X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;h=c4f308e3572564debd3074a31cb7f88f4319a913;hb=4bc1cd2cbab7e95e770abb5c438f2c054d0a432d;hp=aaa8a6118ae3c12ffb14f1ac4610708aff932fdd;hpb=256638175cb9041da39d5c79090f537971e43df3;p=jalview.git

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index aaa8a61..c4f308e 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -72,27 +72,43 @@ public class ContactMapRenderer implements AnnotationRowRendererI
         return;
       }
       int contact_height = contacts.getContactHeight();
-      // fractional pixel height to render each contact cell
-      double pixels_per_contact = ((double) _aa.graphHeight)
-                      / (double) contact_height;
       // fractional number of contacts covering each pixel
-      double contacts_per_pixel = 1d/pixels_per_contact;
-      // number of contacts to render at a time
-      int step = (pixels_per_contact<1) ? (int) Math.floor(contacts_per_pixel) : (int) Math.ceil(pixels_per_contact);
-      
-      int pixels_step = (int) Math.ceil(step*pixels_per_contact);
-      int cstart, cend = -1;
-      for (int ht = y2, eht = y2 - _aa.graphHeight; ht >= eht; ht -= pixels_step)
+      double contacts_per_pixel = ((double) contact_height)
+              / ((double) _aa.graphHeight);
+
+      int pixels_step;
+
+      if (contacts_per_pixel >= 1)
+      {
+        // many contacts rendered per pixel
+        pixels_step = 1;
+      }
+      else
+      {
+        // pixel height for each contact
+        pixels_step = (int) Math
+                .ceil(((double) _aa.graphHeight) / (double) contact_height);
+      }
+
+      int cstart = 0, cend;
+
+      for (int ht = y2,
+              eht = y2 - _aa.graphHeight; ht >= eht; ht -= pixels_step)
       {
-        cstart = cend + 1;
-        cend = (int) Math.min(contact_height, cstart + step);
+        cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
+        cend = (int) Math.min(contact_height,
+                Math.ceil(cstart + contacts_per_pixel * pixels_step));
+
         // TODO show maximum colour for range - sort of done
-        // also need a 'getMaxPosForRange(start,end)'
-        g.setColor(getColorForRange(min, max, contacts, cstart, cend));
+        // also need a 'getMaxPosForRange(start,end)' to accurately render
+        Color col = getColorForRange(min, max, contacts, cstart, cend);
 
-        if (pixels_step>1)
         {
-          g.fillRect(x * charWidth, ht, charWidth, 1 + (int) pixels_step);
+          g.setColor(col);
+        }
+        if (pixels_step > 1)
+        {
+          g.fillRect(x * charWidth, ht, charWidth, 1 + pixels_step);
         }
         else
         {
@@ -106,7 +122,6 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
   Color minColor = Color.white, maxColor = Color.magenta;
 
-
   Color shadeFor(float min, float max, float value)
   {
     return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,