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

NAME

       Bio::SearchIO::Writer::ResultTableWriter - Outputs tab-delimited data for each Bio::Search::Result::ResultI object.

SYNOPSIS

   Example 1: Using the default columns
	   use Bio::SearchIO;
	   use Bio::SearchIO::Writer::ResultTableWriter;

	   my $in = Bio::SearchIO->new();

	   my $writer = Bio::SearchIO::Writer::ResultTableWriter->new();

	   my $out = Bio::SearchIO->new( -writer => $writer );

	   while ( my $result = $in->next_result() ) {
	       $out->write_result($result, ($in->report_count - 1 ? 0 : 1) );
	   }

   Example 2: Specifying a subset of columns
	   use Bio::SearchIO;
	   use Bio::SearchIO::Writer::ResultTableWriter;

	   my $in = Bio::SearchIO->new();

	   my $writer = Bio::SearchIO::Writer::ResultTableWriter->new(
					 -columns => [qw(
							 query_name
							 query_length
							 num_hits
							 )]  );

	   my $out = Bio::SearchIO->new( -writer => $writer,
					 -file	 => ">result.out" );

	   while ( my $result = $in->next_result() ) {
	       $out->write_result($result, ($in->report_count - 1 ? 0 : 1) );
	   }

   Custom Labels
       You can also specify different column labels if you don't want to use the defaults.  Do this by specifying a "-labels" hash reference
       parameter when creating the ResultTableWriter object.  The keys of the hash should be the column number (left-most column = 1) for the
       label(s) you want to specify. Here's an example:

	   my $writer = Bio::SearchIO::Writer::ResultTableWriter->new(
				      -columns => [qw( query_name
						       query_length
						       query_description
						       num_hits)],
				      -labels  => { 1 => 'QUERY_GI',
						    2 => 'QUERY_LENGTH' } );

DESCRIPTION

       Bio::SearchIO::Writer::ResultTableWriter outputs data in tab-delimited format for each search result, one row per search result. This is a
       very coarse-grain level of information since it only includes data stored in the Bio::Search::Result::ResultI object itself and does not
       include any information about hits or HSPs.

       You most likely will never use this object but instead will use one of its subclasses: Bio::SearchIO::Writer::HitTableWriter or
       Bio::SearchIO::Writer::HSPTableWriter.

   Available Columns
       Here are the columns that can be specified in the "-columns" parameter when creating a ResultTableWriter object.  If a "-columns" parameter
       is not specified, this list, in this order, will be used as the default.

	   query_name
	   query_length
	   query_description

       For more details about these columns, see the documentation for the corresponding method in Bio::Search::Result::ResultI.

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 one
       of the Bioperl mailing lists.  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 the bugs and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR

       Steve Chervitz <sac@bioperl.org>

       See the FEEDBACK section  for where to send bug reports and comments.

COPYRIGHT

       Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

SEE ALSO

       Bio::SearchIO::Writer::HitTableWriter, Bio::SearchIO::Writer::HSPTableWriter

METHODS

   to_string()
       Note: this method is not intended for direct use. The SearchIO::write_result() method calls it automatically if the writer is hooked up to
       a SearchIO object as illustrated in the SYNOPSIS section .

	Title	  : to_string()
		  :
	Usage	  : print $writer->to_string( $result_obj, [$include_labels] );
		  :
	Argument  : $result_obj = A Bio::Search::Result::ResultI object
		  : $include_labels = boolean, if true column labels are included (default: false)
		  :
	Returns   : String containing tab-delimited set of data for each hit
		  : in a ResultI object. Some data is summed across multiple HSPs.
		  :
	Throws	  : n/a

   column_labels
	Usage	  : print $result_obj->column_labels();
	Purpose   : Get column labels for to_string().
	Returns   : String containing column labels. Tab-delimited.
	Argument  : n/a
	Throws	  : n/a

   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.  Nothing for
		  a text message.
	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::Writer::ResultTableWriter(3pm)