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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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).