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Bio::SearchIO::SearchWriterI.3pm

NAME

Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results

SYNOPSIS

Bio::SearchIO::SearchWriterI objects cannot be instantiated since this module defines a pure interface.

Given an object that implements the Bio::SearchIO::SearchWriterI interface, you can do the following things with it:

     print $writer->to_string( $result_obj, @args );
 
 

DESCRIPTION

This module defines abstract methods that all subclasses must implement to be used for outputting results from Bio::Search::Result::ResultI objects.

AUTHOR

Steve Chervitz <sac-at-bioperl.org>

DISCLAIMER

This software is provided ``as is'' without warranty of any kind.

APPENDIX

The rest of the documentation details each of the object methods.

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
 
 

start_report

  Title   : start_report
  Usage   : $self->start_report()
  Function: The method to call when starting a report. You can override it
            to make a custom header
  Returns : string
  Args    : none
 
 

end_report

  Title   : end_report
  Usage   : $self->end_report()
  Function: The method to call when ending a report, this is
            mostly for cleanup for formats which require you to 
            have something at the end of the document (</BODY></HTML>)
            for HTML
  Returns : string
  Args    : none
 
 

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