X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreeColorSet.java;h=b11494499b75373f39bd717e8decdf640041a6e7;hb=299c529fea070487998aee60ed7810af57f3a071;hp=9881efac503cd5b63d05c22b853afc32585ae8fc;hpb=03e51d179caedf757b09e2872f9500318bd85a53;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
index 9881efa..b114944 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
@@ -22,7 +22,7 @@
 // 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;
 
@@ -103,9 +103,9 @@ public final class TreeColorSet {
             new Color( 0, 0, 0 ), // box_color
             new Color( 0, 0, 0 ), // collapesed_fill_color
             new Color( 255, 0, 0 ), // found_color
-            new Color( 0, 0, 0 ), // duplication_box_color
-            new Color( 200, 200, 200 ), // speciation_box_color
-            new Color( 0, 0, 0 ), // duplication_speciation_color
+            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 ), // domains_color
             new Color( 0, 0, 0 ), // binary_domain_combinations_color
             new Color( 0, 0, 0 ) // annotation
@@ -121,8 +121,8 @@ public final class TreeColorSet {
             new Color( 140, 140, 140 ), // collapesed_fill_color
             new Color( 255, 0, 0 ), // found_color
             new Color( 255, 0, 0 ), // duplication_box_color
-            new Color( 200, 200, 200 ), // speciation_box_color
-            new Color( 140, 140, 140 ), // duplication_speciation_color
+            new Color( 0, 255, 0 ), // speciation_box_color
+            new Color( 255, 255, 0 ), // duplication_speciation_color
             new Color( 180, 180, 180 ), // domains_color
             new Color( 180, 180, 180 ), // binary_domain_combinations_color
             new Color( 140, 140, 140 ) // annotation
@@ -137,9 +137,9 @@ public final class TreeColorSet {
             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, 255, 255 ), // duplication_box_color
+            new Color( 255, 0, 0 ), // duplication_box_color
             new Color( 0, 255, 0 ), // speciation_box_color
-            new Color( 120, 120, 120 ), // duplication_speciation_color
+            new Color( 255, 255, 0 ), // duplication_speciation_color
             new Color( 0, 235, 0 ), // domains_color
             new Color( 0, 235, 0 ), // binary_domain_combinations_color
             new Color( 0, 235, 0 ) // annotation
@@ -205,9 +205,9 @@ public final class TreeColorSet {
             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, 255 ), // duplication_box_color
-            new Color( 255, 255, 255 ), // speciation_box_color
-            new Color( 100, 100, 100 ), // duplication_speciation_color
+            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 ), // domains_color
             new Color( 255, 255, 255 ), // binary_domain_combinations_color
             new Color( 255, 255, 255 ) // annotation