class Bio::Assembly::Read
Attributes
clear_range_from[RW]
clear_range_to[RW]
from[RW]
name[RW]
orientation[RW]
seq[RW]
to[RW]
Public Class Methods
new(str="")
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# File lib/bio-assembly/read.rb, line 9 def initialize(str="") @seq = Bio::Sequence::NA.new(str) end
Public Instance Methods
<=>(other)
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# File lib/bio-assembly/read.rb, line 41 def <=>(other) unless other.kind_of?(Bio::Assembly::Read) raise "[Error] markers are not comparable" end if self.from == other.from # sort by to if froms are identical return self.to.<=>(other.to) else return self.from.<=>(other.from) end end
==(other_read)
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# File lib/bio-assembly/read.rb, line 13 def ==(other_read) name == other_read.name end
clear_range_from=(new_clear_range_from)
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# File lib/bio-assembly/read.rb, line 33 def clear_range_from=(new_clear_range_from) @clear_range_from = new_clear_range_from.to_i end
clear_range_to=(new_clear_range_to)
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# File lib/bio-assembly/read.rb, line 37 def clear_range_to=(new_clear_range_to) @clear_range_to = new_clear_range_to.to_i end
from=(new_from)
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# File lib/bio-assembly/read.rb, line 21 def from=(new_from) @from = new_from.to_i end
num_bases()
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# File lib/bio-assembly/read.rb, line 17 def num_bases seq.length end
seq=(str)
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# File lib/bio-assembly/read.rb, line 29 def seq=(str) @seq = Bio::Sequence::NA.new(str) end
to=(new_to)
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# File lib/bio-assembly/read.rb, line 25 def to=(new_to) @to = new_to.to_i end