X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=24085d22be1159a777bfd1cbf88d69c7052f90b7;hb=a7bec763a3e4f17a549115f8f9f19ee4c742c26b;hp=dca2d0c4759d47a67efc24385bc047586f5adac7;hpb=8d3d3b4edf47e543b8b352c1b2c247cfc59122a4;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index dca2d0c..24085d2 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
@@ -32,25 +32,41 @@
     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"
+        };
+
 
         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");
-        }
+
+        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!
@@ -64,41 +80,57 @@
         public SequenceI[] readFile(String inFile, String type, String format)
             throws java.io.IOException
         {
+            this.inFile = inFile;
             try
             {
-                if (format.equals("FASTA"))
-                {
-                    afile = new FastaFile(inFile, type);
-                }
-                else if (format.equals("MSF"))
-                {
-                    afile = new MSFfile(inFile, type);
-                }
-                else if (format.equals("PileUp"))
-                {
-                    afile = new PileUpfile(inFile, type);
-                }
-                else if (format.equals("CLUSTAL"))
-                {
-                    afile = new ClustalFile(inFile, type);
-                }
-                else if (format.equals("BLC"))
-                {
-                    afile = new BLCFile(inFile, type);
-                }
-                else if (format.equals("PIR"))
-                {
-                    afile = new PIRFile(inFile, type);
-                }
-                else if (format.equals("PFAM"))
-                {
-                    afile = new PfamFile(inFile, type);
-                }
+              if (format.equals("FASTA"))
+              {
+                afile = new FastaFile(inFile, type);
+              }
+              else if (format.equals("MSF"))
+              {
+                afile = new MSFfile(inFile, type);
+              }
+              else if (format.equals("PileUp"))
+              {
+                afile = new PileUpfile(inFile, type);
+              }
+              else if (format.equals("CLUSTAL"))
+              {
+                afile = new ClustalFile(inFile, type);
+              }
+              else if (format.equals("BLC"))
+              {
+                afile = new BLCFile(inFile, type);
+              }
+              else if (format.equals("PIR"))
+              {
+                afile = new PIRFile(inFile, type);
+              }
+              else if (format.equals("PFAM"))
+              {
+                afile = new PfamFile(inFile, type);
+              }
+              else if (format.equals("JnetFile"))
+              {
+                afile = new JPredFile(inFile, type);
+                ( (JPredFile) afile).removeNonSequences();
+              }
+              else if (format.equals("PDB"))
+              {
+                afile = new MCview.PDBfile(inFile, type);
+              }
+              else if (format.equals("STH"))
+              {
+                afile = new StockholmFile(inFile, type);
+              }
+
 
-                return afile.getSeqsAsArray();
+              return afile.getSeqsAsArray();
             }
             catch (Exception e)
             {
+              e.printStackTrace();
               System.err.println("Failed to read alignment using the '" + format +
                                  "' reader.\n"+e);
 
@@ -177,6 +209,11 @@
                 {
                     afile = new PfamFile();
                 }
+                else if (format.equalsIgnoreCase("STH"))
+                {
+                  afile = new StockholmFile();
+                }
+
 
                 afile.addJVSuffix(jvsuffix);