Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results
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 );
This module defines abstract methods that all subclasses must implement to be used for outputting results from Bio::Search::Result::ResultI objects.
Steve Chervitz <sac-at-bioperl.org>
This software is provided "as is" without warranty of any kind.
The rest of the documentation details each of the object methods.
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
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
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
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
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.