find colours uncommented

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 1b65c48..773b263 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -105,7 +105,7 @@ public class PDBChain {
                 return null;
             sq = sq.getDatasetSequence();
         }
-        /** 
+        /**
          * Remove any existing features for this chain if they exist ?
          * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures();
             int totfeat=seqsfeatures.length;
@@ -198,11 +198,11 @@ public class PDBChain {
 
             //Make a new Residue object with the new atoms vector
             residues.addElement(new Residue(resAtoms, resNumber - 1, count));
-            
+
             Residue tmpres = (Residue) residues.lastElement();
             Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
             // Make A new SequenceFeature for the current residue numbering
-            SequenceFeature sf = 
+            SequenceFeature sf =
                 new SequenceFeature("RESNUM",tmpat.resName+":"+tmpat.resNumIns+" "+pdbid+id,
                         "",offset+count,offset+count,MCview.PDBChain.PDBFILEFEATURE);
             resFeatures.addElement(sf);
@@ -222,8 +222,8 @@ public class PDBChain {
 
         if(id.length()<1 || id.equals(" "))
            id = "_";
-        
-        sequence = new Sequence(id, seq.toString(), offset, resNumber-1); // Note: resNumber-offset ~= seq.size() 
+
+        sequence = new Sequence(id, seq.toString(), offset, resNumber-1); // Note: resNumber-offset ~= seq.size()
       //  System.out.println("PDB Sequence is :\nSequence = " + seq);
      //   System.out.println("No of residues = " + residues.size());
         for (i=0,iSize=resFeatures.size(); i<iSize; i++) {
@@ -246,8 +246,7 @@ public class PDBChain {
                 } 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;
+                  b.startCol = Color.lightGray;
                 }
 
                 if (b.at2.resName.equalsIgnoreCase("ASP") ||
@@ -259,8 +258,7 @@ public class PDBChain {
                 } else if (b.at2.resName.equalsIgnoreCase("CYS")) {
                     b.endCol = Color.yellow;
                 } else {
-                    //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
-                    b.endCol = Color.lightGray;
+                  b.endCol = Color.lightGray;
                 }
             } catch (Exception e) {
                 Bond b = (Bond) bonds.elementAt(i);
@@ -274,19 +272,18 @@ public class PDBChain {
     public void setChainColours(jalview.schemes.ColourSchemeI cs)
     {
         Bond b;
+        int index;
         for (int i = 0; i < bonds.size(); i++) {
             try {
               b = (Bond) bonds.elementAt(i);
 
-            /*  ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
-                  ResidueProperties.codonTranslate(
-                      ResidueProperties.aa3Hash.get(b.at1.resName).toString().charAt(0)
-                  );
+              index = ( (Integer) ResidueProperties.aa3Hash.get(b.at1.
+                  resName)).intValue();
+              b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
 
-              b.endCol = cs.findColour(
-                  ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
-                                         get(b.at2.resName)).intValue()]
-                  );*/
+              index = ( (Integer) ResidueProperties.aa3Hash.get(b.at2.resName)).
+                  intValue();
+              b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
 
             } catch (Exception e)
             {