NAME

       Bio::Map::Prediction - An object representing the predictions of something that can have
       multiple locations in several maps.

SYNOPSIS

         use Bio::Map::Prediction;
         use Bio::Map::Position;

         # normally you would get predictions from a run wrapper like
         # Bio::Tools::Run::Meme, but here we create some manually:
         my $pred1 = Bio::Map::Prediction->new(-source => 'meme');
         Bio::Map::Position->new(-element => $prediction1,
                                                         -map => Bio::Map::GeneMap->get(-gene => 'gene1',
                                                                                        -species => 'species1'),
                                                         -start => 950,
                                                         -end => 960);
         Bio::Map::Position->new(-element => $prediction1,
                                 -map => Bio::Map::GeneMap->get(-gene => 'gene1',
                                                                                        -species => 'species2'),
                                 -start => 1950,
                                 -end => 1960);
         Bio::Map::Position->new(-element => $prediction1,
                                 -map => Bio::Map::GeneMap->get(-gene => 'gene2',
                                                                                        -species => 'species1'),
                                 -start => 955,
                                 -end => 965);
         Bio::Map::Position->new(-element => $prediction1,
                                 -map => Bio::Map::GeneMap->get(-gene => 'gene2',
                                                                                -species => 'species2'),
                                 -start => 1955,
                                 -end => 1965);

         my $pred2 = Bio::Map::Prediction->new(-source => 'gerp');
         Bio::Map::Position->new(-element => $prediction2,
                                 -map => Bio::Map::GeneMap->get(-gene => 'gene1',
                                                                                        -species => 'species1'),
                                 -start => 950,
                                 -end => 960);
         # etc.

         # find the places where predictions agree
         use Bio::Map::GeneRelative;
         my $rel = Bio::Map::GeneRelative->new(-gene => 0);
         my $di = Bio::Map::Mappable->disconnected_intersections([$pred1, $pred2],
                                                       -min_mappables_percent => 100,
                                                       -min_map_percent => 100,
                                                       -relative => $rel);
         my @positions = $di->get_positions;

DESCRIPTION

       For example, used to model transcription factor binding site predictions, which can have
       multiple locations in several maps.

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

AUTHOR - Sendu Bala

       Email bix@sendu.me.uk

APPENDIX

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

   new
        Title   : new
        Usage   : my $prediction = Bio::Map::Prediction->new();
        Function: Builds a new Bio::Map::Prediction object
        Returns : Bio::Map::Prediction
        Args    : -name   => string : name of the mappable element
                  -id     => string : id of the mappable element
                  -source => string : name of the prediction program

   source
        Title   : name
        Usage   : $mappable->name($new_name);
                      my $name = $mappable->name();
        Function: Get/Set the name for this Mappable
        Returns : A scalar representing the current name of this Mappable
        Args    : none to get
                  string to set