- /*\r
- * Jalview - A Sequence Alignment Editor and Viewer\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
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
- package jalview.io;\r
-\r
- import jalview.datamodel.*;\r
-\r
- import java.util.Vector;\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
- public class AppletFormatAdapter\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package jalview.io;\r
+\r
+import jalview.datamodel.*;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AppletFormatAdapter\r
+{\r
+ /** DOCUMENT ME!! */\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" //, "AMSA"\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
+ 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
+ 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