From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 1 Jul 2016 10:08:43 +0000 (+0100)
Subject: JAL-2135 bugfix for error preventing processing of secondary structure annotation... 
X-Git-Tag: Release_2_10_0~146
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=44cbaf5e4c094d90ef1294dd47c75a652e5f2509

JAL-2135 bugfix for error preventing processing of secondary structure annotation for model produced by Phyre2
---

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 073772a..248cf29 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -82,7 +82,7 @@ public class PDBChain
 
   public PDBChain(String pdbid, String id)
   {
-    this.pdbid = pdbid.toLowerCase();
+    this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
     this.id = id;
   }
 
diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 31ed1b7..309e196 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -206,8 +206,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     List<Atom> significantAtoms = new ArrayList<Atom>();
     for (org.jmol.modelset.Atom atom : ms.at)
     {
-      System.out.println("Seq Id : " + atom.getSeqID());
-      System.out.println("To String : " + atom.toString());
+      // System.out.println("Seq Id : " + atom.getSeqID());
+      // System.out.println("To String : " + atom.toString());
       if (atom.isHetero())
       {
         continue;