uk.ac.man.bioinf.io.parsers
Class MotProteinParser

java.lang.Object
  |
  +--uk.ac.man.bioinf.io.parsers.MotProteinParser
All Implemented Interfaces:
AlignmentOutputParser

public class MotProteinParser
extends Object
implements AlignmentOutputParser

MotProteinParser.java Mot files are used by several of the applications that are used to produce PRINTS. Its a very simple format. One line per sequence (motif files tend to be fairly short alignments). Comments are designated with a #. PRINTS motif's can't contain gaps so by definition here this parser does not like gaps and will not write them out. Created: Mon Jan 22 16:44:15 2001

Version:
$Id: MotProteinParser.java,v 1.3 2001/04/11 17:04:43 lord Exp $
Author:
Phillip Lord

Constructor Summary
MotProteinParser()
           
 
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.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MotProteinParser

public MotProteinParser()
Method Detail

write

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

Specified by:
write in interface AlignmentOutputParser
Parameters:
sa - the sequence alignment
eh - the exception handler
Returns:
the writer for output

getDescription

public String getDescription()
Description copied from interface: AlignmentOutputParser
Returns the description of this alignment output parser, and should be human readable/understandable.

Specified by:
getDescription in interface AlignmentOutputParser
Returns:
the description