From 5963dedafa1af673a588f0d30710f7391eb822c4 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Feb 2006 15:45:06 +0000
Subject: [PATCH] Use original colour scheme as base for annotation colouring

---
 src/jalview/schemes/AnnotationColourGradient.java |   55 +++++++++++++++++----
 1 file changed, 45 insertions(+), 10 deletions(-)

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 433af79..3cb7e17 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -34,7 +34,31 @@ public class AnnotationColourGradient extends ResidueColourScheme
     GraphLine annotationThreshold;
 
     float r1, g1, b1, rr, gg, bb, dr, dg, db;
-    float range;
+    float range = 0;
+
+    ColourSchemeI colourScheme;
+
+    /**
+     * Creates a new AnnotationColourGradient object.
+     */
+    public AnnotationColourGradient(AlignmentAnnotation annotation,
+                                    ColourSchemeI originalColour,
+                                    int aboveThreshold)
+    {
+      if(originalColour instanceof AnnotationColourGradient)
+      {
+        colourScheme = ((AnnotationColourGradient)originalColour).colourScheme;
+      }
+      else
+        colourScheme = originalColour;
+
+      this.annotation = annotation;
+
+      aboveAnnotationThreshold = aboveThreshold;
+
+      if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
+        annotationThreshold = annotation.threshold;
+    }
 
     /**
      * Creates a new AnnotationColourGradient object.
@@ -80,7 +104,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
      */
     public Color findColour(String n)
     {
-      System.out.println("AnnotationColourGradient findColour(string)");
         return Color.red;
     }
 
@@ -104,17 +127,29 @@ public class AnnotationColourGradient extends ResidueColourScheme
                || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
                || (annotationThreshold!=null && aboveAnnotationThreshold==BELOW_THRESHOLD && annotation.annotations[j].value<=annotationThreshold.value))
             {
+              if(colourScheme!=null)
+              {
+                currentColour = colourScheme.findColour(n, j);
+              }
+              else if(range!=0)
+              {
                 dr = rr *
-                     ((annotation.annotations[j].value-annotation.graphMin) / range )
-                     +r1;
+                    ( (annotation.annotations[j].value - annotation.graphMin) /
+                     range)
+                    + r1;
                 dg = gg *
-                     ((annotation.annotations[j].value-annotation.graphMin)  / range )
-                     +g1;
+                    ( (annotation.annotations[j].value - annotation.graphMin) /
+                     range)
+                    + g1;
                 db = bb *
-                     ((annotation.annotations[j].value-annotation.graphMin) / range )
-                     +b1;
-
-                 currentColour = new Color( (int) dr, (int) dg, (int) db);
+                    ( (annotation.annotations[j].value - annotation.graphMin) /
+                     range)
+                    + b1;
+
+                currentColour = new Color( (int) dr, (int) dg, (int) db);
+              }
+              else
+                currentColour = Color.white;
             }
             else
               currentColour = Color.white;
-- 
1.7.10.2