From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 18 Jan 2019 14:06:09 +0000 (+0000)
Subject: Merge branch 'develop' into feature/JAL-3063jaxbNoCastor
X-Git-Tag: Release_2_11_0~17^2~97^2~29^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=228413670a113d52552ad1248e6baa20d12feb70;hp=1d6ce1bd2d0cf108d6207694e4aa6b845de11049;p=jalview.git

Merge branch 'develop' into feature/JAL-3063jaxbNoCastor
---

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 86282c7..d97bf69 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -178,16 +178,12 @@ public class Uniprot extends DbSourceProxyImpl
   SequenceI uniprotEntryToSequence(Entry entry)
   {
     String id = getUniprotEntryId(entry);
-    String seqString = entry.getSequence().getValue();
-
     /*
-     * for backwards compatibility with Castor processing,
-     * remove any internal spaces
+     * Sequence should not include any whitespace, but JAXB leaves these in
      */
-    if (seqString.indexOf(' ') > -1)
-    {
-      seqString = seqString.replace(" ", "");
-    }
+    String seqString = entry.getSequence().getValue().replaceAll("\\s*",
+            "");
+
     SequenceI sequence = new Sequence(id,
             seqString);
     sequence.setDescription(getUniprotEntryDescription(entry));
diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index e835724..86f5602 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -216,6 +216,8 @@ public class UniprotTest
     SequenceI seq = new Uniprot().uniprotEntryToSequence(entry);
     assertNotNull(seq);
     assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
+    assertEquals(seq.getSequenceAsString(),
+            seq.createDatasetSequence().getSequenceAsString());
 
   }