NAME

       Bio::Map::PositionWithSequence - A position with a sequence.

SYNOPSIS

           use Bio::Map::PositionWithSequence;

           my $pos = Bio::Map::PositionWithSequence->new(-map => $map,
                                       -element => $element,
                                       -start => 0,
                                       -seq => 'ATGC');

DESCRIPTION

       Have a position with a sequence, eg. define what the binding site sequence of a certain
       transcription factor binding site is by modelling it as one of these objects with the
       -element assigned to a Bio::Map::TranscriptionFactor instance.

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 - 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 $obj = Bio::Map::PositionWithSequence->new();
        Function: Builds a new Bio::Map::PositionWithSequence object
        Returns : Bio::Map::PositionWithSequence
        Args    : -map      => Bio::Map::GeneMap object
                  -element  => Bio::Map::Gene object
                  -relative => Bio::Map::GeneRelative object
                  -seq      => string, length of this string will set the length
                               of this position's range

                  * If this position has no range, or if a single value can describe
                    the range *
                  -value => scalar             : something that describes the single
                                                 point position or range of this
                                                 Position, most likely an int

                  * Or if this position has a range, at least two of *
                  -start => int                : value of the start co-ordinate
                  -end => int                  : value of the end co-ordinate
                  -length => int               : length of the range

   seq
        Title   : seq
        Usage   : my $string = $obj->seq();
        Function: Get/set the sequence as a string of letters.
        Returns : scalar
        Args    : Optionally on set the new value (a string). An optional second
                  argument presets the alphabet (otherwise it will be guessed).