Merge branch 'develop' into develop_m2_8_1_2

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 2fc6d12..eac7cf2 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -45,8 +45,7 @@ public class AppletFormatAdapter
    * method
    */
   public static final String[] WRITEABLE_FORMATS = new String[]
-  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "AMSA" };
+  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
@@ -520,47 +519,43 @@ public class AppletFormatAdapter
         {
           System.out.println("Reading file: " + f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
-          String fName = f.getName();
+          Runtime r = Runtime.getRuntime();
+          System.gc();
+          long memf = -r.totalMemory() + r.freeMemory();
+          long t1 = -System.currentTimeMillis();
+          Alignment al = afa.readFile(args[i], FILE,
+                  new IdentifyFile().Identify(args[i], FILE));
+          t1 += System.currentTimeMillis();
+          System.gc();
+          memf += r.totalMemory() - r.freeMemory();
+          if (al != null)
           {
-            Runtime r = Runtime.getRuntime();
-            System.gc();
-            long memf = -r.totalMemory() + r.freeMemory();
-            long t1 = -System.currentTimeMillis();
-            Alignment al = afa.readFile(args[i], FILE,
-                    new IdentifyFile().Identify(args[i], FILE));
-            t1 += System.currentTimeMillis();
-            System.gc();
-            memf += r.totalMemory() - r.freeMemory();
-            if (al != null)
+            System.out.println("Alignment contains " + al.getHeight()
+                    + " sequences and " + al.getWidth() + " columns.");
+            try
             {
-              System.out.println("Alignment contains " + al.getHeight()
-                      + " sequences and " + al.getWidth() + " columns.");
-              try
-              {
-                System.out.println(new AppletFormatAdapter()
-                        .formatSequences("FASTA", al, true));
-              } catch (Exception e)
-              {
-                System.err
-                        .println("Couln't format the alignment for output as a FASTA file.");
-                e.printStackTrace(System.err);
-              }
-            }
-            else
+              System.out.println(new AppletFormatAdapter().formatSequences(
+                      "FASTA", al, true));
+            } catch (Exception e)
             {
-              System.out.println("Couldn't read alignment");
+              System.err
+                      .println("Couln't format the alignment for output as a FASTA file.");
+              e.printStackTrace(System.err);
             }
-            System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
-            System.out
-                    .println("Difference between free memory now and before is "
-                            + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
           }
+          else
+          {
+            System.out.println("Couldn't read alignment");
+          }
+          System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
+          System.out
+                  .println("Difference between free memory now and before is "
+                          + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
         } catch (Exception e)
         {
           System.err.println("Exception when dealing with " + i
                   + "'th argument: " + args[i] + "\n" + e);
         }
-
       }
       else
       {
@@ -741,5 +736,4 @@ public class AppletFormatAdapter
     }
     return null;
   }
-
 }