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## 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

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