JAL-2349 colour shade computation refactored to annotation row renderer

[jalview.git] / src / jalview / renderer / ContactMapRenderer.java

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 809ced0..35b73a4 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -8,6 +8,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactRange;
 import jalview.renderer.api.AnnotationRowRendererI;
 
 import java.awt.Color;
@@ -63,7 +64,8 @@ public class ContactMapRenderer implements AnnotationRowRendererI
        * {profile type, #values, total count, char1, pct1, char2, pct2...}
        */
       ContactListI contacts = viewport.getContactList(_aa, column);
-
+      min = _aa.graphMin;
+      max = _aa.graphMax;
       if (contacts == null)
       {
         return;
@@ -81,7 +83,7 @@ public class ContactMapRenderer implements AnnotationRowRendererI
                 + (contacts.getContactHeight() * (ht - eht) / _aa.graphHeight);
         // TODO show maximum colour for range - sort of done
         // also need a 'getMaxPosForRange(start,end)'
-        g.setColor(contacts.getColorForRange(cstart, cend));
+        g.setColor(getColorForRange(contacts, cstart, cend));
 
         if (scale > 1)
         {
@@ -96,4 +98,22 @@ public class ContactMapRenderer implements AnnotationRowRendererI
     }
 
   }
+
+  Color minColor = Color.white, maxColor = Color.magenta;
+
+  float min, max;
+
+  Color shadeFor(float value)
+  {
+    return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,
+            max, maxColor);
+  }
+
+  public Color getColorForRange(ContactListI cl, int i, int j)
+  {
+    ContactRange cr = cl.getRangeFor(i, j);
+    // average for moment - probably more interested in maxIntProj though
+    return shadeFor((float) cr.getMean());
+  }
+
 }