From 34eab5424aff7f653637d8664893f829f50758eb Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 16 Nov 2004 15:27:06 +0000
Subject: [PATCH] Add only colours that currently work

---
 src/jalview/schemes/ColourProperties.java |   75 +++++++++++++++++++----------
 1 file changed, 50 insertions(+), 25 deletions(-)

diff --git a/src/jalview/schemes/ColourProperties.java b/src/jalview/schemes/ColourProperties.java
index ff2c6bc..ae6cd1e 100755
--- a/src/jalview/schemes/ColourProperties.java
+++ b/src/jalview/schemes/ColourProperties.java
@@ -34,30 +34,10 @@ public class ColourProperties {
 					       prefix + "TaylorColourScheme",
 					       "Taylor colours"));
 
-    colourSchemes.add(new ColourSchemeProperty("PID",
-					       prefix + "PIDColourScheme",
-					       "By PID"));
-
-    colourSchemes.add(new ColourSchemeProperty("BLOSUM62",
-					       prefix + "Blosum62ColourScheme",
-					       "By BLOSUM62 Score"));
-
-    colourSchemes.add(new ColourSchemeProperty("Secondary structure",
-					       prefix + "SecondaryColourScheme",
-					       "By Secondary Structure"));
-
-    colourSchemes.add(new ColourSchemeProperty("User defined",
-					       prefix + "ZappoColourScheme",
-					       "User defined colours"));
-
     colourSchemes.add(new ColourSchemeProperty("Hydrophobic",
 					       prefix + "HydrophobicColourScheme",
 					       "By Hydrophobicity"));
 
-   colourSchemes.add(new ColourSchemeProperty("Conservation",
-                                                   prefix + "ZappoColourScheme",
-                                                   null));
-
     colourSchemes.add(new ColourSchemeProperty("Helix",
 					       prefix + "HelixColourScheme",
 					       "Helix propensity"));
@@ -74,13 +54,33 @@ public class ColourProperties {
 					       prefix + "BuriedColourScheme",
 					       "Buried index"));
 
-    //    colourSchemes.add(new ColourSchemeProperty("Features",
-    //                                               prefix + "FeatureColourScheme",
-    //                                               null));
+    colourSchemes.add(new ColourSchemeProperty("BLOSUM62",
+                                            prefix + "Blosum62ColourScheme",
+                                            "By BLOSUM62 Score"));
+
+   colourSchemes.add(new ColourSchemeProperty("User defined",
+                                            prefix + "ZappoColourScheme",
+                                            "User defined colours"));
+
+    /*   colourSchemes.add(new ColourSchemeProperty("PID",
+                                                  prefix + "PIDColourScheme",
+                                                  "By PID"));*/
+
+  /*  colourSchemes.add(new ColourSchemeProperty("Secondary structure",
+                                               prefix + "SecondaryColourScheme",
+                                               "By Secondary Structure"));*/
+
+  /* colourSchemes.add(new ColourSchemeProperty("Conservation",
+                                                   prefix + "ZappoColourScheme",
+                                                   null));*/
+
+    /*  colourSchemes.add(new ColourSchemeProperty("Features",
+                                                   prefix + "FeatureColourScheme",
+                                                   null));
 
     colourSchemes.add(new ColourSchemeProperty("Clustalx",
                                                prefix + "ClustalXColourScheme",
-                                               "ClustalX colours"));
+                                               "ClustalX colours"));*/
   }
 
   static int indexOf(String scheme) {
@@ -91,7 +91,7 @@ public class ColourProperties {
     }
   }
 
-  static int indexOfClass(ColourSchemeI scheme) {
+  public static int indexOfClass(ColourSchemeI scheme) {
     return colourSchemes.indexOfClass(scheme);
   }
 
@@ -114,6 +114,31 @@ public class ColourProperties {
   protected static String getDefaultClassPrefix() {
     return "jalview.schemes.";
   }
+
+  public static ColourSchemeI getColourScheme(int i)
+  {
+    switch(i)
+    {
+        case ColourProperties.HYDROPHOBIC: return new HydrophobicColourScheme();
+
+        case  ColourProperties.TAYLOR:   return new TaylorColourScheme();
+        case  ColourProperties.HELIX:    return new HelixColourScheme();
+        case  ColourProperties.STRAND:   return new StrandColourScheme();
+        case  ColourProperties.TURN:     return new TurnColourScheme();
+        case  ColourProperties.BURIED:   return new BuriedColourScheme();
+        case  ColourProperties.PID:      return new PIDColourScheme();
+        case  ColourProperties.BLOSUM62: return new Blosum62ColourScheme(null);
+        case  ColourProperties.SECONDARY:return new SecondaryColourScheme();
+
+        case  ColourProperties.ZAPPO:
+        case  ColourProperties.USER:
+        case  ColourProperties.CONSERVATION:
+        case  ColourProperties.FEATURES:
+        case  ColourProperties.CLUSTALX:
+       default: return new ZappoColourScheme();
+    }
+
+  }
 }
 
 
-- 
1.7.10.2