uk.ac.man.bioinf.io
Interface AlignmentOutputParser

All Known Implementing Classes:
MotProteinParser, PIRProteinAlignmentParser

public interface AlignmentOutputParser

This is an interface that provides a definition for any sequence output parsing. It takes a sequence alignment and returns a writer. Parsers may or may not have state attached to them, and furthermore, they may be re-entered or alternately they may not. You have been warned!

One thing that cannot be enforced in the interface is, every parser should have a default constructor (i.e., no arguments to the constructor). This is because the parsers are generated through Class.newInstance(). Created: Mon Jul 31 13:04:06 2000

Version:
$Id: AlignmentOutputParser.java,v 1.3 2001/04/11 17:04:43 lord Exp $
Author:
Julian Selley

Method Summary
 String getDescription()
          Returns the description of this alignment output parser, and should be human readable/understandable.
 Writer write(SequenceAlignment sa, Writer writer, ParserExceptionHandler eh)
          Returns a writer for output, when provided with a sequence alignment.
 

Method Detail

write

public Writer write(SequenceAlignment sa,
                    Writer writer,
                    ParserExceptionHandler eh)
Returns a writer for output, when provided with a sequence alignment. Exceptions are handled by the supplied exception handler.

Parameters:
sa - the sequence alignment
eh - the exception handler
Returns:
the writer for output

getDescription

public String getDescription()
Returns the description of this alignment output parser, and should be human readable/understandable.

Returns:
the description