Merge branch 'JAL-1199-Stk_writing' into rnaml_test

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 85ea8e0..2fc6d12 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -45,21 +45,24 @@ public class AppletFormatAdapter
    * method
    */
   public static final String[] WRITEABLE_FORMATS = new String[]
-  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "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,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+  { "fa,faa,fasta,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" };
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+      "STH" };
 
   /**
    * List of readable format file extensions by application in order
@@ -455,7 +458,7 @@ public class AppletFormatAdapter
       }
       else if (format.equalsIgnoreCase("STH"))
       {
-        afile = new StockholmFile();
+        afile = new StockholmFile(alignment);
       }
       else if (format.equalsIgnoreCase("AMSA"))
       {
@@ -517,44 +520,47 @@ 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
       {
@@ -735,4 +741,5 @@ public class AppletFormatAdapter
     }
     return null;
   }
+
 }