Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource - Abstract base class for Transcript sources
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.
my $source = Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSourceSubClass->new();
Builds a new Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource inheriting object
Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource object initialized with parameter values
Hash of parameter values, the actual keys/values required depend on the sub class.
$source->setDumpRegion($genomicPosition);
Sets the GenomicRegion to seed Transcript/Gene set retrieval
Nothing
Any Sanger::CGP::Vagrent::Data::AbstractGenomicPosition implementing object
my $region = $source->getDumpRegion();
Gets the GenomicRegion used to seed Transcript/Gene set retrieval
A Sanger::CGP::Vagrent::Data::AbstractGenomicPosition implementing object or undef
if($source->isDumpRegionACompleteSequence()){ ...... }
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
A Boolean, 1 if it is a complete sequence, 0 if is isn't or undef if it doesn't know
my @transList = $source->getTranscripts($genomicPosition);
Abstract function, must be overridden by a subclass. Retrieves a list of Transcripts objects overlapping the specified GenomicPosition
An array of Sanger::CGP::Vagrent::Data::Transcript objects
Any Sanger::CGP::Vagrent::Data::AbstractGenomicPosition implementing object
while (my @transList = $source->getTranscriptsForNextGeneInDumpRegion()){ .... }
Abstract function, must be overridden by a subclass. Retrieves a list of Transcripts objects belonging to the next gene inside the previously specified GenomicRegion
An array of Sanger::CGP::Vagrent::Data::Transcript objects
None
$self->_init(@params);
Abstract internal function, must be overridden by a subclass. This method is used to handle constructor parameters, its called by new.
None
The flattened array of key/value pairs passed in from new.