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Versions: 9
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Stored size: 1.57 KB
Contents
module Bio
class SQL
class Seqfeature <DummyBase
set_sequence_name "seqfeature_pk_seq"
belongs_to :bioentry
#, :class_name => "Bioentry"
belongs_to :type_term, :class_name => "Term", :foreign_key => "type_term_id"
belongs_to :source_term, :class_name => "Term", :foreign_key =>"source_term_id"
has_many :seqfeature_dbxrefs, :class_name => "SeqfeatureDbxref", :foreign_key => "seqfeature_id"
has_many :seqfeature_qualifier_values, :order=>'rank', :foreign_key => "seqfeature_id"
#, :class_name => "SeqfeatureQualifierValue"
has_many :locations, :class_name => "Location", :order=>'rank'
has_many :object_seqfeature_paths, :class_name => "SeqfeaturePath", :foreign_key => "object_seqfeature_id"
has_many :subject_seqfeature_paths, :class_name => "SeqfeaturePath", :foreign_key => "subject_seqfeature_id"
has_many :object_seqfeature_relationships, :class_name => "SeqfeatureRelationship", :foreign_key => "object_seqfeature_id"
has_many :subject_seqfeature_relationships, :class_name => "SeqfeatureRelationship", :foreign_key => "subject_seqfeature_id"
#get the subsequence described by the locations objects
def sequence
return self.locations.inject(Bio::Sequence::NA.new("")){|seq, location| seq<<location.sequence}
end
#translate the subsequences represented by the feature and its locations
#not considering the qualifiers
#Return a Bio::Sequence::AA object
def translate(*args)
self.sequence.translate(*args)
end
end
end #SQL
end #Bio
Version data entries
9 entries across 9 versions & 4 rubygems