X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreeColorSet.java;h=9ab1846141086a86b30299bafc5aec42a764ca82;hb=693353f5ea85d3e50a77f9b1cd9d87711d23412b;hp=c127885bb9460bc605d5b8cc3eb40e8b891e9390;hpb=d33a5a1d64863f9b0207e1da71151396cea74a38;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java index c127885..9ab1846 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java +++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java @@ -31,69 +31,72 @@ import java.util.Map; import org.forester.util.ForesterUtil; -/* - * Maintains the color schemes and a set of colors for drawing a tree. - */ 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 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 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 }; - // All the color sets; better be the same # of sets as there are names! + 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( 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( 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, 0 ), // collapesed_fill_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( 123, 104, 238 ), // domains_color - new Color( 65, 105, 255 ), // binary_domain_combinations_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( 220, 220, 220 ), // sequence __ Black + new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 230, 230, 230 ), // sequence __ Black new Color( 180, 180, 180 ), // taxonomy - new Color( 56, 176, 222 ), // support + 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, 0 ), // collapesed_fill_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( 123, 104, 238 ), // domains_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 @@ -101,7 +104,7 @@ public final class TreeColorSet { 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 ), // support new Color( 0, 0, 0 ), // branch_length_color new Color( 0, 0, 0 ), // branch_color new Color( 0, 0, 0 ), // box_color @@ -112,26 +115,61 @@ public final class TreeColorSet { 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 ), // domains_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( 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 ), // 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( 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( 180, 180, 180 ), // domains_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 @@ -139,18 +177,19 @@ public final class TreeColorSet { 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, 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( 0, 155, 0 ), // collapesed_fill_color new Color( 255, 0, 0 ), // found_color 0 - new Color( 0, 255, 0 ), // found_color 1 + 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( 0, 235, 0 ), // domains_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 @@ -158,18 +197,19 @@ public final class TreeColorSet { 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( 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, 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( 123, 104, 238 ), // domains_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 @@ -177,18 +217,19 @@ public final class TreeColorSet { 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( 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, 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( 123, 104, 238 ), // domains_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 @@ -196,18 +237,19 @@ public final class TreeColorSet { 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 ), // 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, 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( 150, 150, 150 ), // domains_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 @@ -215,18 +257,19 @@ public final class TreeColorSet { 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 ), // 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( 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 ), // domains_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 @@ -234,18 +277,19 @@ public final class TreeColorSet { 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( 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( 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 ), // domains_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 @@ -253,49 +297,61 @@ public final class TreeColorSet { 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( 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 ), // collapsed_fill_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, 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( 27, 255, 0 ), // domains_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 } }; - // 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 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_1; private Color found_color_0_and_1; - private Color duplication_or_specation_color; - private Color domains_color; - private Color binary_domain_combinations_color; - private Color annotation_color; + 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. } + public Color getDomainBaseColor() { + return domain_base_color; + } + + public Color getDomainLabelColor() { + return domain_label_color; + } + + private void setColorForDefault( final int i, final Color color ) { + _color_schemes[ 0 ][ i ] = color; + } + void cycleColorScheme() { if ( getCurrentColorScheme() >= ( _color_schemes.length - 1 ) ) { setColorSchema( 0 ); @@ -318,7 +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; @@ -328,7 +384,7 @@ public final class TreeColorSet { return box_color; } - Color getBranchColor() { + public Color getBranchColor() { return branch_color; } @@ -360,10 +416,6 @@ public final class TreeColorSet { return SCHEME_NAMES[ getCurrentColorScheme() ]; } - Color getDomainsColor() { - return domains_color; - } - Color getDuplicationBoxColor() { return dup_box_color; } @@ -372,18 +424,18 @@ public final class TreeColorSet { return duplication_or_specation_color; } - Color getFoundColor0() { + public Color getFoundColor0() { return found_color_0; } - - Color getFoundColor1() { - return found_color_1; - } - - Color getFoundColor0and1() { + + public Color getFoundColor0and1() { return found_color_0_and_1; } + public Color getFoundColor1() { + return found_color_1; + } + Color getGainedCharactersColor() { return Color.GREEN; } @@ -425,10 +477,6 @@ public final class TreeColorSet { } } - private void setColorForDefault( final int i, final Color color ) { - _color_schemes[ 0 ][ i ] = color; - } - /** * Switches colors between different schemes. */ @@ -444,19 +492,16 @@ public final class TreeColorSet { box_color = _color_schemes[ scheme ][ 7 ]; collapse_fill_color = _color_schemes[ scheme ][ 8 ]; found_color_0 = _color_schemes[ scheme ][ 9 ]; - found_color_1 = _color_schemes[ scheme ][ 10 ]; - - found_color_0_and_1 = _color_schemes[ scheme ][11 ]; - - + 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 ]; + domain_label_color = _color_schemes[ scheme ][ 15 ]; + domain_base_color = _color_schemes[ scheme ][ 16 ]; + binary_domain_combinations_color = _color_schemes[ scheme ][ 17 ]; + annotation_color = _color_schemes[ scheme ][ 18 ]; + ov_color = _color_schemes[ scheme ][ 19 ]; } void setCurrentColorScheme( final int color_scheme ) { @@ -480,7 +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() ); } } }