X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=ac88d96b81898a2467db6bdfb7d6f6e22d73f62b;hb=52fd681e0f239e20df19fd7560d4b999104ba222;hp=bc4455958425dd83439cbca9bf273bf928606081;hpb=1c1f44c47bfd8151d846928eda2d95aeff6f8e92;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index bc44559..ac88d96 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -24,22 +24,55 @@ import jalview.datamodel.*;
 
 public class AnnotationColourGradient extends ResidueColourScheme
 {
+    public static int NO_THRESHOLD = -1;
+    public static int BELOW_THRESHOLD = 0;
+    public static int ABOVE_THRESHOLD = 1;
+
     AlignmentAnnotation annotation;
-    boolean aboveAnnotationThreshold = false;
+    int aboveAnnotationThreshold = -1;
+
+    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.
      */
     public AnnotationColourGradient(AlignmentAnnotation annotation,
-        Color minColour, Color maxColour, boolean aboveThreshold)
+        Color minColour, Color maxColour, int aboveThreshold)
     {
       this.annotation = annotation;
 
       aboveAnnotationThreshold = aboveThreshold;
 
+      if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
+        annotationThreshold = annotation.threshold;
+
       r1 = minColour.getRed();
       g1 = minColour.getGreen();
       b1 = minColour.getBlue();
@@ -52,6 +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);
@@ -71,7 +128,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
      */
     public Color findColour(String n)
     {
-      System.out.println("AnnotationColourGradient findColour(string)");
         return Color.red;
     }
 
@@ -85,35 +141,42 @@ public class AnnotationColourGradient extends ResidueColourScheme
      */
     public Color findColour(String n, int j)
     {
+        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 || (annotation.graphLines!=null
-               && annotation.annotations[j].value>=annotation.getGraphLine(0).value))
+            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);