Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::Tools::Pseudowise - Results of one Pseudowise run

SYNOPSIS

         use Bio::Tools::Pseudowise;

         my $parser = Bio::Tools::Pseudowise->new(-file=>"pw.out");
         while(my $feat = $parser->next_result){
             push @feat, $feat;
         }

DESCRIPTION

       Pseudowise is a pseudogene prediction program written by Ewan Birney as part of the Wise
       Package. This module is the parser for the output of the program.

       http://www.sanger.ac.uk/software/wise2

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Previous committed by the Fugu Team

       Re-written by Jason Stajich jason-at-bioperl-dot-org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   analysis_method
        Usage     : $pseudowise->analysis_method();
        Purpose   : Inherited method. Overridden to ensure that the name matches
                    /pseudowise/i.
        Returns   : String
        Argument  : n/a

   next_feature
        Title   : next_feature
        Usage   : $seqfeature = $obj->next_feature();
        Function: Returns the next feature available in the analysis result, or
                  undef if there are no more features.
        Example :
        Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
                  more features.
        Args    : none

       See Also  Bio::SeqFeatureI

   next_prediction
        Title   : next_prediction
        Usage   : while($gene = $pseudowise->next_prediction()) {
                         # do something
                  }
        Function: Returns the gene of the Pseudowise result
                  file. Call this method repeatedly until FALSE is returned.

        Example :
        Returns : a Bio::SeqFeature::Generic
        Args    : none

       See Also Bio::SeqFeature::Generic

   _parse_predictions
        Title   : _parse_predictions()
        Usage   : $obj->_parse_predictions()
        Function: Parses the prediction section. Automatically called by
                  next_prediction() if not yet done.
        Example :
        Returns :

_prediction

        Title   : _prediction()
        Usage   : $gene = $obj->_prediction()
        Function: internal
        Example :
        Returns :

   _add_prediction
        Title   : _add_prediction()
        Usage   : $obj->_add_prediction($gene)
        Function: internal
        Example :
        Returns :

   _predictions_parsed
        Title   : _predictions_parsed
        Usage   : $obj->_predictions_parsed
        Function: internal
        Example :
        Returns : TRUE or FALSE