X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=cc71355f85e9ee1d57130db16d395b40e220a80b;hb=312153432da8f952a2f2dff9bfd6d727a9f3d361;hp=5176b1545203dcbac50cb5fbac4338666a906f54;hpb=2df814c67726e12955cb9f7e1bbce797234c5fb6;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 5176b15..cc71355 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -98,7 +98,8 @@ public class PDBChain
 
   /**
    * Annotate the residues with their corresponding positions in s1 using the
-   * alignment in as
+   * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+   * structure.
    * 
    * @param as
    * @param s1
@@ -107,7 +108,12 @@ public class PDBChain
   {
     int pdbpos = as.getSeq2Start() - 2;
     int alignpos = s1.getStart() + as.getSeq1Start() - 3;
-
+    // first clear out any old alignmentMapping values:
+    for (Atom atom : (Vector<Atom>) atoms)
+    {
+      atom.alignmentMapping = -1;
+    }
+    // and now trace the alignment onto the atom set.
     for (int i = 0; i < as.astr1.length(); i++)
     {
       if (as.astr1.charAt(i) != '-')
@@ -243,6 +249,7 @@ public class PDBChain
   {
     int count = 0;
     Object symbol;
+    boolean deoxyn = false;
     boolean nucleotide = false;
     StringBuffer seq = new StringBuffer();
     Vector resFeatures = new Vector();
@@ -297,8 +304,13 @@ public class PDBChain
       if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
         String nucname = tmpat.resName.trim();
+        // use the aaIndex rather than call 'toLower' - which would take a bit
+        // more time.
+        deoxyn = nucname.length() == 2
+                && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
         if (tmpat.name.equalsIgnoreCase("CA")
-                || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+                || ResidueProperties.nucleotideIndex[nucname
+                        .charAt((deoxyn ? 1 : 0))] == -1)
         {
           seq.append("X");
           // System.err.println("PDBReader:Null aa3Hash for " +
@@ -308,7 +320,7 @@ public class PDBChain
         {
           // nucleotide flag
           nucleotide = true;
-          seq.append(nucname.charAt(0));
+          seq.append(nucname.charAt((deoxyn ? 1 : 0)));
         }
       }
       else