X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=4a78aa12e6d2be61938ba1d82e4515525a9ed951;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=58256122b6f8cfabdc6c279c933c85636173a2eb;hpb=df227ed4042d4c9fa2affb391fa09b662f3b8a2a;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 5825612..4a78aa1 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
@@ -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.
@@ -46,8 +70,8 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
       aboveAnnotationThreshold = aboveThreshold;
 
-      if(aboveThreshold!=NO_THRESHOLD && annotation.graphLines!=null)
-        annotationThreshold = annotation.getGraphLine(0);
+      if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
+        annotationThreshold = annotation.threshold;
 
       r1 = minColour.getRed();
       g1 = minColour.getGreen();
@@ -61,6 +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);
@@ -80,7 +128,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
      */
     public Color findColour(String n)
     {
-      System.out.println("AnnotationColourGradient findColour(string)");
         return Color.red;
     }
 
@@ -94,39 +141,45 @@ public class AnnotationColourGradient extends ResidueColourScheme
      */
     public Color findColour(String n, int j)
     {
+        Color currentColour = Color.white;
+
         if ((threshold == 0) || aboveThreshold(n, j))
         {
-          if( j+1>annotation.annotations.length || annotation.annotations[j]==null)
-            currentColour = Color.white;
-          else
+          if( j<annotation.annotations.length
+              && annotation.annotations[j]!=null
+              && !jalview.util.Comparison.isGap(n.charAt(0)))
           {
             if(  aboveAnnotationThreshold==NO_THRESHOLD
                || (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;
+                    ( (annotation.annotations[j].value - annotation.graphMin) /
+                     range)
+                    + b1;
 
-                 currentColour = new Color( (int) dr, (int) dg, (int) db);
+                currentColour = new Color( (int) dr, (int) dg, (int) db);
+              }
             }
-            else
-              currentColour = Color.white;
           }
         }
-        else
-        {
-            return Color.white;
-        }
 
         if(conservationColouring)
-         applyConservation(j);
+         currentColour = applyConservation(currentColour, j);
 
        return currentColour;
     }