From 93ad1bb6b4e849dbca2c7a0ce04ec4080752b9ce Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 9 Jan 2018 15:34:36 +0000
Subject: [PATCH] JAL-2805 added check for null node sequences during parsing
 (such as in internal nodes)

---
 src/jalview/ext/archaeopteryx/Tree.java |    6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/jalview/ext/archaeopteryx/Tree.java b/src/jalview/ext/archaeopteryx/Tree.java
index 76808e8..d0133a1 100644
--- a/src/jalview/ext/archaeopteryx/Tree.java
+++ b/src/jalview/ext/archaeopteryx/Tree.java
@@ -160,8 +160,12 @@ public class Tree implements TreeI
     int i = 0;
     while (iter.hasNext())
     {
+
       SequenceI nodeSeq = iter.next().getSequence();
-      treeSeqs[i++] = nodeSeq;
+      if (nodeSeq != null)
+      {
+        treeSeqs[i++] = nodeSeq;
+      }
     }
     return treeSeqs;
   }
-- 
1.7.10.2