X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=8338c63e6a160554cf02ee3c7940e436d2b20d73;hb=c07ef0cc5eabc7df4eb15bb3541a702278783f05;hp=d5597de1480381f412e2e42d2e8bfb0302bab44f;hpb=cbb5b519ea1986d0e2016a6472e7583ec98c5294;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index d5597de..8338c63 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package MCview;
 
@@ -98,7 +99,8 @@ 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 +109,12 @@ 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) != '-')
@@ -243,7 +250,7 @@ public class PDBChain
   {
     int count = 0;
     Object symbol;
-    boolean deoxyn=false;
+    boolean deoxyn = false;
     boolean nucleotide = false;
     StringBuffer seq = new StringBuffer();
     Vector resFeatures = new Vector();
@@ -298,10 +305,13 @@ 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'];
+        // 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)
+                || ResidueProperties.nucleotideIndex[nucname
+                        .charAt((deoxyn ? 1 : 0))] == -1)
         {
           seq.append("X");
           // System.err.println("PDBReader:Null aa3Hash for " +