Sanger::CGP::Vagrent::Data::AbstractGenomicPosition - Abstract Data object representing Genomic position
This is an abstract data class designed to be extended, it provides basic functionality for holding genomic position. Child classes must implement an _init method to handle parameter values handed to the object when the constructor is called.
my $gp = Sanger::CGP::Vagrent::Data::AbstractGenomicPositionSubClass->new(%params);
Builds a new Sanger::CGP::Vagrent::Data::AbstractGenomicPosition inheriting object
Sanger::CGP::Vagrent::Data::AbstractGenomicPosition sub class object initialized with parameter values
species => Species string (eg Human) genomeVersion => Genome version String (eg GRCh37) chr => Chromosome/contig name minpos => Lowest coordinate of the feature maxpos => Highest coordinate of the feature id => Identifier (Optional)
Abstract internal initialisation method, must be implemented in subclasses. All parameters are passed through from the constructor.
my $id = $gp->getId;
Returns the value of Id
String
my $species = $gp->getSpecies;
Returns the species name
String
my $gVers = $gp->getGenomeVersion;
Returns the genome version string
String
my $chr = $gp->getChr;
Returns the chromosome/contig name
String
my $min = $gp->getMinPos;
Returns the lowest coordinate of the feature on the sequence
Integer
$gp->setMinPos($newPos);
Sets the lowest coordinate of the feature on the sequence
Integer, new position
None
my $max = $gp->getMaxPos;
Returns the highest coordinate of the feature on the sequence
Integer
$gp->setMaxPos($newPos);
Sets the highest coordinate of the feature on the sequence
Integer, new position
None