uk.ac.man.bioinf.io
Interface AlignmentInputParser

All Known Implementing Classes:

AbstractProteinAlignmentInputParser

public interface AlignmentInputParser

This is an interface that provides a definition for any sequence parsers. It takes input and returns a sequence alignment object. Parsers may or may not have state attached to them. Furthermore they may be re-entered or alternatively they may not. You have been warned.

One thing which cannot be enforced in the interface is that every parser should have a default constructor (ie no arguments to the constructor). This is because the parsers are generated through Class.newInstance(). Created: Thu May 25 23:01:02 2000

Version:

$Id: AlignmentInputParser.java,v 1.4 2001/04/11 17:04:43 lord Exp $

Author:

Julian

Method Summary

String	getDescription() Returns the description of this alignment parser, and should be human readable/understandable.
SequenceAlignment	parse(Identifier ident, Reader reader, ParserExceptionHandler eh)
SequenceAlignment	parse(Reader reader, ParserExceptionHandler eh) This method returns a sequence alignment from a buffered reader input stream.

Method Detail

parse

public SequenceAlignment parse(Identifier ident,
                               Reader reader,
                               ParserExceptionHandler eh)
                        throws IOException

IOException

parse

public SequenceAlignment parse(Reader reader,
                               ParserExceptionHandler eh)
                        throws IOException

This method returns a sequence alignment from a buffered reader input stream.

Parameters:

reader - the input stream

eh - exception handler

Returns:

the sequence alignment

IOException

getDescription

public String getDescription()

Returns the description of this alignment parser, and should be human readable/understandable.

Returns:

the description