X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=00fcb9c39c598d12dc6d285b5b9720bb080ba129;hb=f41806761ec9086c852941a7f91c890190fb522a;hp=6db04a09a546dfa26f902ca1967bc12a2198e5d5;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 6db04a0..00fcb9c 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,6 +20,8 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
 import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
@@ -152,14 +154,17 @@ public class AppletFormatAdapter
   {
     return readFile(null, file, sourceType, fileFormat);
   }
-  
-  public AlignmentI readFile(File selectedFile, String file, DataSourceType sourceType,
-          FileFormatI fileFormat) throws IOException
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat)
+          throws IOException
   {
 
     this.selectedFile = selectedFile;
     if (selectedFile != null)
+    {
       this.inFile = selectedFile.getPath();
+    }
     this.inFile = file;
     try
     {
@@ -175,7 +180,8 @@ public class AppletFormatAdapter
         if (isParseWithJMOL)
         {
           // needs a File option
-          alignFile = new JmolParser(selectedFile == null ? inFile : selectedFile, sourceType);
+          alignFile = new JmolParser(
+                  selectedFile == null ? inFile : selectedFile, sourceType);
         }
         else
         {
@@ -188,9 +194,12 @@ public class AppletFormatAdapter
         ((StructureFile) alignFile).setDbRefType(
                 FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
       }
-      else if (selectedFile != null) {
-        alignFile = fileFormat.getReader(new FileParse(selectedFile, sourceType));
-      } else 
+      else if (selectedFile != null)
+      {
+        alignFile = fileFormat
+                .getReader(new FileParse(selectedFile, sourceType));
+      }
+      else
       {
         // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
         alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
@@ -422,24 +431,26 @@ public class AppletFormatAdapter
     return null;
   }
 
-
   /**
    * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
    * data
    * 
    * BH 2018 allows File or String, and can return RELATIVE_URL
    *
-   * @param dataObject File or String
+   * @param dataObject
+   *          File or String
    * @return the protocol for the input data
    */
   public static DataSourceType checkProtocol(Object dataObject)
   {
-    if(dataObject instanceof File)
+    if (dataObject instanceof File)
+    {
       return DataSourceType.FILE;
-    
+    }
+
     String data = dataObject.toString();
     DataSourceType protocol = DataSourceType.PASTE;
-    String ft = data.toLowerCase().trim();
+    String ft = data.toLowerCase(Locale.ROOT).trim();
     if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
             || ft.indexOf("file:") == 0)
     {
@@ -456,6 +467,10 @@ public class AppletFormatAdapter
     return protocol;
   }
 
+  /**
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     int i = 0;