X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2FMCview%2FPDBChain.java;h=65504e4bdebcfec7077acedced1811dd6700c6a9;hb=723d0cff35b408c12fc13b44ff50193c588d6ff1;hp=779b4f0155a49b9d8581a459224259ff1804d953;hpb=e601d78bc7762386f570e346a803684c43a66ff1;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 779b4f0..65504e4 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -66,18 +66,22 @@ public class PDBChain
     this.pdbid = pdbid.toLowerCase();
     this.id = id;
   }
+
   /**
-   * character used to write newlines 
+   * character used to write newlines
    */
   protected String newline = System.getProperty("line.separator");
+
   public void setNewlineString(String nl)
   {
     newline = nl;
   }
+
   public String getNewlineString()
   {
     return newline;
   }
+
   public String print()
   {
     String tmp = "";
@@ -92,11 +96,22 @@ public class PDBChain
     return tmp;
   }
 
+  /**
+   * Annotate the residues with their corresponding positions in s1 using the
+   * alignment in as
+   * NOTE: This clears all atom.alignmentMapping values on the structure.
+   * @param as
+   * @param s1
+   */
   public void makeExactMapping(AlignSeq as, SequenceI s1)
   {
     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) != '-')
@@ -232,6 +247,7 @@ public class PDBChain
   {
     int count = 0;
     Object symbol;
+    boolean deoxyn=false;
     boolean nucleotide = false;
     StringBuffer seq = new StringBuffer();
     Vector resFeatures = new Vector();
@@ -286,7 +302,10 @@ public class PDBChain
       if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
         String nucname = tmpat.resName.trim();
-        if (tmpat.name.equalsIgnoreCase("CA") || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+        // 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((deoxyn ? 1 : 0))] == -1)
         {
           seq.append("X");
           // System.err.println("PDBReader:Null aa3Hash for " +
@@ -296,7 +315,7 @@ public class PDBChain
         {
           // nucleotide flag
           nucleotide = true;
-          seq.append(nucname.charAt(0));
+          seq.append(nucname.charAt((deoxyn ? 1 : 0)));
         }
       }
       else