Classes for parsing clustal formatted files.

For example:
try {

// Get Parser.
ClustalFileParserFactory cfpf = ClustalFileParserFactory.newInstance();
ClustalFileParser parser = cfpf.newParser();

// Initialise handler.
MyClustalFileHandler handler = new MyClustalFileHandler();

// Parse clustal file.
parser.parse(_file, handler);

// Subsequent code depends on handler.
// ...
// ...

}
catch(Exception e) {
JOptionPane.showMessageDialog(
this,
e.getMessage(),
"Exception",
JOptionPane.ERROR_MESSAGE
);
e.printStackTrace();
}