Classes for parsing Fasta formatted files.
For example:
try {
// Get Parser.
FastaFileParserFactory ffpf = FastaFileParserFactory.newInstance();
FastaFileParser parser = ffpf.newParser();
// Initialise handler.
MyFastaFileHandler handler = new MyFastaFileHandler();
// Parse file.
parser.parse(reader, handler);
// Subsequent code depends on handler.
// ...
// ...
}
catch (IOException ioe) {
System.err.println("Input/Output Exception: " + ioe.getMessage());
}
catch (DatabaseParserException dpe) {
System.err.println("Database Parser Exception: " + dpe.getMessage());
}
catch (RecordConflictException rce) {
System.err.println("Record Conflict Exception: " + rce.getMessage());
}
catch (NonIUBCharacterException nice) {
System.err.println("Non IUB Character: " + nice.getMessage());
}