X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=278cf6afcafad8b8de0d3f8c2cdc364ca805bfa1;hb=ca26cdb914e0a8885bb0a3986750481bde71383a;hp=d27dcf012972f2a43fd081f4a29e20748803ec61;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index d27dcf0..278cf6a 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -40,28 +40,32 @@ public class ColourSchemeProperty
     public static final int ZAPPO = 3;
 
     /** DOCUMENT ME!! */
-    public static final int HYDROPHOBIC = 4;
+    public static final int TAYLOR = 4;
 
     /** DOCUMENT ME!! */
-    public static final int HELIX = 5;
+    public static final int HYDROPHOBIC = 5;
 
     /** DOCUMENT ME!! */
-    public static final int STRAND = 6;
+    public static final int HELIX = 6;
 
     /** DOCUMENT ME!! */
-    public static final int TURN = 7;
+    public static final int STRAND = 7;
 
     /** DOCUMENT ME!! */
-    public static final int BURIED = 8;
+    public static final int TURN = 8;
 
     /** DOCUMENT ME!! */
-    public static final int NUCLEOTIDE = 9;
+    public static final int BURIED = 9;
 
     /** DOCUMENT ME!! */
-    public static final int USER_DEFINED = 10;
+    public static final int NUCLEOTIDE = 10;
 
     /** DOCUMENT ME!! */
-    public static final int NONE = 11;
+    public static final int USER_DEFINED = 11;
+
+
+    /** DOCUMENT ME!! */
+    public static final int NONE = 12;
 
     /**
      * DOCUMENT ME!
@@ -72,7 +76,7 @@ public class ColourSchemeProperty
      */
     public static int getColourIndexFromName(String name)
     {
-        int ret = 11;
+        int ret = 12;
 
         if (name.equalsIgnoreCase("Clustal"))
         {
@@ -90,6 +94,10 @@ public class ColourSchemeProperty
         {
             ret = ZAPPO;
         }
+        else if (name.equalsIgnoreCase("Taylor"))
+        {
+          ret = TAYLOR;
+        }
         else if (name.equalsIgnoreCase("Hydrophobic"))
         {
             ret = HYDROPHOBIC;
@@ -131,12 +139,8 @@ public class ColourSchemeProperty
      */
     public static String getColourName(ColourSchemeI cs)
     {
-        if (cs instanceof ConservationColourScheme)
-        {
-            cs = ((ConservationColourScheme) cs).cs;
-        }
 
-        int index = 11;
+        int index = 12;
 
         if (cs instanceof ClustalxColourScheme)
         {
@@ -154,6 +158,10 @@ public class ColourSchemeProperty
         {
             index = ZAPPO;
         }
+        else if (cs instanceof TaylorColourScheme)
+        {
+            index = TAYLOR;
+        }
         else if (cs instanceof HydrophobicColourScheme)
         {
             index = HYDROPHOBIC;
@@ -219,6 +227,10 @@ public class ColourSchemeProperty
 
             break;
 
+        case TAYLOR:
+            ret = "Taylor";
+            break;
+
         case HYDROPHOBIC:
             ret = "Hydrophobic";
 
@@ -328,6 +340,10 @@ public class ColourSchemeProperty
 
             break;
 
+        case TAYLOR:
+            cs = new TaylorColourScheme();
+            break;
+
         case HYDROPHOBIC:
             cs = new HydrophobicColourScheme();
 
@@ -359,8 +375,10 @@ public class ColourSchemeProperty
             break;
 
         case USER_DEFINED:
-            cs = new UserColourScheme(new Color[0]);
-
+          Color[] col = new Color[24];
+          for (int i = 0; i < 24; i++)
+            col[i] = Color.white;
+          cs = new UserColourScheme(col);
             break;
 
         default: