X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreeColorSet.java;h=44e050bcebb6e16c95cfc033c94d913322b68c47;hb=4e20c9132065232b26afd38e8ce371b353a2686d;hp=b11494499b75373f39bd717e8decdf640041a6e7;hpb=5ddbd83b67f268536509c2382425b1f2d69298af;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java index b114944..44e050b 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java +++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java @@ -36,39 +36,46 @@ import org.forester.util.ForesterUtil; */ public final class TreeColorSet { - public static final String OVERVIEW = "Overview"; 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 DOMAINS = "Domains"; - public static final String DUPLICATION_OR_SPECATION = "Duplication or Specation"; - public static final String SPECIATION = "Speciation"; - public static final String DUPLICATION = "Duplication"; - public static final String MATCHING_NODES = "Matching Nodes"; - public static final String COLLAPSED = "Collapsed"; - public static final String NODE_BOX = "Node Box"; 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 TAXONOMY = "Taxonomy"; + public static final String DOMAINS = "Domains"; + 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 BACKGROUND_GRADIENT_BOTTOM = "Background Gradient Bottom"; - public static final String BACKGROUND = "Background"; - static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", - "The Matrix", "White & Blue", "Cyan", "Clockwork", "Blue", "Blue & White", "Neon" }; + 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, DUPLICATION, SPECIATION, - DUPLICATION_OR_SPECATION, DOMAINS, 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, DOMAINS, + BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW }; + static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", "Green", + "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" }; + // Color schemes: + private int _color_scheme; // 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( 230, 230, 230 ), // sequence __ Default (same as Black) new Color( 180, 180, 180 ), // taxonomy - new Color( 56, 176, 222 ), // support + new Color( 56, 176, 255 ), // 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, 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 @@ -78,14 +85,16 @@ public final class TreeColorSet { , 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( 230, 230, 230 ), // sequence __ Black new Color( 180, 180, 180 ), // taxonomy - new Color( 56, 176, 222 ), // support + new Color( 56, 176, 255 ), // 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, 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 @@ -102,7 +111,9 @@ public final class TreeColorSet { 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( 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 @@ -118,8 +129,10 @@ public final class TreeColorSet { 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( 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 @@ -135,8 +148,10 @@ public final class TreeColorSet { 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( 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 @@ -152,8 +167,10 @@ public final class TreeColorSet { 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( 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 @@ -169,8 +186,10 @@ public final class TreeColorSet { 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( 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 @@ -186,8 +205,10 @@ public final class TreeColorSet { 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, 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 @@ -203,8 +224,10 @@ public final class TreeColorSet { 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( 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 @@ -220,8 +243,10 @@ public final class TreeColorSet { 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( 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 @@ -237,8 +262,10 @@ public final class TreeColorSet { 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( 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 @@ -247,26 +274,26 @@ public final class TreeColorSet { new Color( 27, 255, 0 ) // annotation , new Color( 77, 77, 255 ) // ov } }; - // Color schemes: - private int _color_scheme; - // The drawing colors - private Color seq_color; - private Color taxonomy_color; - private Color bootstrap_color; - private Color branch_length_color; - private Color branch_color; - private Color box_color; + private Color annotation_color; private Color background_color; private Color background_color_gradient_bottom; - private Color dup_box_color; - private Color spec_box_color; + 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 found_color; - private Color duplication_or_specation_color; private Color domains_color; - private Color binary_domain_combinations_color; - private Color annotation_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; + // The drawing colors + private Color seq_color; + private Color spec_box_color; + private Color taxonomy_color; private TreeColorSet() { // Hidden constructor. @@ -348,8 +375,16 @@ public final class TreeColorSet { return duplication_or_specation_color; } - Color getFoundColor() { - return found_color; + Color getFoundColor0() { + return found_color_0; + } + + Color getFoundColor0and1() { + return found_color_0_and_1; + } + + Color getFoundColor1() { + return found_color_1; } Color getGainedCharactersColor() { @@ -393,10 +428,6 @@ public final class TreeColorSet { } } - private void setColorForDefault( final int i, final Color color ) { - _color_schemes[ 0 ][ i ] = color; - } - /** * Switches colors between different schemes. */ @@ -411,20 +442,26 @@ public final class TreeColorSet { branch_color = _color_schemes[ scheme ][ 6 ]; box_color = _color_schemes[ scheme ][ 7 ]; collapse_fill_color = _color_schemes[ scheme ][ 8 ]; - found_color = _color_schemes[ scheme ][ 9 ]; - dup_box_color = _color_schemes[ scheme ][ 10 ]; - spec_box_color = _color_schemes[ scheme ][ 11 ]; - duplication_or_specation_color = _color_schemes[ scheme ][ 12 ]; - domains_color = _color_schemes[ scheme ][ 13 ]; - binary_domain_combinations_color = _color_schemes[ scheme ][ 14 ]; - annotation_color = _color_schemes[ scheme ][ 15 ]; - ov_color = _color_schemes[ scheme ][ 16 ]; + found_color_0 = _color_schemes[ scheme ][ 9 ]; + found_color_1 = _color_schemes[ scheme ][ 10 ]; + found_color_0_and_1 = _color_schemes[ scheme ][ 11 ]; + dup_box_color = _color_schemes[ scheme ][ 12 ]; + spec_box_color = _color_schemes[ scheme ][ 13 ]; + duplication_or_specation_color = _color_schemes[ scheme ][ 14 ]; + domains_color = _color_schemes[ scheme ][ 15 ]; + binary_domain_combinations_color = _color_schemes[ scheme ][ 16 ]; + annotation_color = _color_schemes[ scheme ][ 17 ]; + ov_color = _color_schemes[ scheme ][ 18 ]; } void setCurrentColorScheme( final int color_scheme ) { _color_scheme = color_scheme; } + private void setColorForDefault( final int i, final Color color ) { + _color_schemes[ 0 ][ i ] = color; + } + static TreeColorSet createInstance() { final TreeColorSet tcs = new TreeColorSet(); tcs.setColorSchema( 0 );