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Fixed issue with reading from TreeBase
[jalview.git] / forester / java / src / org / forester / archaeopteryx / TreeColorSet.java
diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
index c83d135..f90ec22 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
@@ -54,233 +54,233 @@ public final class TreeColorSet {
     public static final String SPECIATION                 = "Speciation";
     public static final String TAXONOMY                   = "Taxonomy";
     static final String[]      COLOR_FIELDS               = { BACKGROUND, BACKGROUND_GRADIENT_BOTTOM, SEQUENCE,
-        TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B,
-        MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAIN_LABEL, DOMAIN_BASE,
-        BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW };
+            TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B,
+            MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAIN_LABEL, DOMAIN_BASE,
+            BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW };
     static final String[]      SCHEME_NAMES               = { "Default", "Black", "Black & White", "Silver", "Green",
-        "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" };
+            "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" };
     private int                _color_scheme;
     private final Color[][]    _color_schemes             = { { new Color( 0, 0, 0 ), // background_color
-        new Color( 0, 100, 100 ), // background_color_gradient_bottom
-        new Color( 230, 230, 230 ), // sequence  __ Default (same as Black)
-        new Color( 180, 180, 180 ), // taxonomy
-        new Color( 180, 180, 180 ), // support
-        new Color( 140, 140, 140 ), // branch_length_color
-        new Color( 255, 255, 255 ), // branch_color
-        new Color( 255, 255, 255 ), // box_color
-        new Color( 255, 255, 255 ), // collapesed_fill_color
-        new Color( 0, 255, 0 ), // found_color 0
-        new Color( 255, 0, 0 ), // found_color 1
-        new Color( 255, 255, 0 ), // found_color 1 + 2
-        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( 230, 230, 230 ), // domain_label
-        new Color( 100, 100, 100 ), // domains_base
-        new Color( 65, 105, 255 ), // binary_domain_combinations_color
-        new Color( 173, 255, 47 ) // annotation
-    , new Color( 130, 130, 130 )                 // overview
-    }, { new Color( 0, 0, 0 ), // background_color
-        new Color( 0, 255, 255 ), // background_color_gradient_bottom
-        new Color( 230, 230, 230 ), // sequence  __ Black
-        new Color( 180, 180, 180 ), // taxonomy
-        new Color( 180, 180, 180 ), // support
-        new Color( 140, 140, 140 ), // branch_length_color
-        new Color( 255, 255, 255 ), // branch_color
-        new Color( 255, 255, 255 ), // box_color
-        new Color( 255, 255, 255 ), // collapesed_fill_color
-        new Color( 0, 255, 0 ), // found_color 0
-        new Color( 255, 0, 0 ), // found_color 1
-        new Color( 255, 255, 0 ), // found_color 1 + 2
-        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( 230, 230, 230 ), // domain_label
-        new Color( 100, 100, 100 ), // domains_base
-        new Color( 65, 105, 255 ), // binary_domain_combinations_color
-        new Color( 173, 255, 47 ) // annotation
-    , new Color( 130, 130, 130 ) // ov
-    }, { new Color( 255, 255, 255 ), // background_color
-        new Color( 0, 255, 255 ), // background_color_gradient_bottom
-        new Color( 0, 0, 0 ), // sequence  __ Black & White
-        new Color( 0, 0, 0 ), // taxonomy
-        new Color( 0, 0, 0 ), // support
-        new Color( 0, 0, 0 ), // branch_length_color
-        new Color( 0, 0, 0 ), // branch_color
-        new Color( 0, 0, 0 ), // box_color
-        new Color( 0, 0, 0 ), // collapesed_fill_color
-        new Color( 255, 0, 0 ), // found_color 0
-        new Color( 0, 255, 0 ), // found_color 1
-        new Color( 0, 0, 255 ), // found_color 1 + 2
