X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=d9dd79d2bcba215458556f66cb88afc41e8d8593;hb=6129931bfa23eec90e6556a4d0412ef34aff5759;hp=1dbfdefeb8d2e92e58dd734fc16541522a9278fd;hpb=4815037f13748676b04b91dc761b73cf6f2d6ecd;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 1dbfdef..d9dd79d 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -155,84 +155,13 @@ public class FormatAdapter extends AppletFormatAdapter
    */
   public String formatSequences(FileFormatI format, SequenceI[] seqs)
   {
-    //
-    // try
-    // {
     boolean withSuffix = getCacheSuffixDefault(format);
-    return format.getAlignmentFile().print(seqs, withSuffix);
-      // null;
-      //
-      // if (format.equalsIgnoreCase("FASTA"))
-      // {
-      // afile = new FastaFile();
-      // afile.addJVSuffix(jalview.bin.Cache.getDefault("FASTA_JVSUFFIX",
-      // true));
-      // }
-      // else if (format.equalsIgnoreCase("MSF"))
-      // {
-      // afile = new MSFfile();
-      // afile.addJVSuffix(jalview.bin.Cache
-      // .getDefault("MSF_JVSUFFIX", true));
-      // }
-      // else if (format.equalsIgnoreCase("PileUp"))
-      // {
-      // afile = new PileUpfile();
-      // afile.addJVSuffix(jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX",
-      // true));
-      // }
-      // else if (format.equalsIgnoreCase("CLUSTAL"))
-      // {
-      // afile = new ClustalFile();
-      // afile.addJVSuffix(jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX",
-      // true));
-      // }
-      // else if (format.equalsIgnoreCase("BLC"))
-      // {
-      // afile = new BLCFile();
-      // afile.addJVSuffix(jalview.bin.Cache
-      // .getDefault("BLC_JVSUFFIX", true));
-      // }
-      // else if (format.equalsIgnoreCase("PIR"))
-      // {
-      // afile = new PIRFile();
-      // afile.addJVSuffix(jalview.bin.Cache
-      // .getDefault("PIR_JVSUFFIX", true));
-      // }
-      // else if (format.equalsIgnoreCase("PFAM"))
-      // {
-      // afile = new PfamFile();
-      // afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX",
-      // true));
-      // }
-      // /*
-      // * amsa is not supported by this function - it requires an alignment
-      // * rather than a sequence vector else if
-      // (format.equalsIgnoreCase("AMSA"))
-      // * { afile = new AMSAFile(); afile.addJVSuffix(
-      // * jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true)); }
-      // */
-
-//      afile.setSeqs(seqs);
-//      String afileresp = afile.print();
-//      if (afile.hasWarningMessage())
-//      {
-//        System.err.println("Warning raised when writing as " + format
-//                + " : " + afile.getWarningMessage());
-//      }
-//      return afileresp;
-//    } catch (Exception e)
-//    {
-//      System.err.println("Failed to write alignment as a '" + format
-//              + "' file\n");
-//      e.printStackTrace();
-//    }
-//
-//    return null;
+    return format.getWriter(null).print(seqs, withSuffix);
   }
 
   public boolean getCacheSuffixDefault(FileFormatI format)
   {
-    return Cache.getDefault(format.toString() + "_JVSUFFIX", true);
+    return Cache.getDefault(format.getName() + "_JVSUFFIX", true);
   }
 
   public String formatSequences(FileFormatI format, AlignmentI alignment,
@@ -329,8 +258,8 @@ public class FormatAdapter extends AppletFormatAdapter
             selectedOnly);
   }
 
-  public AlignmentI readFromFile(AlignmentFileI source, FileFormatI format)
-          throws IOException
+  public AlignmentI readFromFile(AlignmentFileReaderI source,
+          FileFormatI format) throws IOException
   {
     FileParse fp = new FileParse(source.getInFile(),
             source.getDataSourceType());