-public class FormatAdapter {\r
- public static Vector formats = new Vector();\r
-\r
- static {\r
- formats.addElement("FASTA");\r
- formats.addElement("MSF");\r
- formats.addElement("PileUp");\r
- formats.addElement("CLUSTAL");\r
- formats.addElement("BLC");\r
- formats.addElement("PIR");\r
- formats.addElement("PFAM");\r
- }\r
-\r
- public static SequenceI[] readFile(String inFile, String type, String format) {\r
- try {\r
- AlignFile afile = null;\r
-\r
- if (format.equals("FASTA")) {\r
- afile = new FastaFile(inFile, type);\r
- } else if (format.equals("MSF")) {\r
- afile = new MSFfile(inFile, type);\r
- } else if (format.equals("PileUp")) {\r
- afile = new PileUpfile(inFile, type);\r
- } else if (format.equals("CLUSTAL")) {\r
- afile = new ClustalFile(inFile, type);\r
- } else if (format.equals("BLC")) {\r
- afile = new BLCFile(inFile, type);\r
- } else if (format.equals("PIR")) {\r
- afile = new PIRFile(inFile, type);\r
- } else if (format.equals("PFAM")) {\r
- afile = new PfamFile(inFile, type);\r
- }\r
-\r
- return afile.getSeqsAsArray();\r
- } catch (Exception e) {\r
- System.err.println("Failed to read alignment using the '" + format +\r
- "' reader.");\r
- e.printStackTrace();\r
- }\r
-\r
- return null;\r
- }\r
-\r
- public static String formatSequences(String format, Vector seqs) {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class FormatAdapter extends AppletFormatAdapter\r
+{\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param format DOCUMENT ME!\r
+ * @param seqs DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String formatSequences(String format, Vector seqs)\r
+ {\r