JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...

[jalview.git] / src / jalview / ws / sifts / SiftsClient.java

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index ae58082..5a03aea 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws.sifts;
 
+import java.util.Locale;
+
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -219,7 +221,7 @@ public class SiftsClient implements SiftsClientI
     }
 
     String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
-            + pdbId.toLowerCase() + ".xml.gz";
+            + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz";
     File siftsFile = new File(siftsFileName);
     if (siftsFile.exists())
     {
@@ -233,7 +235,7 @@ public class SiftsClient implements SiftsClientI
         BackupFiles.moveFileToFile(siftsFile, oldSiftsFile);
         try
         {
-          siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+          siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT));
           oldSiftsFile.delete();
           return siftsFile;
         } catch (IOException e)
@@ -250,7 +252,7 @@ public class SiftsClient implements SiftsClientI
     }
     try
     {
-      siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+      siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT));
     } catch (IOException e)
     {
       throw new SiftsException(e.getMessage());
@@ -356,7 +358,7 @@ public class SiftsClient implements SiftsClientI
   public static boolean deleteSiftsFileByPDBId(String pdbId)
   {
     File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
-            + pdbId.toLowerCase() + ".xml.gz");
+            + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz");
     if (siftsFile.exists())
     {
       return siftsFile.delete();
@@ -431,7 +433,7 @@ public class SiftsClient implements SiftsClientI
         for (MapRegion mapRegion : mapRegions)
         {
           accessions
-                  .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
+                  .add(mapRegion.getDb().getDbAccessionId().toLowerCase(Locale.ROOT));
         }
       }
     }
@@ -501,9 +503,9 @@ public class SiftsClient implements SiftsClientI
     HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
     for (DBRefEntry dbref : seq.getDBRefs())
     {
-      dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
+      dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase(Locale.ROOT));
     }
-    dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase());
+    dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase(Locale.ROOT));
 
     curDBRefAccessionIdsString = dbRefAccessionIdsString;
     curSourceDBRef = sourceDBRef.getAccessionId();
@@ -891,14 +893,14 @@ public class SiftsClient implements SiftsClientI
   {
     boolean isStrictMatch = true;
     return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
-            : curDBRefAccessionIdsString.contains(accession.toLowerCase());
+            : curDBRefAccessionIdsString.contains(accession.toLowerCase(Locale.ROOT));
   }
 
   private boolean isFoundInSiftsEntry(String accessionId)
   {
     Set<String> siftsDBRefs = getAllMappingAccession();
     return accessionId != null
-            && siftsDBRefs.contains(accessionId.toLowerCase());
+            && siftsDBRefs.contains(accessionId.toLowerCase(Locale.ROOT));
   }
 
   /**