Allow threshold to be min/max

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