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:
$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 :
$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
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