public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
+ public final static boolean SPECIAL_DOMAIN_COLORING = true;
final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
RenderableDomainArchitecture rds = null;
if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
- rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture() );
+ if ( SPECIAL_DOMAIN_COLORING ) {
+ rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
+ .getDomainArchitecture(), node.getName() );
+ }
+ else {
+ rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
+ .getDomainArchitecture() );
+ }
node.getNodeData().getSequence().setDomainArchitecture( rds );
}
else {
final void sortDescendants( final PhylogenyNode node ) {
if ( !node.isExternal() ) {
- DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
- if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
- .isShowTaxonomyCommonNames() ) ) {
- if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowSeqNames() || getControlPanel()
- .isShowSeqSymbols() ) ) {
- pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
- }
- else if ( getControlPanel().isShowNodeNames() ) {
- pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
- }
+ DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
+ if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
+ pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
+ }
+ else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols()
+ || getControlPanel().isShowGeneNames() ) {
+ pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
}
PhylogenyMethods.sortNodeDescendents( node, pri );
setNodeInPreorderToNull();
getControlPanel().getUseVisualStylesCb().setSelected( true );
}
}
+ setEdited( true );
repaint();
}
al = new NodeColorizationActionListener( _color_chooser, node );
}
final JDialog dialog = JColorChooser.createDialog( this, "Node colorization", true, _color_chooser, al, null );
+ setEdited( true );
dialog.setVisible( true );
}
}
final JDialog dialog = JColorChooser
.createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
+ setEdited( true );
dialog.setVisible( true );
}
if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
|| ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
|| ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
+ || ( getOptions().isShowDefaultNodeShapesForMarkedNodes()
+ && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData()
+ .getNodeVisualData().isEmpty() ) )
|| ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node
.getNodeData().getNodeVisualData().getNodeColor() != null )
|| ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )