X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=2e4ddc4438700055fb745beb09d299c093e0b2fc;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=8d2d796ae98cff03a278d8d13c64b99e2b9a73e5;hpb=a6afc82877599e6ad2c52f01249c36338f251983;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 8d2d796..2e4ddc4 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,6 +1,6 @@
     /*
     * Jalview - A Sequence Alignment Editor and Viewer
-    * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+    * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
     *
     * This program is free software; you can redistribute it and/or
     * modify it under the terms of the GNU General Public License
@@ -20,9 +20,6 @@
 
     import jalview.datamodel.*;
 
-    import java.util.Vector;
-
-
     /**
      * DOCUMENT ME!
      *
@@ -32,34 +29,42 @@
     public class AppletFormatAdapter
     {
         /** DOCUMENT ME!! */
-        public static final Vector formats = new Vector();
+        public static final String [] READABLE_FORMATS = new String[]
+        {
+            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"
+        };
+
+        public static final String [] WRITEABLE_FORMATS = new String[]
+        {
+            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"  //, "AMSA"
+        };
+
 
         public static String INVALID_CHARACTERS = "Contains invalid characters";
 
         public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
                                                  "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
 
-        static
-        {
-            formats.addElement("BLC");
-            formats.addElement("CLUSTAL");
-            formats.addElement("FASTA");
-            formats.addElement("MSF");
-            formats.addElement("PileUp");
-            formats.addElement("PIR");
-            formats.addElement("PFAM");
-            formats.addElement("PDB");
-        }
-
 
         public static String FILE = "File";
         public static String URL = "URL";
         public static String PASTE = "Paste";
         public static String CLASSLOADER = "ClassLoader";
 
+
         AlignFile afile = null;
         String inFile;
 
+        public static final boolean isValidFormat(String format)
+        {
+          boolean valid = false;
+          for(int i=0; i<READABLE_FORMATS.length; i++)
+            if(READABLE_FORMATS[i].equalsIgnoreCase(format))
+              return true;
+
+          return valid;
+        }
+
         /**
          * DOCUMENT ME!
          *
@@ -69,7 +74,7 @@
          *
          * @return DOCUMENT ME!
          */
-        public SequenceI[] readFile(String inFile, String type, String format)
+        public Alignment readFile(String inFile, String type, String format)
             throws java.io.IOException
         {
             this.inFile = inFile;
@@ -112,8 +117,16 @@
               {
                 afile = new MCview.PDBfile(inFile, type);
               }
+              else if (format.equals("STH"))
+              {
+                afile = new StockholmFile(inFile, type);
+              }
 
-              return afile.getSeqsAsArray();
+              Alignment al = new Alignment(afile.getSeqsAsArray());
+
+              afile.addAnnotations(al);
+
+              return al;
             }
             catch (Exception e)
             {
@@ -130,7 +143,10 @@
                 try{
                   // Possible sequence is just residues with no label
                   afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
-                  return afile.getSeqsAsArray();
+                  Alignment al = new Alignment(afile.getSeqsAsArray());
+                  afile.addAnnotations(al);
+                  return al;
+
                 }
                 catch(Exception ex)
                 {
@@ -156,14 +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;
@@ -196,10 +207,18 @@
                 {
                     afile = new PfamFile();
                 }
+                else if (format.equalsIgnoreCase("STH"))
+                {
+                  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();
             }