From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 31 Aug 2016 13:18:53 +0000 (+0100)
Subject: JAL-2148 further enhancment to CA HETATM processing
X-Git-Tag: Release_2_10_0~60^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=43522cd06017137882e382baad33cbeef02bbbe9;p=jalview.git

JAL-2148 further enhancment to CA HETATM processing
---

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 848e7db..7c3ff42 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -257,6 +257,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       // diff < 5 then mark as valid and update termination Atom
       if (chainTerMap.containsKey(curAtomChId))
       {
+        if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+        {
+          return false;
+        }
         if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
         {
           chainTerMap.put(curAtomChId, curAtom);
@@ -268,6 +272,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     // atom with previously terminated chain encountered
     else if (chainTerMap.containsKey(curAtomChId))
     {
+      if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+      {
+        return false;
+      }
       if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
       {
         chainTerMap.put(curAtomChId, curAtom);