Bio::SearchIO::SearchWUserrContributed Perl DocBio::SearchIO::SearchWriterI(3)NAMEBio::SearchIO::SearchWriterI - Interface for outputting parsed Search
results
SYNOPSISBio::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
perl v5.14.1 2011-07-22 Bio::SearchIO::SearchWriterI(3)
