Merge branch 'patch/JAL-3874_newJmolAndGradleDedup' into develop

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index d1da9de..a80a530 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws.dbsources;
 
+import java.util.Locale;
+
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -139,7 +141,7 @@ public class Uniprot extends DbSourceProxyImpl
     startQuery();
     try
     {
-      queries = queries.toUpperCase().replaceAll(
+      queries = queries.toUpperCase(Locale.ROOT).replaceAll(
               "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
       AlignmentI al = null;
 
@@ -180,16 +182,12 @@ 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));
@@ -199,10 +197,12 @@ public class Uniprot extends DbSourceProxyImpl
      */
     final String dbVersion = getDbVersion();
     List<DBRefEntry> dbRefs = new ArrayList<>();
+    boolean canonical=true;
     for (String accessionId : entry.getAccession())
     {
       DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
-              accessionId);
+              accessionId,null,canonical);
+      canonical=false;
       dbRefs.add(dbRef);
     }