<<

NAME

Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource - Abstract base class for Transcript sources

DESCRIPTION

This is a base utility class all TranscriptSources should inherit from, its little more than an interface with the vast majority of the functionality being implemented in the sub class.

Sub classes must implement a getTranscripts method and an internal _init method.

METHODS

Constructor

new

Usage :
 my $source = Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSourceSubClass->new();
Function :

Builds a new Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource inheriting object

Returns :

Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource object initialized with parameter values

Params :

Hash of parameter values, the actual keys/values required depend on the sub class.

Attributes

setDumpRegion

Usage :
 $source->setDumpRegion($genomicPosition);
Function :

Sets the GenomicRegion to seed Transcript/Gene set retrieval

Returns :

Nothing

Params :

Any Sanger::CGP::Vagrent::Data::AbstractGenomicPosition implementing object

getDumpRegion

Usage :
 my $region = $source->getDumpRegion();
Function :

Gets the GenomicRegion used to seed Transcript/Gene set retrieval

Returns :

A Sanger::CGP::Vagrent::Data::AbstractGenomicPosition implementing object or undef

Functions

isDumpRegionACompleteSequence

Usage :
 if($source->isDumpRegionACompleteSequence()){
        ......
 }
Function :

Returns boolean status for the current dump region being a complete sequence (eg. a whole chromosome/contig). The value behind this is populated by getTranscriptsForNextGeneInDumpRegion method when processing the specified gene region

Returns :

A Boolean, 1 if it is a complete sequence, 0 if is isn't or undef if it doesn't know

Abstract

getTranscripts

Usage :
 my @transList = $source->getTranscripts($genomicPosition);
Function :

Abstract function, must be overridden by a subclass. Retrieves a list of Transcripts objects overlapping the specified GenomicPosition

Returns :

An array of Sanger::CGP::Vagrent::Data::Transcript objects

Params :

Any Sanger::CGP::Vagrent::Data::AbstractGenomicPosition implementing object

getTranscriptsForNextGeneInDumpRegion

Usage :
 while (my @transList = $source->getTranscriptsForNextGeneInDumpRegion()){
        ....
 }
Function :

Abstract function, must be overridden by a subclass. Retrieves a list of Transcripts objects belonging to the next gene inside the previously specified GenomicRegion

Returns :

An array of Sanger::CGP::Vagrent::Data::Transcript objects

Params :

None

_init

Usage :
 $self->_init(@params);
Function :

Abstract internal function, must be overridden by a subclass. This method is used to handle constructor parameters, its called by new.

Returns :

None

Params :

The flattened array of key/value pairs passed in from new.

<<