X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainPanel.java;h=6551f1bd01ee4b3c387d4dc5f7a326eb05073aad;hb=8d6e81da091d432309f2f7034cf93dbc5ba5e82a;hp=62b7d00ad42dabb61fe06860a5dc5254a6e5befe;hpb=52d04b647ce1ca1cb9652e72e42972b9c8ad748c;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainPanel.java b/forester/java/src/org/forester/archaeopteryx/MainPanel.java
index 62b7d00..6551f1b 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainPanel.java
@@ -24,7 +24,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -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;
 
@@ -222,7 +222,7 @@ public class MainPanel extends JPanel implements ComponentListener {
         // Do nothing.
     }
 
-    private Configuration getConfiguration() {
+    Configuration getConfiguration() {
         return _configuration;
     }
 
@@ -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() );
     }