bio::searchio::searchwriteri(3pm) [debian man page]

Bio::SearchIO::SearchWriterI(3pm)			User Contributed Perl Documentation			 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

perl v5.14.2							    2012-03-02					 Bio::SearchIO::SearchWriterI(3pm)

Bio::SearchIO::Writer::BSMLResultWriter(3pm)		User Contributed Perl Documentation	      Bio::SearchIO::Writer::BSMLResultWriter(3pm)

NAME

       Bio::SearchIO::Writer::BSMLResultWriter - BSML output writer

SYNOPSIS

	 use Bio::SearchIO;
	 my $in = Bio::SearchIO->new(-file   => 'result.blast',
				    -format => 'blast');
	 my $out = Bio::SearchIO->new(-output_format  => 'BSMLResultWriter',
				     -file	     => ">result.bsml");
	 while( my $r = $in->next_result ) {
	   $out->write_result($r);
	 }

DESCRIPTION

       This is a writer to produce BSML for a search result.

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/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   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 the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason-at-bioperl-dot-org

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 = Bio::SearchIO::Writer::BSMLResultWriter->new();
	Function: Builds a new Bio::SearchIO::Writer::BSMLResultWriter object
	Returns : an instance of Bio::SearchIO::Writer::BSMLResultWriter
	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

perl v5.14.2							    2012-03-02			      Bio::SearchIO::Writer::BSMLResultWriter(3pm)