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" };
+ 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", "Simple", "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
- } };
+ 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( 255, 255, 255 ), // background_color
+ new Color( 0, 255, 255 ), // background_color_gradient_bottom
+ new Color( 0, 0, 153 ), //sequence __ NEW
+ new Color( 0, 0, 102 ), // taxonomy
+ new Color( 0, 0, 204 ), // support
+ new Color( 0, 51, 255 ), // branch_length_color
+ new Color( 0, 0, 0 ), // branch_color
+ new Color( 0, 51, 255 ), // box_color
+ new Color( 0, 51, 255 ), // collapesed_fill_color
+ new Color( 0, 0, 255 ), // found_color 0
+ new Color( 0, 255, 0 ), // found_color 1
+ new Color( 0, 255, 255 ), // found_color 0 + 1
+ new Color( 102, 51, 255 ), // duplication_box_color
+ new Color( 153, 153, 153 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 51, 51, 51), // domain_label
+ new Color( 51, 51, 51 ), // domains_base
+ new Color( 0, 0, 153 ), // binary_domain_combinations_color
+ new Color( 0, 0, 153 ),// annotation
+ new Color( 51, 51, 51 ) // 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;
}
Color getBinaryDomainCombinationsColor() {
- if ( Constants.SPECIAL_CUSTOM ) {
+ if ( AptxConstants.SPECIAL_CUSTOM ) {
return new Color( 50, 50, 50 );
}
return binary_domain_combinations_color;
return box_color;
}
- Color getBranchColor() {
+ public Color getBranchColor() {
return branch_color;
}
return duplication_or_specation_color;
}
- Color getFoundColor0() {
+ public Color getFoundColor0() {
return found_color_0;
}
- Color getFoundColor0and1() {
+ public Color getFoundColor0and1() {
return found_color_0_and_1;
}
- Color getFoundColor1() {
+ public Color getFoundColor1() {
return found_color_1;
}
tcs.setColorforDefault( field, color );
}
catch ( final IllegalArgumentException ex ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, ex.getMessage() );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, ex.getMessage() );
}
}
}