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

[jalview.git] / src / jalview / analysis / SequenceIdMatcher.java

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 3d4cbe7..3ec162d 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import java.util.Locale;
+
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 
@@ -74,13 +76,13 @@ public class SequenceIdMatcher
       dbseq = dbseq.getDatasetSequence();
     }
     // add in any interesting identifiers
-    if (dbseq.getDBRefs() != null)
+    List<DBRefEntry> dbr = dbseq.getDBRefs(); 
+    if (dbr != null)
     {
-      DBRefEntry dbr[] = dbseq.getDBRefs();
       SeqIdName sid = null;
-      for (int r = 0; r < dbr.length; r++)
+      for (int r = 0, nr = dbr.size(); r < nr; r++)
       {
-        sid = new SeqIdName(dbr[r].getAccessionId());
+        sid = new SeqIdName(dbr.get(r).getAccessionId());
         if (!names.containsKey(sid))
         {
           names.put(sid, seq);
@@ -289,7 +291,7 @@ public class SequenceIdMatcher
     {
       if (s != null)
       {
-        id = s.toLowerCase();
+        id = s.toLowerCase(Locale.ROOT);
       }
       else
       {
@@ -319,7 +321,7 @@ public class SequenceIdMatcher
       {
         if (s instanceof String)
         {
-          return this.stringequals(((String) s).toLowerCase());
+          return this.stringequals(((String) s).toLowerCase(Locale.ROOT));
         }
       }