X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=bb31d7efdf239b047fa02f14737ff3b4fe33d007;hb=06b38f91bc061d8ab1dfea3b6238c94c95a30d26;hp=971afb342a8cb5614a02357ca6101c8bd910afca;hpb=f642399d323502c48c4ccb25ad6a4268a4152e6a;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 971afb3..bb31d7e 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -136,6 +136,7 @@ import org.forester.util.TaxonomyUtil;
 
 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 );
@@ -1096,7 +1097,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     && ( 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 {
@@ -4158,6 +4166,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         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 )