-        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 ), // domain_label
-        new Color( 100, 100, 100 ), // domains_base
-        new Color( 0, 0, 0 ), // binary_domain_combinations_color
-        new Color( 0, 0, 0 ) // annotation
-    , new Color( 220, 220, 220 ) // ov
-    }, { new Color( 0, 0, 0 ), // background_color
-        new Color( 0, 255, 255 ), // background_color_gradient_bottom
-        new Color( 220, 220, 220 ), // sequence __ Silver
-        new Color( 180, 180, 180 ), // taxonomy
-        new Color( 140, 140, 140 ), // support
-        new Color( 140, 140, 140 ), // branch_length_color
-        new Color( 240, 240, 240 ), // branch_color
-        new Color( 140, 140, 140 ), // box_color
-        new Color( 240, 240, 240 ), // collapesed_fill_color
-        new Color( 255, 0, 0 ), // found_color 0
-        new Color( 0, 255, 0 ), // found_color 1
-        new Color( 255, 255, 0 ), // found_color 1 + 2
-        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( 230, 230, 230 ), // domain_label
-        new Color( 100, 100, 100 ), // domains_base
-        new Color( 180, 180, 180 ), // binary_domain_combinations_color
-        new Color( 140, 140, 140 ) // annotation
-    , new Color( 40, 40, 40 ) // ov
-    }, { new Color( 0, 10, 0 ), // background_color
-        new Color( 0, 255, 255 ), // background_color_gradient_bottom
-        new Color( 0, 255, 0 ), // sequence __ the Matrix
-        new Color( 30, 200, 30 ), // taxonomy
-        new Color( 0, 155, 0 ), // support
-        new Color( 0, 100, 0 ), // branch_length_color
-        new Color( 0, 155, 0 ), // branch_color
-        new Color( 0, 255, 0 ), // box_color
-        new Color( 0, 155, 0 ), // collapesed_fill_color
-        new Color( 255, 0, 0 ), // found_color 0
-        new Color( 0, 255, 0 ), // found_color 1
-        new Color( 255, 255, 0 ), // found_color 1 + 2
-        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( 230, 230, 230 ), // domain_label
-        new Color( 100, 100, 100 ), // domains_base
-        new Color( 0, 235, 0 ), // binary_domain_combinations_color
-        new Color( 0, 235, 0 ) // annotation
-    , new Color( 40, 40, 40 ) // ov
-    }, { new Color( 255, 255, 255 ), // background_color
-        new Color( 0, 255, 255 ), // background_color_gradient_bottom
-        new Color( 0, 0, 0 ), //sequence __ White & Blue
-        new Color( 40, 40, 40 ), // taxonomy
-        new Color( 0, 125, 0 ), // support
-        new Color( 70, 70, 0 ), // branch_length_color
-        new Color( 0, 20, 200 ), // branch_color
-        new Color( 0, 20, 200 ), // box_color
-        new Color( 0, 20, 200 ), // collapesed_fill_color
-        new Color( 0, 255, 0 ), // found_color 0
-        new Color( 255, 0, 0 ), // found_color 1
-        new Color( 0, 0, 255 ), // found_color 0 + 1
-        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 ), // domain_label
-        new Color( 50, 50, 50 ), // domains_base
-        new Color( 65, 105, 225 ), // binary_domain_combinations_color
-        new Color( 173, 255, 47 ) // annotation
-    , new Color( 220, 220, 220 ) // ov
-    }, { new Color( 0, 0, 0 ), // background_color
-        new Color( 0, 255, 255 ), // background_color_gradient_bottom
-        new Color( 255, 255, 255 ), // sequence __ Cyan
-        new Color( 200, 200, 200 ), // taxonomy
-        new Color( 255, 255, 255 ), // support
-        new Color( 200, 200, 200 ), // branch_length_color
-        new Color( 0, 255, 255 ), // branch_color
-        new Color( 0, 255, 255 ), // box_color
-        new Color( 0, 255, 255 ), // collapesed_fill_color
-        new Color( 0, 255, 0 ), // found_color 0
-        new Color( 0, 0, 255 ), // found_color 1
-        new Color( 0, 255, 255 ), // found_color 0 + 1
-        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( 230, 230, 230 ), // domain_label
-        new Color( 100, 100, 100 ), // domains_base
-        new Color( 65, 105, 225 ), // binary_domain_combinations_color
-        new Color( 173, 255, 47 ) // annotation
-    , new Color( 0, 120, 120 ) // ov
-    }, { new Color( 0, 0, 0 ), // background_color
-        new Color( 0, 255, 255 ), // background_color_gradient_bottom
-        new Color( 255, 200, 0 ), // sequence __ Clockwork
-        new Color( 255, 200, 0 ), // taxonomy
-        new Color( 255, 200, 0 ), // support
-        new Color( 255, 200, 0 ), // branch_length_color
-        new Color( 255, 200, 0 ), // branch_color
-        new Color( 255, 200, 0 ), // box_color
-        new Color( 255, 200, 0 ), // collapesed_fill_color
-        new Color( 255, 255, 0 ), // found_color 0
-        new Color( 0, 255, 255 ), // found_color 1
-        new Color( 255, 255, 255 ), // found_color 0 + 1
-        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, 200, 0 ), // domain_label
-        new Color( 255, 200, 0 ), // domains_base
-        new Color( 150, 150, 150 ), // binary_domain_combinations_color
-        new Color( 150, 150, 150 ) // annotation
-    , new Color( 150, 150, 150 ) // ov
-    }, { new Color( 0, 0, 100 ), // background_color
-        new Color( 0, 255, 255 ), // background_color_gradient_bottom
-        new Color( 255, 255, 255 ), // sequence __ Blue
-        new Color( 255, 255, 255 ), // taxonomy
-        new Color( 255, 0, 0 ), // support
-        new Color( 255, 0, 0 ), // branch_length_color
-        new Color( 255, 0, 0 ), // branch_color
-        new Color( 255, 0, 0 ), // box_color
-        new Color( 255, 0, 0 ), // collapesed_fill_color
-        new Color( 0, 255, 0 ), // found_color
-        new Color( 255, 0, 0 ), // found_color 1
-        new Color( 255, 255, 0 ), // found_color 1 + 2
-        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 ), // domain_label
-        new Color( 100, 100, 100 ), // domains_base
-        new Color( 255, 255, 255 ), // binary_domain_combinations_color
-        new Color( 255, 255, 255 ) // annotation
-    , new Color( 77, 77, 255 ) // ov
-    }, { new Color( 0, 0, 0 ), // background_color
-        new Color( 0, 255, 255 ), // background_color_gradient_bottom
-        new Color( 255, 255, 255 ), // sequence __ blue &  white
-        new Color( 255, 255, 255 ), // taxonomy
-        new Color( 255, 255, 255 ), // support
-        new Color( 0, 191, 255 ), // branch_length_color
-        new Color( 0, 191, 255 ), // branch_color
-        new Color( 0, 191, 255 ), // box_color
-        new Color( 0, 191, 255 ), // collapesed_fill_color
-        new Color( 255, 0, 0 ), // found_color 0
-        new Color( 0, 255, 0 ), // found_color 1
-        new Color( 255, 255, 0 ), // found_color 0 + 1
-        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 ), // domain_label
-        new Color( 150, 150, 150 ), // domains_base
-        new Color( 255, 255, 255 ), // binary_domain_combinations_color
-        new Color( 255, 255, 255 ) // annotation
-    , new Color( 170, 187, 204 ) // ov
-    }, { new Color( 0, 0, 0 ), // background_color
-        new Color( 255, 255, 0 ), // background_color_gradient_bottom
-        new Color( 127, 255, 0 ), // sequence __ Neon
-        new Color( 255, 110, 199 ), // taxonomy
-        new Color( 234, 173, 234 ), // support
-        new Color( 77, 77, 255 ), // branch_length_color
-        new Color( 234, 173, 234 ), // branch_color
-        new Color( 77, 77, 255 ), // box_color
-        new Color( 234, 173, 234 ), // collapsed_fill_color
-        new Color( 243, 243, 21 ), // found_color 0
-        new Color( 255, 20, 147 ), // found_color 1
-        new Color( 255, 255, 255 ), // found_color 1 + 2
-        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( 127, 255, 0 ), // domain_label
-        new Color( 234, 173, 234 ), // domains_base
-        new Color( 27, 255, 0 ), // binary_domain_combinations_color
-        new Color( 27, 255, 0 ) // annotation
-    , new Color( 77, 77, 255 ) // ov
-    }                                            };
+            new Color( 0, 100, 100 ), // background_color_gradient_bottom
+            new Color( 230, 230, 230 ), // sequence  __ Default (same as Black)
