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

java.lang.Object
  |
  +--uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser
        |
        +--uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser
All Implemented Interfaces:
AlignmentInputParser, AlignmentOutputParser

public class PIRProteinAlignmentParser
extends AbstractProteinAlignmentInputParser
implements AlignmentOutputParser

A filter that reads an alignment in PIR/NBRF protein sequence format and returns a sequence alignment object. This parser has no state attached to it, and may be re-entered (ie it is thread safe). Created: Fri May 26 10:18:02 2000

Version:
$Id: PIRProteinAlignmentParser.java,v 1.15 2001/04/11 17:04:43 lord Exp $
Author:
J Selley

Constructor Summary
PIRProteinAlignmentParser()
           
 
Method Summary
 String getDescription()
          Returns that this is a PIR/NBRF protein sequence parser.
 SequenceAlignment parse(Identifier ident, Reader r, ParserExceptionHandler eh)
           
 SequenceAlignment parse(Reader r, ParserExceptionHandler eh)
          This function parses an input reader which contains a (set of) PIR/NBRF sequence(s), and returns an alignment containing them.
 Writer write(SequenceAlignment sa, Writer writer, ParserExceptionHandler eh)
          This method parses a sequence alignment and writes it out to the supplied writer.
 
Methods inherited from class uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser
toSequence
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PIRProteinAlignmentParser

public PIRProteinAlignmentParser()
Method Detail

parse

public SequenceAlignment parse(Reader r,
                               ParserExceptionHandler eh)
                        throws IOException
This function parses an input reader which contains a (set of) PIR/NBRF sequence(s), and returns an alignment containing them. It only reads the protein version of PIR/NBRF format. Any exceptions thrown up (except the IOException) are packaged up and sent to an exception handler.

Specified by:
parse in interface AlignmentInputParser
Parameters:
r - the input reader
eh - the exception handler
Returns:
the sequence alignment
Throws:
IOException - if there is an error in the reader

parse

public SequenceAlignment parse(Identifier ident,
                               Reader r,
                               ParserExceptionHandler eh)
                        throws IOException
Specified by:
parse in interface AlignmentInputParser
IOException

write

public Writer write(SequenceAlignment sa,
                    Writer writer,
                    ParserExceptionHandler eh)
This method parses a sequence alignment and writes it out to the supplied writer. It formats the output to 80 characters wide.

N.B., this method does nothing with the writer other than write output to it - i.e. it does not close the writer.

Specified by:
write in interface AlignmentOutputParser
Parameters:
sa - the sequence alignment to be written.
writer - the writer to which the sequence is to be written
eh - the exception handler to which exceptions are parsed.
Returns:
the writer for output

getDescription

public String getDescription()
Returns that this is a PIR/NBRF protein sequence parser.

Specified by:
getDescription in interface AlignmentOutputParser
Returns:
the description of this parser