-/*
- * Maintains the color schemes and a set of colors for drawing a tree.
- */
-final class TreeColorSet {
-
- static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", "The Matrix",
- "White & Blue", "Cyan", "Clockwork", "Blue", "Blue & White", "Neon" };
- static final String[] COLOR_FIELDS = { "Background", "Background Gradient Bottom", "Sequence", "Taxonomy",
- "Confidence", "Branch Length", "Branch", "Node Box", "Collapsed", "Matching Nodes", "Duplication",
- "Speciation", "Duplication or Specation", "Domains", "Binary Domain Combinations", "Annotation", "Overview" };
- // All the color sets; better be the same # of sets as there are names!
- private final Color[][] _color_schemes = { { new Color( 0, 0, 0 ), // background_color
- new Color( 0, 100, 100 ), // background_color_gradient_bottom
- new Color( 220, 220, 220 ), // sequence __ Default (same as Black)
- new Color( 180, 180, 180 ), // taxonomy
- new Color( 56, 176, 222 ), // 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, 0 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_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( 123, 104, 238 ), // domains_color
- 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( 220, 220, 220 ), // sequence __ Black
- new Color( 180, 180, 180 ), // taxonomy
- new Color( 56, 176, 222 ), // 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, 0 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_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( 123, 104, 238 ), // domains_color
- 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
- 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( 0, 0, 0 ), // domains_color
- 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( 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( 180, 180, 180 ), // domains_color
- 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, 255, 0 ), // collapesed_fill_color
- new Color( 255, 255, 255 ), // found_color
- new Color( 255, 255, 255 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 120, 120, 120 ), // 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
- , 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( 255, 255, 0 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_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( 123, 104, 238 ), // domains_color
- 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( 255, 255, 0 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_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( 123, 104, 238 ), // domains_color
- 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, 255, 255 ), // collapesed_fill_color
- new Color( 255, 255, 255 ), // found_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( 150, 150, 150 ), // domains_color
- 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( 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, 255, 255 ), // domains_color
- 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( 255, 255, 255 ), // collapesed_fill_color
- new Color( 255, 0, 0 ), // found_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
- , 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( 77, 77, 255 ), // collapesed_fill_color
- new Color( 243, 243, 21 ), // found_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( 27, 255, 0 ), // domains_color
- new Color( 27, 255, 0 ), // binary_domain_combinations_color
- new Color( 27, 255, 0 ) // annotation
- , new Color( 77, 77, 255 ) // ov
- } };
- // Color schemes:
- private int _color_scheme;
+public final class TreeColorSet {
+
+ public static final String ANNOTATION = "Annotation";
+ public static final String BACKGROUND = "Background";
+ public static final String BACKGROUND_GRADIENT_BOTTOM = "Background Gradient Bottom";
+ public static final String BINARY_DOMAIN_COMBINATIONS = "Binary Domain Combinations";
+ public static final String BRANCH = "Branch";
+ public static final String BRANCH_LENGTH = "Branch Length";
+ public static final String COLLAPSED = "Collapsed";
+ public static final String CONFIDENCE = "Confidence";
+ public static final String DOMAIN_LABEL = "Domain Label";
+ public static final String DOMAIN_BASE = "Domain Base";
+ public static final String DUPLICATION = "Duplication";
+ public static final String DUPLICATION_OR_SPECATION = "Duplication or Specation";
+ public static final String MATCHING_NODES_A = "Matching A";
+ public static final String MATCHING_NODES_A_AND_B = "Matching A and B";
+ public static final String MATCHING_NODES_B = "Matching B";
+ public static final String NODE_BOX = "Node Box";
+ public static final String OVERVIEW = "Overview";
+ public static final String SEQUENCE = "Sequence";
+ 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 };
+ static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", "Green",
+ "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
+ } };
+ private Color annotation_color;
+ private Color background_color;
+ private Color background_color_gradient_bottom;
+ private Color binary_domain_combinations_color;
+ private Color bootstrap_color;
+ private Color box_color;
+ private Color branch_color;
+ private Color branch_length_color;
+ private Color collapse_fill_color;
+ private Color domain_label_color;
+ private Color domain_base_color;
+ private Color dup_box_color;
+ private Color duplication_or_specation_color;
+ private Color found_color_0;
+ private Color found_color_0_and_1;
+ private Color found_color_1;
+ private Color ov_color;