogenyNode n, final double x, final double y, final Graphics2D g ) {
final int box_size = getOptions().getDefaultNodeShapeSize();
- final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
- g.setColor( getTreeColorSet().getFoundColor() );
- g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
+ final double half_box_size = getOptions().getDefaultNodeShapeSize() / 2.0;
+
+
+
+
+ g.setColor( getColorForFoundNode( n ) );
+ //g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
+ //TODO check me
+ //FIXME
+ _rectangle.setRect( x - half_box_size, y - half_box_size, box_size, box_size );
+ g.fill( _rectangle );
}
final private void paintGainedAndLostCharacters( final Graphics2D g,
final PhylogenyNode node,
final Graphics2D g,
final boolean to_pdf,
- final boolean to_graphics_file,
- final boolean is_in_found_nodes ) {
+ final boolean to_graphics_file ) {
if ( node.isCollapse() ) {
return;
}
// if this node should be highlighted, do so
if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getTreeColorSet().getFoundColor0() );
drawOval( x - 8, y - 8, 16, 16, g );
drawOval( x - 9, y - 8, 17, 17, g );
drawOval( x - 9, y - 9, 18, 18, g );
}
- if ( is_in_found_nodes ) {
- paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
+ if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
+ paintFoundNode( node, x , y , g );
}
else {
Color outline_color = null;
g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( node ) );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( node ) );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
return;
}
if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( node ) );
drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
}
float new_x = 0;
child_node.setYcoord( y2 );
y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
- paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
- || isInCurrentExternalNodes( node ) );
+ paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
}
if ( dynamically_hide
&& !is_in_found_nodes
final float height = getOvMaxHeight() / h_ratio;
final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getTreeColorSet().getFoundColor0() );
getOvRectangle().setRect( x, y, width, height );
final Stroke s = g.getStroke();
g.setStroke( STROKE_1 );
final double w = PhylogenyMethods.getBranchWidthValue( root );
drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
}
- paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
+ paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file );
}
final private void paintScale( final Graphics2D g,
}
else if ( is_in_found_nodes ) {
g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( node ) );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
current_angle += arc_size;
assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
drawLine( x, y, new_x, new_y, g );
- paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc )
- || isInCurrentExternalNodes( desc ) );
+ paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file );
}
if ( n.isRoot() ) {
- paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
+ paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file );
}
}
desc.setXSecondary( new_x );
desc.setYSecondary( new_y );
if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( desc ) );
drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
g.setColor( getTreeColorSet().getOvColor() );
}
private void showExtDescNodeData( final PhylogenyNode node ) {
final List<String> data = new ArrayList<String>();
final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
- if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
- for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) {
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
+ for( final PhylogenyNode n : getFoundNodes0AsListOfPhylogenyNodes() ) {
+ if ( !nodes.contains( n ) ) {
+ nodes.add( n );
+ }
+ }
+ }
+ if ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() ) {
+ for( final PhylogenyNode n : getFoundNodes1AsListOfPhylogenyNodes() ) {
if ( !nodes.contains( n ) ) {
nodes.add( n );
}
else {
setCurrentExternalNodesDataBuffer( sb );
String title;
- if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
: obtainTitleForExtDescNodeData() )
+ " for "
_rollover_popup
.setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
_rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
- if ( isInFoundNodes( node ) ) {
- _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
+ if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
+ }
+ else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
+ }
+ else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
_rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
git://source.jalview.org / jalview.git / commitdiff