X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=6679a03a907e3e01224a66c4b7385aa0088761cb;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=a8485550d2494ac13e7832a7be10ab0e95759e13;hpb=91f6f98109a5c9ffda2ed8da3875773e3469f2f2;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index a848555..6679a03 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -45,28 +46,31 @@ 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", "STH",
+      "AMSA" };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
    * that are writable by the application.
    */
   public static final String[] WRITABLE_EXTENSIONS = new String[]
-  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar", "sto,stk" };
+  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+      "sto,stk" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
    * WRITABLE_EXTENSIONS list of formats.
    */
   public static final String[] WRITABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", "STH"};
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+      "STH" };
 
   /**
    * List of readable format file extensions by application in order
    * corresponding to READABLE_FNAMES
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
-  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
       "sto,stk" }; // ,
 
   // ".blast"
@@ -502,44 +506,47 @@ public class AppletFormatAdapter
         {
           System.out.println("Reading file: " + f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
-          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)
+          String fName = f.getName();
           {
-            System.out.println("Alignment contains " + al.getHeight()
-                    + " sequences and " + al.getWidth() + " columns.");
-            try
+            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(new AppletFormatAdapter().formatSequences(
-                      "FASTA", al, true));
-            } catch (Exception e)
+              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.err
-                      .println("Couln't format the alignment for output as a FASTA file.");
-              e.printStackTrace(System.err);
+              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");
           }
-          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
       {
@@ -720,4 +727,5 @@ public class AppletFormatAdapter
     }
     return null;
   }
+
 }