X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=0a47a196d811d06c66faaa86b7ce1b3e09c6d23e;hb=ecef9bc6e3c5c651f2e03fe8fb6597b5dc3dcf05;hp=d42157b3e70c2821a18e04f1302bf8bd0c9d5405;hpb=e601d78bc7762386f570e346a803684c43a66ff1;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d42157b..0a47a19 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -45,29 +45,32 @@ 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, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+  { "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" };
+  { "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",
-      "sto" }; // ,
+  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+      "sto,stk" }; // ,
 
   // ".blast"
   // };
@@ -117,18 +120,22 @@ public class AppletFormatAdapter
   AlignFile afile = null;
 
   String inFile;
+
   /**
-   * character used to write newlines 
+   * character used to write newlines
    */
   protected String newline = System.getProperty("line.separator");
+
   public void setNewlineString(String nl)
   {
     newline = nl;
   }
+
   public String getNewlineString()
   {
     return newline;
   }
+
   /**
    * check that this format is valid for reading
    * 
@@ -441,7 +448,7 @@ public class AppletFormatAdapter
       }
       else if (format.equalsIgnoreCase("STH"))
       {
-        afile = new StockholmFile();
+        afile = new StockholmFile(alignment);
       }
       else if (format.equalsIgnoreCase("AMSA"))
       {
@@ -477,8 +484,9 @@ public class AppletFormatAdapter
   public static String checkProtocol(String file)
   {
     String protocol = FILE;
-  
-    if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+    String ft = file.toLowerCase().trim();
+    if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+            || ft.indexOf("file:") == 0)
     {
       protocol = URL;
     }
@@ -497,44 +505,47 @@ 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
       {
@@ -715,4 +726,5 @@ public class AppletFormatAdapter
     }
     return null;
   }
+
 }