From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 20 Oct 2022 09:07:57 +0000 (+0100)
Subject: JAL-3855 RGB colours from the alphafold paE scale.
X-Git-Tag: Release_2_11_4_0~539
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=444daa160575f54ff61f6e1a793a82dca0aca3b7;p=jalview.git

JAL-3855 RGB colours from the alphafold paE scale.
---

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 7a435c3..58fb984 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -140,8 +140,11 @@ public class ContactMapRenderer implements AnnotationRowRendererI
   }
 
   // Shading parameters
-  Color minColor = Color.white, maxColor = Color.green.darker().darker(),
-          selMaxColor = Color.magenta.darker();
+  // currently hardwired for alphafold
+  Color maxColor = new Color(246, 252, 243),
+          minColor = new Color(0, 60, 26),
+          selMinColor = new Color(26, 0, 60),
+          selMaxColor = new Color(243, 246, 252);
 
   Color shadeFor(float min, float max, float value)
   {
@@ -163,7 +166,7 @@ public class ContactMapRenderer implements AnnotationRowRendererI
     ContactRange cr = cl.getRangeFor(i, j);
     // average for moment - probably more interested in maxIntProj though
     return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(),
-            0, minColor, max, selMaxColor);
+            0, selMinColor, max, selMaxColor);
   }
 
 }