after merge

[jalview.git] / src / jalview / schemes / ColourSchemeProperty.java

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index d27dcf0..b586a0a 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -40,28 +40,32 @@ public class ColourSchemeProperty
     public static final int ZAPPO = 3;\r
 \r
     /** DOCUMENT ME!! */\r
-    public static final int HYDROPHOBIC = 4;\r
+    public static final int TAYLOR = 4;\r
 \r
     /** DOCUMENT ME!! */\r
-    public static final int HELIX = 5;\r
+    public static final int HYDROPHOBIC = 5;\r
 \r
     /** DOCUMENT ME!! */\r
-    public static final int STRAND = 6;\r
+    public static final int HELIX = 6;\r
 \r
     /** DOCUMENT ME!! */\r
-    public static final int TURN = 7;\r
+    public static final int STRAND = 7;\r
 \r
     /** DOCUMENT ME!! */\r
-    public static final int BURIED = 8;\r
+    public static final int TURN = 8;\r
 \r
     /** DOCUMENT ME!! */\r
-    public static final int NUCLEOTIDE = 9;\r
+    public static final int BURIED = 9;\r
 \r
     /** DOCUMENT ME!! */\r
-    public static final int USER_DEFINED = 10;\r
+    public static final int NUCLEOTIDE = 10;\r
 \r
     /** DOCUMENT ME!! */\r
-    public static final int NONE = 11;\r
+    public static final int USER_DEFINED = 11;\r
+\r
+\r
+    /** DOCUMENT ME!! */\r
+    public static final int NONE = 12;\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -72,7 +76,7 @@ public class ColourSchemeProperty
      */\r
     public static int getColourIndexFromName(String name)\r
     {\r
-        int ret = 11;\r
+        int ret = 12;\r
 \r
         if (name.equalsIgnoreCase("Clustal"))\r
         {\r
@@ -90,6 +94,10 @@ public class ColourSchemeProperty
         {\r
             ret = ZAPPO;\r
         }\r
+        else if (name.equalsIgnoreCase("Taylor"))\r
+        {\r
+          ret = TAYLOR;\r
+        }\r
         else if (name.equalsIgnoreCase("Hydrophobic"))\r
         {\r
             ret = HYDROPHOBIC;\r
@@ -131,12 +139,8 @@ public class ColourSchemeProperty
      */\r
     public static String getColourName(ColourSchemeI cs)\r
     {\r
-        if (cs instanceof ConservationColourScheme)\r
-        {\r
-            cs = ((ConservationColourScheme) cs).cs;\r
-        }\r
 \r
-        int index = 11;\r
+        int index = 12;\r
 \r
         if (cs instanceof ClustalxColourScheme)\r
         {\r
@@ -154,6 +158,10 @@ public class ColourSchemeProperty
         {\r
             index = ZAPPO;\r
         }\r
+        else if (cs instanceof TaylorColourScheme)\r
+        {\r
+            index = TAYLOR;\r
+        }\r
         else if (cs instanceof HydrophobicColourScheme)\r
         {\r
             index = HYDROPHOBIC;\r
@@ -219,6 +227,10 @@ public class ColourSchemeProperty
 \r
             break;\r
 \r
+        case TAYLOR:\r
+            ret = "Taylor";\r
+            break;\r
+\r
         case HYDROPHOBIC:\r
             ret = "Hydrophobic";\r
 \r
@@ -328,6 +340,10 @@ public class ColourSchemeProperty
 \r
             break;\r
 \r
+        case TAYLOR:\r
+            cs = new TaylorColourScheme();\r
+            break;\r
+\r
         case HYDROPHOBIC:\r
             cs = new HydrophobicColourScheme();\r
 \r
@@ -359,8 +375,10 @@ public class ColourSchemeProperty
             break;\r
 \r
         case USER_DEFINED:\r
-            cs = new UserColourScheme(new Color[0]);\r
-\r
+          Color[] col = new Color[24];\r
+          for (int i = 0; i < 24; i++)\r
+            col[i] = Color.white;\r
+          cs = new UserColourScheme(col);\r
             break;\r
 \r
         default:\r