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, #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.
443
444
445
446
|
# File 'lib/bio/maf/maf.rb', line 443
def initialize(*args)
super(*args[0..4])
@status = args[5]
end
|
Instance Attribute Details
#status ⇒ Object
441
442
443
|
# File 'lib/bio/maf/maf.rb', line 441
def status
@status
end
|
Instance Method Details
#empty? ⇒ Boolean
465
466
467
|
# File 'lib/bio/maf/maf.rb', line 465
def empty?
true
end
|
#join(o) ⇒ Object
456
457
458
459
460
461
462
463
|
# File 'lib/bio/maf/maf.rb', line 456
def join(o)
EmptySequence.new(source,
start,
size + o.size,
strand,
src_size,
@status)
end
|
#slice(offset, len) ⇒ Object
452
453
454
|
# File 'lib/bio/maf/maf.rb', line 452
def slice(offset, len)
self
end
|
#text ⇒ Object
448
449
450
|
# File 'lib/bio/maf/maf.rb', line 448
def text
''
end
|
#write_fasta(writer) ⇒ Object
469
470
471
|
# File 'lib/bio/maf/maf.rb', line 469
def write_fasta(writer)
raise "empty sequence output not implemented!"
end
|