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

NAME

       Bio::SearchIO::wise - Parsing of wise output as alignments

SYNOPSIS

	 use Bio::SearchIO;
	 my $parser = Bio::SearchIO->new(-file	  => 'file.genewise',
					-format  => 'wise',
					-wisetype=> 'genewise');

	 while( my $result = $parser->next_result ) {}

DESCRIPTION

       This object parsers Wise output using Bio::Tools::Genewise or Bio::Tools::Genomewise as a helper.

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::wise->new();
	Function: Builds a new Bio::SearchIO::wise object
	Returns : an instance of Bio::SearchIO::wise
	Args	: -wise => a Bio::Tools::Genewise or Bio::Tools::Genomewise object

   next_result
	Title	: next_result
	Usage	: my $hit = $searchio->next_result;
	Function: Returns the next Result from a search
	Returns : Bio::Search::Result::ResultI object
	Args	: none

   start_element
	Title	: start_element
	Usage	: $eventgenerator->start_element
	Function: Handles a start element event
	Returns : none
	Args	: hashref with at least 2 keys 'Data' and 'Name'

   end_element
	Title	: start_element
	Usage	: $eventgenerator->end_element
	Function: Handles an end element event
	Returns : none
	Args	: hashref with at least 2 keys 'Data' and 'Name'

   element
	Title	: element
	Usage	: $eventhandler->element({'Name' => $name, 'Data' => $str});
	Function: Convience method that calls start_element, characters, end_element
	Returns : none
	Args	: Hash ref with the keys 'Name' and 'Data'

   characters
	Title	: characters
	Usage	: $eventgenerator->characters($str)
	Function: Send a character events
	Returns : none
	Args	: string

   within_element
	Title	: within_element
	Usage	: if( $eventgenerator->within_element($element) ) {}
	Function: Test if we are within a particular element
		  This is different than 'in' because within can be tested
		  for a whole block.
	Returns : boolean
	Args	: string element name

   in_element
	Title	: in_element
	Usage	: if( $eventgenerator->in_element($element) ) {}
	Function: Test if we are in a particular element
		  This is different than 'in' because within can be tested
		  for a whole block.
	Returns : boolean
	Args	: string element name

   start_document
	Title	: start_document
	Usage	: $eventgenerator->start_document
	Function: Handle a start document event
	Returns : none
	Args	: none

   end_document
	Title	: end_document
	Usage	: $eventgenerator->end_document
	Function: Handles an end document event
	Returns : Bio::Search::Result::ResultI object
	Args	: none

   wise
	Title	: wise
	Usage	: $obj->wise($newval)
	Function: Get/Set the Wise object parser
	Returns : value of wise (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   wisetype
	Title	: wisetype
	Usage	: $obj->wisetype($newval)
	Function: Wise program type
	Returns : value of wisetype (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

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