+            new Color( 180, 180, 180 ), // taxonomy
+            new Color( 180, 180, 180 ), // support
+            new Color( 140, 140, 140 ), // branch_length_color
+            new Color( 255, 255, 255 ), // branch_color
+            new Color( 255, 255, 255 ), // box_color
+            new Color( 255, 255, 255 ), // collapesed_fill_color
+            new Color( 0, 255, 0 ), // found_color 0
+            new Color( 255, 0, 0 ), // found_color 1
+            new Color( 255, 255, 0 ), // found_color 1 + 2
+            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( 230, 230, 230 ), // domain_label
+            new Color( 100, 100, 100 ), // domains_base
+            new Color( 65, 105, 255 ), // binary_domain_combinations_color
+            new Color( 173, 255, 47 ) // annotation
+            , new Color( 130, 130, 130 )                 // overview
+            }, { new Color( 0, 0, 0 ), // background_color
+            new Color( 0, 255, 255 ), // background_color_gradient_bottom
+            new Color( 230, 230, 230 ), // sequence  __ Black
+            new Color( 180, 180, 180 ), // taxonomy
+            new Color( 180, 180, 180 ), // support
+            new Color( 140, 140, 140 ), // branch_length_color
+            new Color( 255, 255, 255 ), // branch_color
+            new Color( 255, 255, 255 ), // box_color
+            new Color( 255, 255, 255 ), // collapesed_fill_color
+            new Color( 0, 255, 0 ), // found_color 0
+            new Color( 255, 0, 0 ), // found_color 1
+            new Color( 255, 255, 0 ), // found_color 1 + 2
+            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( 230, 230, 230 ), // domain_label
+            new Color( 100, 100, 100 ), // domains_base
+            new Color( 65, 105, 255 ), // binary_domain_combinations_color
+            new Color( 173, 255, 47 ) // annotation
+            , new Color( 130, 130, 130 ) // ov
+            }, { new Color( 255, 255, 255 ), // background_color
+            new Color( 0, 255, 255 ), // background_color_gradient_bottom
+            new Color( 0, 0, 0 ), // sequence  __ Black & White
+            new Color( 0, 0, 0 ), // taxonomy
+            new Color( 0, 0, 0 ), // support
+            new Color( 0, 0, 0 ), // branch_length_color
+            new Color( 0, 0, 0 ), // branch_color
+            new Color( 0, 0, 0 ), // box_color
+            new Color( 0, 0, 0 ), // collapesed_fill_color
+            new Color( 255, 0, 0 ), // found_color 0
+            new Color( 0, 255, 0 ), // found_color 1
+            new Color( 0, 0, 255 ), // found_color 1 + 2
+            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 ), // domain_label
+            new Color( 100, 100, 100 ), // domains_base
+            new Color( 0, 0, 0 ), // binary_domain_combinations_color
+            new Color( 0, 0, 0 ) // annotation
+            , new Color( 220, 220, 220 ) // ov
+            }, { new Color( 0, 0, 0 ), // background_color
+            new Color( 0, 255, 255 ), // background_color_gradient_bottom
+            new Color( 220, 220, 220 ), // sequence __ Silver
+            new Color( 180, 180, 180 ), // taxonomy
+            new Color( 140, 140, 140 ), // support
+            new Color( 140, 140, 140 ), // branch_length_color
+            new Color( 240, 240, 240 ), // branch_color
+            new Color( 140, 140, 140 ), // box_color
+            new Color( 240, 240, 240 ), // collapesed_fill_color
+            new Color( 255, 0, 0 ), // found_color 0
+            new Color( 0, 255, 0 ), // found_color 1
+            new Color( 255, 255, 0 ), // found_color 1 + 2
+            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( 230, 230, 230 ), // domain_label
+            new Color( 100, 100, 100 ), // domains_base
+            new Color( 180, 180, 180 ), // binary_domain_combinations_color
+            new Color( 140, 140, 140 ) // annotation
+            , new Color( 40, 40, 40 ) // ov
+            }, { new Color( 0, 10, 0 ), // background_color
