From 415f149083cc1a2112b922a18688adce0e1025d8 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 23 May 2016 14:34:22 +0100
Subject: [PATCH] JAL-2113 remove spaces in sequence from unmarshalling
 newlines

---
 src/jalview/datamodel/xdb/embl/EmblSequence.java    |    3 ++-
 test/jalview/datamodel/xdb/embl/EmblTestHelper.java |    4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/xdb/embl/EmblSequence.java b/src/jalview/datamodel/xdb/embl/EmblSequence.java
index 5a18929..92c424b 100644
--- a/src/jalview/datamodel/xdb/embl/EmblSequence.java
+++ b/src/jalview/datamodel/xdb/embl/EmblSequence.java
@@ -43,6 +43,7 @@ public class EmblSequence
    */
   public void setSequence(String sequence)
   {
-    this.sequence = sequence;
+    // remove spaces introduced by unmarshalling of newline characters
+    this.sequence = sequence.replace(" ", "");
   }
 }
diff --git a/test/jalview/datamodel/xdb/embl/EmblTestHelper.java b/test/jalview/datamodel/xdb/embl/EmblTestHelper.java
index 8f631df..71ca508 100644
--- a/test/jalview/datamodel/xdb/embl/EmblTestHelper.java
+++ b/test/jalview/datamodel/xdb/embl/EmblTestHelper.java
@@ -17,7 +17,9 @@ public class EmblTestHelper
           + "<xref db=\"GOA\" id=\"P00340\" secondaryId=\"2.1\" /><xref db=\"InterPro\" id=\"IPR001236\" />"
           + "<qualifier name=\"note\"><value>L-lactate dehydrogenase A-chain</value><value>pickle</value></qualifier>"
           + "<qualifier name=\"translation\"><value>MSLKDHLIHN</value><evidence>Keith</evidence></qualifier>"
-          + "</feature>" + "<sequence>GTGACG</sequence></entry></ROOT>";
+          // emulate EMBL XML 1.2 which splits sequence data every 60 characters
+          // see EmblSequence.setSequence
+          + "</feature>" + "<sequence>GTG\nACG</sequence></entry></ROOT>";
 
   static EmblFile getEmblFile()
   {
-- 
1.7.10.2