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

       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 v5.32.1                                       2021-08-15                           Bio::SearchIO::wise(3pm)

       Email jason-at-bioperl-dot-org

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

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       at the problem and quickly address it. Please include a thorough description of the problem with code and
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       Bug reports can be submitted via the web:

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

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

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