JAL-2349 debugged and simplified (a little) the scaled rendering of contact maps...

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

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 7413e65..c4f308e 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -61,32 +61,54 @@ public class ContactMapRenderer implements AnnotationRowRendererI
         x++;
         continue;
       }
-      /*
-       * {profile type, #values, total count, char1, pct1, char2, pct2...}
-       */
+      if (_aa.sequenceRef != null)
+      {
+        // get the sequence position for the column
+        column = _aa.sequenceRef.findPosition(column) - 1;
+      }
       ContactListI contacts = viewport.getContactList(_aa, column);
       if (contacts == null)
       {
         return;
       }
+      int contact_height = contacts.getContactHeight();
+      // fractional number of contacts covering each pixel
+      double contacts_per_pixel = ((double) contact_height)
+              / ((double) _aa.graphHeight);
 
-      // cell height to render
-      double scale = (_aa.graphHeight < contacts.getContactHeight()) ? 1
-              : ((double) _aa.graphHeight)
-                      / (double) contacts.getContactHeight();
-      int cstart, cend = -1;
-      for (int ht = y2, eht = y2 - _aa.graphHeight; ht >= eht; ht -= scale)
+      int pixels_step;
+
+      if (contacts_per_pixel >= 1)
       {
-        cstart = cend + 1;
-        cend = Math.max(cstart + 1, contacts.getContactHeight()
-                * ((ht - y2) / _aa.graphHeight));
+        // 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 = (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 (scale > 1)
         {
-          g.fillRect(x * charWidth, ht, charWidth, 1 + (int) scale);
+          g.setColor(col);
+        }
+        if (pixels_step > 1)
+        {
+          g.fillRect(x * charWidth, ht, charWidth, 1 + pixels_step);
         }
         else
         {
@@ -100,7 +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,