X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=2e4ddc4438700055fb745beb09d299c093e0b2fc;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=232de57345a4e6c57637233ecd67dadb65bd3156;hpb=ed8d18abc302ac802ad1d0611f3fe2fef570ab5e;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 232de57..2e4ddc4 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,9 +20,6 @@
 
     import jalview.datamodel.*;
 
-    import java.util.Vector;
-
-
     /**
      * DOCUMENT ME!
      *
@@ -38,8 +35,8 @@
         };
 
         public static final String [] WRITEABLE_FORMATS = new String[]
-            {
-            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"
+        {
+            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"  //, "AMSA"
         };
 
 
@@ -175,14 +172,9 @@
          * @return DOCUMENT ME!
          */
         public String formatSequences(String format,
-                                      Vector seqs,
+                                      AlignmentI alignment,
                                       boolean jvsuffix)
         {
-            SequenceI[] s = new SequenceI[seqs.size()];
-
-            for (int i = 0; i < seqs.size(); i++)
-                s[i] = (SequenceI) seqs.elementAt(i);
-
             try
             {
                 AlignFile afile = null;
@@ -219,11 +211,14 @@
                 {
                   afile = new StockholmFile();
                 }
-
+                else if (format.equals("AMSA"))
+                {
+                  afile = new AMSAFile(alignment);
+                }
 
                 afile.addJVSuffix(jvsuffix);
 
-                afile.setSeqs(s);
+                afile.setSeqs( alignment.getSequencesArray() );
 
                 return afile.print();
             }