fixing lining up of domains.

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainPanel.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainPanel.java b/forester/java/src/org/forester/archaeopteryx/MainPanel.java
index f59a3d4..6551f1b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainPanel.java
@@ -66,7 +66,7 @@ public class MainPanel extends JPanel implements ComponentListener {
     private TreeColorSet                     _colorset;
     private TreeFontSet                      _fontset;
     private Phylogeny                        _cut_or_copied_tree;
-    private Set<Integer>                     _copied_and_pasted_nodes;
+    private Set<Long>                        _copied_and_pasted_nodes;
     private Hashtable<String, BufferedImage> _image_map;
     private static Map<String, String>       _lineage_to_rank_map;
 
@@ -230,7 +230,7 @@ public class MainPanel extends JPanel implements ComponentListener {
         return _control_panel;
     }
 
-    public Set<Integer> getCopiedAndPastedNodes() {
+    public Set<Long> getCopiedAndPastedNodes() {
         return _copied_and_pasted_nodes;
     }
 
@@ -388,7 +388,7 @@ public class MainPanel extends JPanel implements ComponentListener {
         repaint();
     }
 
-    public void setCopiedAndPastedNodes( final Set<Integer> node_ids ) {
+    public void setCopiedAndPastedNodes( final Set<Long> node_ids ) {
         _copied_and_pasted_nodes = node_ids;
     }
 
@@ -409,6 +409,7 @@ public class MainPanel extends JPanel implements ComponentListener {
 
     void setupTreeGraphic( final Configuration config_settings, final ControlPanel control ) {
         control.setSpeciesColors( config_settings.getSpeciesColors() );
+        control.setSequenceColors( config_settings.getSequenceColors() );
         control.setAnnotationColors( config_settings.getAnnotationColors() );
         RenderableDomainArchitecture.setColorMap( config_settings.getDomainColors() );
     }