Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index be0df21..ff959b0 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -72,10 +72,11 @@ public class IdentifyFile
     // preserves original behaviour prior to version 2.3
   }
 
-  public FileFormatI identify(AlignmentFileReaderI file, boolean closeSource)
-          throws IOException
+  public FileFormatI identify(AlignmentFileReaderI file,
+          boolean closeSource) throws IOException
   {
-    FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());
+    FileParse fp = new FileParse(file.getInFile(),
+            file.getDataSourceType());
     return identify(fp, closeSource);
   }
 
@@ -309,9 +310,8 @@ public class IdentifyFile
           break;
         }
 
-        if ((data.indexOf("//") == 0)
-                || ((data.indexOf("!!") > -1) && (data.indexOf("!!") < data
-                        .indexOf("_MULTIPLE_ALIGNMENT "))))
+        if ((data.indexOf("//") == 0) || ((data.indexOf("!!") > -1) && (data
+                .indexOf("!!") < data.indexOf("_MULTIPLE_ALIGNMENT "))))
         {
           reply = FileFormat.MSF;
 
@@ -361,8 +361,8 @@ public class IdentifyFile
     }
     if (trimmedLength == 0)
     {
-      System.err
-              .println("File Identification failed! - Empty file was read.");
+      System.err.println(
+              "File Identification failed! - Empty file was read.");
       throw new FileFormatException("EMPTY DATA FILE");
     }
     System.out.println("File format identified as " + reply.toString());
@@ -428,9 +428,9 @@ public class IdentifyFile
         type = ider.identify(args[i], DataSourceType.FILE);
       } catch (FileFormatException e)
       {
-        System.err.println(String.format(
-                "Error '%s' identifying file type for %s", args[i],
-                e.getMessage()));
+        System.err.println(
+                String.format("Error '%s' identifying file type for %s",
+                        args[i], e.getMessage()));
       }
       System.out.println("Type of " + args[i] + " is " + type);
     }