make PH, aPH, CL selection

[jalview.git] / forester / java / src / org / forester / archaeopteryx / TreeColorSet.java

diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
index 53650d5..56c2cc1 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java
@@ -31,7 +31,6 @@ import java.util.Map;
 
 import org.forester.util.ForesterUtil;
 
-
 public final class TreeColorSet {
 
     public static final String ANNOTATION                 = "Annotation";
@@ -58,16 +57,14 @@ public final class TreeColorSet {
             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",
+    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( 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
@@ -78,16 +75,16 @@ 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( 230, 230, 230 ), // domain_label  
-            new Color( 100, 100, 100 ), // domains_base  
-            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( 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( 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
@@ -98,8 +95,8 @@ 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( 230, 230, 230 ), // domain_label  
-            new Color( 100, 100, 100 ), // domains_base  
+            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
@@ -107,7 +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
@@ -118,16 +115,49 @@ 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 ), // domain_label  
-            new Color( 100, 100, 100 ), // domains_base  
+            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
@@ -138,8 +168,8 @@ 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( 230, 230, 230 ), // domain_label  
-            new Color( 100, 100, 100 ), // domains_base  
+            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
@@ -147,7 +177,7 @@ 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
@@ -158,8 +188,8 @@ 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( 230, 230, 230 ), // domain_label  
-            new Color( 100, 100, 100 ), // domains_base  
+            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
@@ -167,7 +197,7 @@ 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
@@ -178,8 +208,8 @@ 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 ), // domain_label  
-            new Color( 50, 50, 50 ), // domains_base  
+            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
@@ -187,7 +217,7 @@ 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
@@ -198,8 +228,8 @@ 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( 230, 230, 230 ), // domain_label  
-            new Color( 100, 100, 100 ), // domains_base  
+            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
@@ -207,7 +237,7 @@ 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
@@ -218,8 +248,8 @@ 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( 255, 200, 0  ), // domain_label  
-            new Color( 255, 200, 0  ), // domains_base  
+            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
@@ -227,7 +257,7 @@ 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
@@ -238,8 +268,8 @@ 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(255, 255, 255 ), // domain_label  
-            new Color( 100, 100, 100 ), // domains_base  
+            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
@@ -247,7 +277,7 @@ 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
@@ -258,8 +288,8 @@ 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( 255, 255, 255 ), // domain_label  
-            new Color( 150, 150, 150 ), // domains_base  
+            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
@@ -267,7 +297,7 @@ 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
@@ -278,8 +308,8 @@ 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( 127, 255, 0 ), // domain_label  
-            new Color(  234, 173, 234 ), // domains_base  
+            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
@@ -310,6 +340,18 @@ public final class 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 );
@@ -332,7 +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;
@@ -374,14 +416,6 @@ public final class TreeColorSet {
         return SCHEME_NAMES[ getCurrentColorScheme() ];
     }
 
-    public Color getDomainBaseColor() {
-        return domain_base_color;
-    }
-    
-    public Color getDomainLabelColor() {
-        return domain_label_color;
-    }
-
     Color getDuplicationBoxColor() {
         return dup_box_color;
     }
@@ -474,10 +508,6 @@ public final class TreeColorSet {
         _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 );
@@ -495,7 +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() );
                 }
             }
         }