Provided by: libbio-perl-perl_1.7.2-2_all bug


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


           use Bio::Map::PositionWithSequence;

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


       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.


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AUTHOR - Sendu Bala



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

        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

        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).