From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 12 Dec 2016 21:08:44 +0000 (+0000)
Subject: JAL-2349 fixed rendering method and switched to using color from contact range to... 
X-Git-Tag: Release_2_11_3_0~23^2~60^2~9^2~19
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c2e0797f0a114da79ed00e67ec029a3e83496d8d;p=jalview.git

JAL-2349 fixed rendering method and switched to using color from contact range to allow subsampling
---

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 1f235b3..809ced0 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -73,17 +73,15 @@ public class ContactMapRenderer implements AnnotationRowRendererI
       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++)
+      int cstart, cend = -1;
+      for (int ht = y2, eht = y2 - _aa.graphHeight; ht >= eht; ht -= scale)
       {
-        // TODO show maximum colour for range
+        cstart = cend + 1;
+        cend = -1
+                + (contacts.getContactHeight() * (ht - eht) / _aa.graphHeight);
+        // TODO show maximum colour for range - sort of done
         // also need a 'getMaxPosForRange(start,end)'
-        g.setColor(contacts
-                .getColorForScore((int) (stp * step * ((double) _aa.graphHeight / (double) contacts
-                        .getContactHeight()))));
+        g.setColor(contacts.getColorForRange(cstart, cend));
 
         if (scale > 1)
         {