inprogress

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 4573a9d..09e5912 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -43,10 +43,10 @@ public final class Constants {
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
     final static String         VERSION                                                       = "0.9811 A1ST";
-    final static String         PRG_DATE                                                      = "130326";
+    final static String         PRG_DATE                                                      = "130327";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
-    final static String[]       DEFAULT_FONT_CHOICES                                          = { "Verdana", "Tahoma",
-            "Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
+    final static String[]       DEFAULT_FONT_CHOICES                                          = { "Arial", "Helvetica",
+            "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans"  };
     final static boolean        VERBOSE_DEFAULT                                               = false;
     final static int            DOMAIN_STRUCTURE_DEFAULT_WIDTH                                = 200;
     final static String         AUTHOR_EMAIL                                                  = "phyloxml@gmail.com";

diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
index 7e11577..b114944 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
@@ -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