Class: Bio::FANTOM::MaXML::Cluster
Constant Summary
collapse
- Data_XPath =
'maxml-clusters/cluster'
DELIMITER
Instance Attribute Summary
#elem
Instance Method Summary
collapse
#entry_id, #gsub_entities, #initialize, #to_s
Methods inherited from DB
#entry_id, #exists?, #fetch, #get, open, #tags
Instance Method Details
#representative_annotations ⇒ Object
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# File 'lib/bio/db/fantom.rb', line 147
def representative_annotations
e = representative_sequence
e ? e.annotations : nil
end
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#representative_cloneid ⇒ Object
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# File 'lib/bio/db/fantom.rb', line 152
def representative_cloneid
e = representative_sequence
e ? e.cloneid : nil
end
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#representative_seqid ⇒ Object
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# File 'lib/bio/db/fantom.rb', line 118
def representative_seqid
unless defined?(@representative_seqid)
@representative_seqid =
gsub_entities(@elem.text('representative-seqid'))
end
@representative_seqid
end
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#representative_sequence ⇒ Object
Also known as:
representative_clone
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# File 'lib/bio/db/fantom.rb', line 137
def representative_sequence
unless defined?(@representative_sequence)
rid = representative_seqid
@representative_sequence =
rid ? sequences[representative_seqid] : nil
end
@representative_sequence
end
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#sequence(idstr = nil) ⇒ Object
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# File 'lib/bio/db/fantom.rb', line 133
def sequence(idstr = nil)
idstr ? sequences[idstr] : representative_sequence
end
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#sequences ⇒ Object
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# File 'lib/bio/db/fantom.rb', line 126
def sequences
unless defined?(@sequences)
@sequences = MaXML::Sequences.new(@elem)
end
@sequences
end
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