X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=20b08857c757ec16f291d6962d625118173f2762;hb=d70d7e5bc8da1189f44709b6ec59ea1e23f6f557;hp=789667e0b2d49296053fa319b45ff933ebf0b319;hpb=2bdd8fe3e044068769ca42c57bfa1ef5f52e2f2d;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 789667e..20b0885 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.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
@@ -85,6 +85,30 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
     }
 
+
+    public String getAnnotation()
+    {
+      return annotation.label;
+    }
+
+    public int getAboveThreshold()
+    {
+      return aboveAnnotationThreshold;
+    }
+
+    public float getAnnotationThreshold()
+    {
+      if(annotationThreshold==null)
+        return 0;
+      else
+        return annotationThreshold.value;
+    }
+
+    public ColourSchemeI getBaseColour()
+    {
+      return colourScheme;
+    }
+
     public Color getMinColour()
     {
       return new Color( (int) r1, (int) g1, (int) b1);
@@ -102,7 +126,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n)
+    public Color findColour(char c)
     {
         return Color.red;
     }
@@ -115,15 +139,15 @@ public class AnnotationColourGradient extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n, int j)
+    public Color findColour(char c, int j)
     {
-        currentColour = Color.white;
+        Color currentColour = Color.white;
 
-        if ((threshold == 0) || aboveThreshold(n, j))
+        if ((threshold == 0) || aboveThreshold(c, j))
         {
           if( j<annotation.annotations.length
               && annotation.annotations[j]!=null
-              && !jalview.util.Comparison.isGap(n.charAt(0)))
+              && !jalview.util.Comparison.isGap(c))
           {
             if(  aboveAnnotationThreshold==NO_THRESHOLD
                || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
@@ -131,7 +155,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
             {
               if(colourScheme!=null)
               {
-                currentColour = colourScheme.findColour(n, j);
+                currentColour = colourScheme.findColour(c, j);
               }
               else if(range!=0)
               {
@@ -155,7 +179,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
         }
 
         if(conservationColouring)
-         applyConservation(j);
+         currentColour = applyConservation(currentColour, j);
 
        return currentColour;
     }