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