Class: BioInterchange::Genomics::GVFFeature

Inherits:
GFF3Feature
  • Object
show all
Defined in:
lib/biointerchange/genomics/gvf_feature.rb

Overview

Represents a single genomic feature of a GVF file.

Constant Summary

Constants inherited from GFF3Feature

BioInterchange::Genomics::GFF3Feature::NEGATIVE, BioInterchange::Genomics::GFF3Feature::NOT_STRANDED, BioInterchange::Genomics::GFF3Feature::POSITIVE, BioInterchange::Genomics::GFF3Feature::UNKNOWN

Instance Method Summary collapse

Methods inherited from GFF3Feature

#attributes, #end_coordinate, #phase, #score, #sequence_id, #source, #start_coordinate, #strand, #type

Constructor Details

#initialize(sequence_id, source, type, start_coordinate, end_coordinate, score = nil, strand = NOT_STRANDED, attributes = {}) ⇒ GVFFeature

Creates a new feature representation. A feature is described on one line of the GVF file.

sequence_id

an identifier that determines the coordinate system for the feature

source

a text description of the origin of this feature description

type

either a SOFA accession, SOFA term, or textual description (the former are URIs, the latter is a string)

start_coordinate

an integer denoting the start coordinate of the feature

end_coordinate

an integer denoting the end coordinate of the feature, which is equal or larger than the start coordinate

score

a floating point score

strand

a constant determining whether the feature is NOT_STRANDED, the strand is UNKNOWN, or the feature is on the POSITIVE or NEGATIVE strand

attributes

a map of additional attributes associated with the feature



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# File 'lib/biointerchange/genomics/gvf_feature.rb', line 16

def initialize(sequence_id, source, type, start_coordinate, end_coordinate, score = nil, strand = NOT_STRANDED, attributes = {})
  # Fill in phase, which is always omitted in GVF features (after 'strand', before 'attributes'):
  super(sequence_id, source, type, start_coordinate, end_coordinate, score, strand, nil, attributes)
end