Class: Bio::MAF::EmptySequence
Overview
An empty sequence record from an 'e' line.
This indicates that "there isn't aligning DNA for a species but
that the current block is bridged by a chain that connects
blocks before and after this block" (MAF spec).
Constant Summary
Constants inherited
from Sequence
Sequence::I_STATUS
Instance Attribute Summary collapse
Attributes inherited from Sequence
#i_data, #quality, #size, #source, #src_size, #start, #strand
Instance Method Summary
collapse
Methods inherited from Sequence
#decode_status_char, #delete_text, #end, #fasta_desc, #gapped?, #interval, #joinable_with?, #left_count, #left_status, #left_status_char, #right_count, #right_status, #right_status_char, #species, #text_range, #to_bio_alignment
Constructor Details
Returns a new instance of EmptySequence.
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# File 'lib/bio/maf/maf.rb', line 446
def initialize(*args)
super(*(args[0..4] << nil))
@status = args[5]
end
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Instance Attribute Details
#status ⇒ Object
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# File 'lib/bio/maf/maf.rb', line 444
def status
@status
end
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Instance Method Details
#empty? ⇒ Boolean
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# File 'lib/bio/maf/maf.rb', line 468
def empty?
true
end
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#join(o) ⇒ Object
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# File 'lib/bio/maf/maf.rb', line 459
def join(o)
EmptySequence.new(source,
start,
size + o.size,
strand,
src_size,
@status)
end
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#slice(offset, len) ⇒ Object
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# File 'lib/bio/maf/maf.rb', line 455
def slice(offset, len)
self
end
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#text ⇒ Object
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# File 'lib/bio/maf/maf.rb', line 451
def text
''
end
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#write_fasta(writer) ⇒ Object
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# File 'lib/bio/maf/maf.rb', line 472
def write_fasta(writer)
raise "empty sequence output not implemented!"
end
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