From: Jim Procter <jprocter@dundee.ac.uk>
Date: Sat, 19 Apr 2014 12:53:11 +0000 (+0100)
Subject: JAL-1476 JAL-1016 avoid NPE messiness if structures fail to align for some reason
X-Git-Tag: Jalview_2_9~123^2~33
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=653144053dfcfcde800beb1fa81a6870775a8034;p=jalview.git

JAL-1476 JAL-1016 avoid NPE messiness if structures fail to align for some reason
---

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index cc37b66..81b88ac 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -829,7 +829,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
       // need to wait around until script has finished
       while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
-              : (jmb.isFinishedInit() && jmb.getPdbFile().length != jmb.pdbentry.length))
+              : (jmb.isFinishedInit() && jmb.getPdbFile()!=null && jmb.getPdbFile().length != jmb.pdbentry.length))
       {
         try
         {