From 8bde1dc9a0a4538ee0a0d2a320a10540e55da61b Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 Apr 2007 08:21:09 +0000
Subject: [PATCH] Allow threshold to be min/max

---
 src/jalview/schemes/AnnotationColourGradient.java |   61 +++++++++++++++------
 1 file changed, 44 insertions(+), 17 deletions(-)

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 06085da..ff6673a 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -29,16 +29,18 @@ public class AnnotationColourGradient
   public static int BELOW_THRESHOLD = 0;
   public static int ABOVE_THRESHOLD = 1;
 
-  AlignmentAnnotation annotation;
+  public AlignmentAnnotation annotation;
   int aboveAnnotationThreshold = -1;
+  public boolean thresholdIsMinMax = false;
 
   GraphLine annotationThreshold;
 
   float r1, g1, b1, rr, gg, bb, dr, dg, db;
-  float range = 0;
 
   ColourSchemeI colourScheme;
 
+  public boolean predefinedColours = false;
+
   /**
    * Creates a new AnnotationColourGradient object.
    */
@@ -88,9 +90,6 @@ public class AnnotationColourGradient
     rr = maxColour.getRed() - r1;
     gg = maxColour.getGreen() - g1;
     bb = maxColour.getBlue() - b1;
-
-    range = annotation.graphMax - annotation.graphMin;
-
   }
 
   public String getAnnotation()
@@ -160,6 +159,15 @@ public class AnnotationColourGradient
           && annotation.annotations[j] != null
           && !jalview.util.Comparison.isGap(c))
       {
+
+        if (predefinedColours)
+        {
+          if(annotation.annotations[j].colour != null)
+              return annotation.annotations[j].colour;
+          else
+            return currentColour;
+        }
+
         if (aboveAnnotationThreshold == NO_THRESHOLD
             ||
             (annotationThreshold != null && aboveAnnotationThreshold == ABOVE_THRESHOLD &&
@@ -168,24 +176,43 @@ public class AnnotationColourGradient
             (annotationThreshold != null && aboveAnnotationThreshold == BELOW_THRESHOLD &&
              annotation.annotations[j].value <= annotationThreshold.value))
         {
+
+          float range=1f;
+          if (thresholdIsMinMax
+              && annotation.threshold != null
+              && aboveAnnotationThreshold == ABOVE_THRESHOLD
+              && annotation.annotations[j].value>annotation.threshold.value)
+          {
+            range =
+                (annotation.annotations[j].value - annotation.threshold.value) /
+                (annotation.graphMax - annotation.threshold.value);
+          }
+          else if (thresholdIsMinMax
+                   && annotation.threshold != null
+                   && aboveAnnotationThreshold == BELOW_THRESHOLD
+              &&  annotation.annotations[j].value > annotation.graphMin)
+          {
+            range =
+                ( annotation.annotations[j].value - annotation.graphMin ) /
+                (annotation.threshold.value - annotation.graphMin );
+          }
+          else
+          {
+            range = (annotation.annotations[j].value -
+                     annotation.graphMin) /
+                (annotation.graphMax - annotation.graphMin);
+          }
+
+
           if (colourScheme != null)
           {
             currentColour = colourScheme.findColour(c, j);
           }
           else if (range != 0)
           {
-            dr = rr *
-                ( (annotation.annotations[j].value - annotation.graphMin) /
-                 range)
-                + r1;
-            dg = gg *
-                ( (annotation.annotations[j].value - annotation.graphMin) /
-                 range)
-                + g1;
-            db = bb *
-                ( (annotation.annotations[j].value - annotation.graphMin) /
-                 range)
-                + b1;
+            dr = rr * range   + r1;
+            dg = gg * range   + g1;
+            db = bb * range   + b1;
 
             currentColour = new Color( (int) dr, (int) dg, (int) db);
           }
-- 
1.7.10.2