From 72da885aa401e932e73af4a554ea338cd5015efc Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 6 Oct 2016 08:52:55 +0100
Subject: [PATCH] JAL-2245 checks for null added (in case EMBL fetch finds
 nothing)

---
 src/jalview/datamodel/xdb/embl/EmblFile.java |    4 ++++
 src/jalview/ws/dbsources/EmblXmlSource.java  |    2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index 69870b6..a95f6e5 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -152,6 +152,10 @@ public class EmblFile
    */
   static void canonicaliseDbRefs(EmblFile record)
   {
+    if (record.getEntries() == null)
+    {
+      return;
+    }
     for (EmblEntry entry : record.getEntries())
     {
       if (entry.getDbRefs() != null)
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 2049766..f672e8b 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -103,7 +103,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     }
 
     List<SequenceI> peptides = new ArrayList<SequenceI>();
-    if (efile != null)
+    if (efile != null && efile.getEntries() != null)
     {
       for (EmblEntry entry : efile.getEntries())
       {
-- 
1.7.10.2