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NAME

Sanger::CGP::Vagrent::Data::AbstractGenomicPosition - Abstract Data object representing Genomic position

DESCRIPTION

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.

METHODS

Constructor

new

Usage :
 my $gp = Sanger::CGP::Vagrent::Data::AbstractGenomicPositionSubClass->new(%params);
Function :

Builds a new Sanger::CGP::Vagrent::Data::AbstractGenomicPosition inheriting object

Returns :

Sanger::CGP::Vagrent::Data::AbstractGenomicPosition sub class object initialized with parameter values

Params :
 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)

_init

Usage :

Abstract internal initialisation method, must be implemented in subclasses. All parameters are passed through from the constructor.

Attributes

getId

Usage :
 my $id = $gp->getId;
Function :

Returns the value of Id

Returns :

String

getSpecies

Usage :
 my $species = $gp->getSpecies;
Function :

Returns the species name

Returns :

String

getGenomeVersion

Usage :
 my $gVers = $gp->getGenomeVersion;
Function :

Returns the genome version string

Returns :

String

getChr

Usage :
 my $chr = $gp->getChr;
Function :

Returns the chromosome/contig name

Returns :

String

getMinPos

Usage :
 my $min = $gp->getMinPos;
Function :

Returns the lowest coordinate of the feature on the sequence

Returns :

Integer

setMinPos

Usage :
 $gp->setMinPos($newPos);
Function :

Sets the lowest coordinate of the feature on the sequence

Params

Integer, new position

Returns :

None

getMaxPos

Usage :
 my $max = $gp->getMaxPos;
Function :

Returns the highest coordinate of the feature on the sequence

Returns :

Integer

setMaxPos

Usage :
 $gp->setMaxPos($newPos);
Function :

Sets the highest coordinate of the feature on the sequence

Params

Integer, new position

Returns :

None

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