/ 
bioperl-1.2.2
/ Bio::SearchIO::Writer::TextResultWriter

NAME

Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a Bio::Search::ResultI in Text.

SYNOPSIS

  use Bio::SearchIO;
  use Bio::SearchIO::Writer::TextResultWriter;

  my $in = new Bio::SearchIO(-format => 'blast',
			     -file   => shift @ARGV);

  my $writer = new Bio::SearchIO::Writer::TextResultWriter();
  my $out = new Bio::SearchIO(-writer => $writer);
  $out->write_result($in->next_result);

DESCRIPTION

This object implements the SearchWriterI interface which will produce a set of Text for a specific Bio::Search::Report::ReportI interface.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org              - General discussion
http://bioperl.org/MailList.shtml  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $obj = new Bio::SearchIO::Writer::TextResultWriter();
Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object 
Returns : Bio::SearchIO::Writer::TextResultWriter
Args    :

to_string

Purpose   : Produces data for each Search::Result::ResultI in a string.
          : This is an abstract method. For some useful implementations,
          : see ResultTableWriter.pm, HitTableWriter.pm, 
          : and HSPTableWriter.pm.
Usage     : print $writer->to_string( $result_obj, @args );
Argument  : $result_obj = A Bio::Search::Result::ResultI object
          : @args = any additional arguments used by your implementation.
Returns   : String containing data for each search Result or any of its
          : sub-objects (Hits and HSPs).
Throws    : n/a

id_parser

Title   : id_parser
Usage   : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
          parse the ID for record from a string.  Useful
          for (for instance) specifying a different
          parser for different flavours of FASTA file. 
          Returns \&default_id_parser (see below) if not
          set. If you supply your own id_parser
          subroutine, then it should expect a fasta
          description line.  An entry will be added to
          the index for each string in the list returned.
Example : $index->id_parser( \&my_id_parser )
Returns : ref to CODE if called without arguments
Args    : CODE

default_id_parser

Title   : default_id_parser
Usage   : $id = default_id_parser( $header )
Function: The default Fasta ID parser for Fasta.pm
          Returns $1 from applying the regexp /^>\s*(\S+)/
          to $header.
Returns : ID string
Args    : a fasta header line string

algorithm_reference

Title   : algorithm_reference
Usage   : my $reference = $writer->algorithm_reference($result);
Function: Returns the appropriate Bibliographic reference for the 
          algorithm format being produced
Returns : String
Args    : L<Bio::Search::Result::ResultI> to reference

filter

Title   : filter
Usage   : $writer->filter('hsp', \&hsp_filter);
Function: Filter out either at HSP,Hit,or Result level
Returns : none
Args    : string => data type,
          CODE reference