HEADER and ATOM must be position 0

[jalview.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 8d2d796..24085d2 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,6 +1,6 @@
     /*\r
     * Jalview - A Sequence Alignment Editor and Viewer\r
-    * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+    * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
     *\r
     * This program is free software; you can redistribute it and/or\r
     * modify it under the terms of the GNU General Public License\r
@@ -32,34 +32,42 @@
     public class AppletFormatAdapter\r
     {\r
         /** DOCUMENT ME!! */\r
-        public static final Vector formats = new Vector();\r
+        public static final String [] READABLE_FORMATS = new String[]\r
+        {\r
+            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"\r
+        };\r
+\r
+        public static final String [] WRITEABLE_FORMATS = new String[]\r
+            {\r
+            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"\r
+        };\r
+\r
 \r
         public static String INVALID_CHARACTERS = "Contains invalid characters";\r
 \r
         public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +\r
                                                  "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";\r
 \r
-        static\r
-        {\r
-            formats.addElement("BLC");\r
-            formats.addElement("CLUSTAL");\r
-            formats.addElement("FASTA");\r
-            formats.addElement("MSF");\r
-            formats.addElement("PileUp");\r
-            formats.addElement("PIR");\r
-            formats.addElement("PFAM");\r
-            formats.addElement("PDB");\r
-        }\r
-\r
 \r
         public static String FILE = "File";\r
         public static String URL = "URL";\r
         public static String PASTE = "Paste";\r
         public static String CLASSLOADER = "ClassLoader";\r
 \r
+\r
         AlignFile afile = null;\r
         String inFile;\r
 \r
+        public static final boolean isValidFormat(String format)\r
+        {\r
+          boolean valid = false;\r
+          for(int i=0; i<READABLE_FORMATS.length; i++)\r
+            if(READABLE_FORMATS[i].equalsIgnoreCase(format))\r
+              return true;\r
+\r
+          return valid;\r
+        }\r
+\r
         /**\r
          * DOCUMENT ME!\r
          *\r
@@ -112,6 +120,11 @@
               {\r
                 afile = new MCview.PDBfile(inFile, type);\r
               }\r
+              else if (format.equals("STH"))\r
+              {\r
+                afile = new StockholmFile(inFile, type);\r
+              }\r
+\r
 \r
               return afile.getSeqsAsArray();\r
             }\r
@@ -196,6 +209,11 @@
                 {\r
                     afile = new PfamFile();\r
                 }\r
+                else if (format.equalsIgnoreCase("STH"))\r
+                {\r
+                  afile = new StockholmFile();\r
+                }\r
+\r
 \r
                 afile.addJVSuffix(jvsuffix);\r
 \r