X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2FMCview%2FPDBChain.java;h=ddf05e1320e827b35ea4d32d8aef973135ad335f;hb=5655997c202bfcb4ab2778999d785490d3a7dbae;hp=0715b6abd2e8ac892fbd166856e9256b31631e2f;hpb=dbbe146185027d9cb041a83645985a6b1a26cb75;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 0715b6a..ddf05e1 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -228,44 +228,27 @@ public class PDBChain {
         }
     }
 
-    public void setHydrophobicityColours() {
-        float hydmin = (float) ResidueProperties.getHydmin();
-        float hydmax = (float) ResidueProperties.getHydmax();
-        double[] hyd = ResidueProperties.getHyd();
-
-        Hashtable AA3Hash = ResidueProperties.getAA3Hash();
 
+    public void setChainColours(jalview.schemes.ColourSchemeI cs)
+    {
+        Bond b;
         for (int i = 0; i < bonds.size(); i++) {
             try {
-                Bond b = (Bond) bonds.elementAt(i);
-
-                int atno = ((Integer) AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
-                float red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
-
-                if (red > (float) 1.0) {
-                    red = (float) 1.0;
-                }
-
-                if (red < (float) 0.0) {
-                    red = (float) 0.0;
-                }
+              b = (Bond) bonds.elementAt(i);
 
-                b.startCol = new Color(red, (float) 0.0, (float) 1.0 - red);
-                atno = ((Integer) AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
+              ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
+                  ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
+                                         get(b.at1.resName)).intValue()]
+                  );
 
-                red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
+              b.endCol = cs.findColour(
+                  ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
+                                         get(b.at2.resName)).intValue()]
+                  );
 
-                if (red > (float) 1.0) {
-                    red = (float) 1.0;
-                }
-
-                if (red < (float) 0.0) {
-                    red = (float) 0.0;
-                }
-
-                b.endCol = new Color(red, (float) 0.2, (float) 1.0 - red);
-            } catch (Exception e) {
-                Bond b = (Bond) bonds.elementAt(i);
+            } catch (Exception e)
+            {
+                b = (Bond) bonds.elementAt(i);
                 b.startCol = Color.gray;
                 b.endCol = Color.gray;
             }