X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreeColorSet.java;h=56c2cc171ad3669cd3dc570e25d55dee25a319d7;hb=26d8d47ed32a0eb9bd43c409d0e26ff13570b246;hp=c83d135410c27e960dcc73834b24bc42195ab52f;hpb=54d8e3a926c3cf3477199c8b85aca478230e223c;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java index c83d135..56c2cc1 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java +++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java @@ -54,233 +54,266 @@ 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 }; - 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; @@ -341,7 +374,7 @@ 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 +525,7 @@ 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() ); } } }