X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=0cb9f02a260d9e667d44d56fc7f9dc766a40693f;hb=5a60f6428df1108a96524aae0c34d615ae48c227;hp=5f23a266bd21902c84b9ed881177e07bc9ccbf6b;hpb=8893c2ac9824d4c566ae69c73d34889c5316b058;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 5f23a26..0cb9f02 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
@@ -195,26 +195,26 @@ public class PDBChain {
             try {
                 Bond b = (Bond) bonds.elementAt(i);
 
-                if (b.at1.resName.toUpperCase().equals("ASP") ||
-                        b.at1.resName.toUpperCase().equals("GLU")) {
+                if (b.at1.resName.equalsIgnoreCase("ASP") ||
+                        b.at1.resName.equalsIgnoreCase("GLU")) {
                     b.startCol = Color.red;
-                } else if (b.at1.resName.toUpperCase().equals("LYS") ||
-                        b.at1.resName.toUpperCase().equals("ARG")) {
+                } else if (b.at1.resName.equalsIgnoreCase("LYS") ||
+                        b.at1.resName.equalsIgnoreCase("ARG")) {
                     b.startCol = Color.blue;
-                } else if (b.at1.resName.toUpperCase().equals("CYS")) {
+                } else if (b.at1.resName.equalsIgnoreCase("CYS")) {
                     b.startCol = Color.yellow;
                 } else {
                     //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
                     b.startCol = Color.lightGray;
                 }
 
-                if (b.at2.resName.toUpperCase().equals("ASP") ||
-                        b.at2.resName.toUpperCase().equals("GLU")) {
+                if (b.at2.resName.equalsIgnoreCase("ASP") ||
+                        b.at2.resName.equalsIgnoreCase("GLU")) {
                     b.endCol = Color.red;
-                } else if (b.at2.resName.toUpperCase().equals("LYS") ||
-                        b.at2.resName.toUpperCase().equals("ARG")) {
+                } else if (b.at2.resName.equalsIgnoreCase("LYS") ||
+                        b.at2.resName.equalsIgnoreCase("ARG")) {
                     b.endCol = Color.blue;
-                } else if (b.at2.resName.toUpperCase().equals("CYS")) {
+                } else if (b.at2.resName.equalsIgnoreCase("CYS")) {
                     b.endCol = Color.yellow;
                 } else {
                     //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
@@ -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.codonTranslate(
+                      ResidueProperties.aa3Hash.get(b.at1.resName).toString().charAt(0)
+                  );
 
-                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;
             }