X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=5de14a43272af4839a79231ca98976b92b67128d;hb=17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35;hp=8c376fcfbfd3c5ea7f681e09f4d8b32c099a87d8;hpb=b879c4a2d32d3489e63ac06917e81637e6bb4068;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 8c376fc..5de14a4 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,16 +20,20 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
 import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SeqDistanceContactMatrix;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
+import jalview.util.Platform;
 
 import java.io.File;
 import java.io.IOException;
@@ -151,14 +155,17 @@ 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
     {
@@ -174,7 +181,8 @@ 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
         {
@@ -187,9 +195,12 @@ 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));
@@ -421,30 +432,32 @@ 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)
     {
       protocol = DataSourceType.URL;
     }
-    else if (jalview.bin.Jalview.isJS())
+    else if (Platform.isJS())
     {
       protocol = DataSourceType.RELATIVE_URL;
     }
@@ -455,6 +468,10 @@ public class AppletFormatAdapter
     return protocol;
   }
 
+  /**
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     int i = 0;