Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into develop

[jalview.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index c25d3d9..5de14a4 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -155,9 +155,10 @@ 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;
@@ -180,7 +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
         {
@@ -193,9 +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));
@@ -427,23 +432,23 @@ 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(Locale.ROOT).trim();