/*\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
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
{\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
{\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