X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;fp=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;h=a504b4dcae59ecf00f22c895b619f36551a92260;hb=cd9c7864b10bfc0917dfbbfbe11b3af086c9fc4d;hp=313e3dbe07100eb921ed48a9ef30961a7f293761;hpb=a81d5dedad0d679f576a7c0f165d99dbc6cdb63b;p=jalview.git

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 313e3db..a504b4d 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -82,25 +82,29 @@ public class ContactMapRenderer implements AnnotationRowRendererI
       }
 
 
-      int scale = Math
-              .max(1, _aa.graphHeight / contacts.getContactHeight());
-      int step = _aa.graphHeight / scale;
-      int valuesProcessed = 0;
+      // cell height to render
+      double scale = (_aa.graphHeight < contacts.getContactHeight()) ? 1
+              : (((double) _aa.graphHeight) / (double) contacts
+                      .getContactHeight());
+      // distance between contact map per cell
+      int step = (int) ((contacts.getContactHeight()) * scale / _aa.graphHeight);
+
       // profl[1] is the number of values in the profile
-      for (int stp = 0, ht = y2, eht = y2 + _aa.graphHeight; ht < eht; ht += scale, stp++)
+      for (int stp = 0, ht = y2, eht = y2 - _aa.graphHeight; ht > eht; ht -= scale, stp++)
       {
-        valuesProcessed = stp * step;
-        g.setColor(contacts.getColorForScore(stp * step));
+        g.setColor(contacts
+                .getColorForScore((int) (stp * step * ((double) _aa.graphHeight / (double) contacts
+                        .getContactHeight()))));
 
         if (scale > 1)
         {
-          g.fillRect(x * charWidth, ht, charWidth, scale);
+          g.fillRect(x * charWidth, ht, charWidth, 1 + (int) scale);
         } else {
           g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht);
         }
       }
+      x++;
     }
-    x++;
 
   }
 }