JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation

[jalview.git] / src / jalview / ext / ensembl / EnsemblInfo.java

diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index 97a8e74..a32edb3 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -1,5 +1,27 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
+import java.util.Locale;
+
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.util.JSONUtils;
@@ -74,7 +96,7 @@ public class EnsemblInfo extends EnsemblRestClient
     {
       fetchDivisions();
     }
-    return divisions.get(division.toUpperCase());
+    return divisions.get(division.toUpperCase(Locale.ROOT));
   }
 
   /**
@@ -88,17 +110,21 @@ public class EnsemblInfo extends EnsemblRestClient
     /*
      * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
      */
-    divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
+    divisions.put(DBRefSource.ENSEMBL.toUpperCase(Locale.ROOT),
+            ensemblDomain);
     try
     {
       @SuppressWarnings("unchecked")
-         Iterator<Object> rvals = (Iterator<Object>) getJSON(getDivisionsUrl(ensemblGenomesDomain), null, -1, MODE_ITERATOR, null);
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(
+              getDivisionsUrl(ensemblGenomesDomain), null, -1,
+              MODE_ITERATOR, null);
       if (rvals == null)
-         return;
+        return;
       while (rvals.hasNext())
       {
         String division = rvals.next().toString();
-        divisions.put(division.toUpperCase(), ensemblGenomesDomain);
+        divisions.put(division.toUpperCase(Locale.ROOT),
+                ensemblGenomesDomain);
       }
     } catch (IOException | ParseException | NumberFormatException e)
     {
@@ -108,15 +134,17 @@ public class EnsemblInfo extends EnsemblRestClient
 
   /**
    * Constructs the URL for the EnsemblGenomes /info/divisions REST service
-   * @param domain TODO
+   * 
+   * @param domain
+   *          TODO
    * 
    * @return
    * @throws MalformedURLException
    */
   URL getDivisionsUrl(String domain) throws MalformedURLException
   {
-    return new URL(domain
-            + "/info/divisions?content-type=application/json");
+    return new URL(
+            domain + "/info/divisions?content-type=application/json");
   }
 
   /**
@@ -124,7 +152,8 @@ public class EnsemblInfo extends EnsemblRestClient
    * 
    * @return
    */
-  public Set<String> getDivisions() {
+  public Set<String> getDivisions()
+  {
     if (divisions == null)
     {
       fetchDivisions();