+            new Color( 0, 255, 255 ), // background_color_gradient_bottom
+            new Color( 0, 255, 0 ), // sequence __ the Matrix
+            new Color( 30, 200, 30 ), // taxonomy
+            new Color( 0, 155, 0 ), // support
+            new Color( 0, 100, 0 ), // branch_length_color
+            new Color( 0, 155, 0 ), // branch_color
+            new Color( 0, 255, 0 ), // box_color
+            new Color( 0, 155, 0 ), // collapesed_fill_color
+            new Color( 255, 0, 0 ), // found_color 0
+            new Color( 0, 255, 0 ), // found_color 1
+            new Color( 255, 255, 0 ), // found_color 1 + 2
+            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( 230, 230, 230 ), // domain_label
+            new Color( 100, 100, 100 ), // domains_base
+            new Color( 0, 235, 0 ), // binary_domain_combinations_color
+            new Color( 0, 235, 0 ) // annotation
+            , new Color( 40, 40, 40 ) // ov
+            }, { new Color( 255, 255, 255 ), // background_color
+            new Color( 0, 255, 255 ), // background_color_gradient_bottom
+            new Color( 0, 0, 0 ), //sequence __ White & Blue
+            new Color( 40, 40, 40 ), // taxonomy
+            new Color( 0, 125, 0 ), // support
+            new Color( 70, 70, 0 ), // branch_length_color
+            new Color( 0, 20, 200 ), // branch_color
+            new Color( 0, 20, 200 ), // box_color
+            new Color( 0, 20, 200 ), // collapesed_fill_color
+            new Color( 0, 255, 0 ), // found_color 0
+            new Color( 255, 0, 0 ), // found_color 1
+            new Color( 0, 0, 255 ), // found_color 0 + 1
+            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 ), // domain_label
+            new Color( 50, 50, 50 ), // domains_base
+            new Color( 65, 105, 225 ), // binary_domain_combinations_color
+            new Color( 173, 255, 47 ) // annotation
+            , new Color( 220, 220, 220 ) // ov
+            }, { new Color( 0, 0, 0 ), // background_color
+            new Color( 0, 255, 255 ), // background_color_gradient_bottom
+            new Color( 255, 255, 255 ), // sequence __ Cyan
+            new Color( 200, 200, 200 ), // taxonomy
+            new Color( 255, 255, 255 ), // support
+            new Color( 200, 200, 200 ), // branch_length_color
+            new Color( 0, 255, 255 ), // branch_color
+            new Color( 0, 255, 255 ), // box_color
+            new Color( 0, 255, 255 ), // collapesed_fill_color
+            new Color( 0, 255, 0 ), // found_color 0
+            new Color( 0, 0, 255 ), // found_color 1
+            new Color( 0, 255, 255 ), // found_color 0 + 1
+            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( 230, 230, 230 ), // domain_label
+            new Color( 100, 100, 100 ), // domains_base
+            new Color( 65, 105, 225 ), // binary_domain_combinations_color
+            new Color( 173, 255, 47 ) // annotation
+            , new Color( 0, 120, 120 ) // ov
+            }, { new Color( 0, 0, 0 ), // background_color
+            new Color( 0, 255, 255 ), // background_color_gradient_bottom
+            new Color( 255, 200, 0 ), // sequence __ Clockwork
+            new Color( 255, 200, 0 ), // taxonomy
+            new Color( 255, 200, 0 ), // support
+            new Color( 255, 200, 0 ), // branch_length_color
+            new Color( 255, 200, 0 ), // branch_color
+            new Color( 255, 200, 0 ), // box_color
+            new Color( 255, 200, 0 ), // collapesed_fill_color
+            new Color( 255, 255, 0 ), // found_color 0
+            new Color( 0, 255, 255 ), // found_color 1
+            new Color( 255, 255, 255 ), // found_color 0 + 1
+            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, 200, 0 ), // domain_label
+            new Color( 255, 200, 0 ), // domains_base
+            new Color( 150, 150, 150 ), // binary_domain_combinations_color
+            new Color( 150, 150, 150 ) // annotation
+            , new Color( 150, 150, 150 ) // ov
