Bio::SearchIO::wise - Parsing of wise output as alignments use Bio::SearchIO; my $parser = new Bio::SearchIO(-file => 'file.genewise', -format => 'wise', -wisetype=> 'genewise'); while( my $result = $parser->next_result ) {} This object parsers Wise output using Bio::Tools::Genewise or Bio::Tools::Genomewise as a helper.

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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: http://bugzilla.bioperl.org/ Email jason-at-bioperl-dot-org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::SearchIO::wise(); 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)