X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=ca90d6085bb23c37339ba31a94bf3a2cf40a20ad;hb=8474476096a0bbce03c7748aa3c267fbf6258249;hp=0236d441e5ca38fd16ed17bd492cfbb84131a370;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 0236d44..ca90d60 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -64,13 +64,13 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     {
       reply = dbFetch.fetchDataAsFile(
               emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
-              ".xml");
+              "xml");
     } catch (Exception e)
     {
       stopQuery();
       throw new Exception(MessageManager.formatMessage(
-              "exception.ebiembl_retrieval_failed_on", new String[] {
-                  emprefx.toLowerCase(), query.trim() }), e);
+              "exception.ebiembl_retrieval_failed_on", new String[]
+              { emprefx.toLowerCase(), query.trim() }), e);
     }
     return getEmblSequenceRecords(emprefx, query, reply);
   }
@@ -91,7 +91,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
           File reply) throws Exception
   {
     EmblFile efile = null;
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
 
     if (reply != null && reply.exists())
     {
@@ -102,8 +102,13 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       }
     }
 
-    List<SequenceI> peptides = new ArrayList<SequenceI>();
-    if (efile != null)
+    /*
+     * invalid accession gets a reply with no <entry> elements, text content of
+     * EmbFile reads something like (e.g.) this ungrammatical phrase
+     * Entry: <acc> display type is either not supported or entry is not found.
+     */
+    List<SequenceI> peptides = new ArrayList<>();
+    if (efile != null && efile.getEntries() != null)
     {
       for (EmblEntry entry : efile.getEntries())
       {