+            }, { new Color( 0, 0, 100 ), // background_color
+            new Color( 0, 255, 255 ), // background_color_gradient_bottom
+            new Color( 255, 255, 255 ), // sequence __ Blue
+            new Color( 255, 255, 255 ), // taxonomy
+            new Color( 255, 0, 0 ), // support
+            new Color( 255, 0, 0 ), // branch_length_color
+            new Color( 255, 0, 0 ), // branch_color
+            new Color( 255, 0, 0 ), // box_color
+            new Color( 255, 0, 0 ), // collapesed_fill_color
+            new Color( 0, 255, 0 ), // found_color
+            new Color( 255, 0, 0 ), // found_color 1
+            new Color( 255, 255, 0 ), // found_color 1 + 2
+            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 ), // domain_label
+            new Color( 100, 100, 100 ), // domains_base
+            new Color( 255, 255, 255 ), // binary_domain_combinations_color
+            new Color( 255, 255, 255 ) // annotation
+            , new Color( 77, 77, 255 ) // ov
+            }, { new Color( 0, 0, 0 ), // background_color
+            new Color( 0, 255, 255 ), // background_color_gradient_bottom
+            new Color( 255, 255, 255 ), // sequence __ blue &  white
+            new Color( 255, 255, 255 ), // taxonomy
+            new Color( 255, 255, 255 ), // support
+            new Color( 0, 191, 255 ), // branch_length_color
+            new Color( 0, 191, 255 ), // branch_color
+            new Color( 0, 191, 255 ), // box_color
+            new Color( 0, 191, 255 ), // collapesed_fill_color
+            new Color( 255, 0, 0 ), // found_color 0
+            new Color( 0, 255, 0 ), // found_color 1
+            new Color( 255, 255, 0 ), // found_color 0 + 1
+            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 ), // domain_label
+            new Color( 150, 150, 150 ), // domains_base
+            new Color( 255, 255, 255 ), // binary_domain_combinations_color
+            new Color( 255, 255, 255 ) // annotation
+            , new Color( 170, 187, 204 ) // ov
+            }, { new Color( 0, 0, 0 ), // background_color
+            new Color( 255, 255, 0 ), // background_color_gradient_bottom
+            new Color( 127, 255, 0 ), // sequence __ Neon
+            new Color( 255, 110, 199 ), // taxonomy
+            new Color( 234, 173, 234 ), // support
+            new Color( 77, 77, 255 ), // branch_length_color
+            new Color( 234, 173, 234 ), // branch_color
+            new Color( 77, 77, 255 ), // box_color
+            new Color( 234, 173, 234 ), // collapsed_fill_color
+            new Color( 243, 243, 21 ), // found_color 0
+            new Color( 255, 20, 147 ), // found_color 1
+            new Color( 255, 255, 255 ), // found_color 1 + 2
+            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( 127, 255, 0 ), // domain_label
+            new Color( 234, 173, 234 ), // domains_base
+            new Color( 27, 255, 0 ), // binary_domain_combinations_color
+            new Color( 27, 255, 0 ) // annotation
+            , new Color( 77, 77, 255 ) // ov
+            }                                            };
     private Color              annotation_color;
     private Color              background_color;
     private Color              background_color_gradient_bottom;
@@ -341,7 +341,7 @@ public final class TreeColorSet {
     }
 
     Color getBinaryDomainCombinationsColor() {
-        if ( Constants.SPECIAL_CUSTOM ) {
+        if ( AptxConstants.SPECIAL_CUSTOM ) {
             return new Color( 50, 50, 50 );
         }
         return binary_domain_combinations_color;
@@ -492,7 +492,7 @@ public final class TreeColorSet {
                     tcs.setColorforDefault( field, color );
                 }
                 catch ( final IllegalArgumentException ex ) {
-                    ForesterUtil.printWarningMessage( Constants.PRG_NAME, ex.getMessage() );
+                    ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, ex.getMessage() );
                 }
             }
         }