class Sequence
@author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com> @author Luis (Coto) Orellana @license artistic license 2.0 @update Jan-22-2015
Attributes
aln[R]
id[R]
seq[R]
Public Class Methods
new(id, aln)
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# File lib/rocker/sequence.rb, line 10 def initialize(id, aln) @id = id @aln = aln.gsub(/[-\.]/,'-').gsub(/[^A-Za-z-]/, '').upcase @seq = aln.gsub(/[^A-Za-z]/, '').upcase end
Public Instance Methods
col2pos(col)
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# File lib/rocker/sequence.rb, line 24 def col2pos(col) pos = 1 self.aln.split(//).each do |c| col-=1 pos+=1 unless c=='-' return pos if col==0 end pos end
cols()
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# File lib/rocker/sequence.rb, line 33 def cols() self.aln.length end
length()
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# File lib/rocker/sequence.rb, line 34 def length() self.seq.length end
pos2col(pos)
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# File lib/rocker/sequence.rb, line 15 def pos2col(pos) col = 0 self.aln.split(//).each do |c| col+=1 pos-=1 unless c=='-' return col if pos==0 end col end
to_s()
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# File lib/rocker/sequence.rb, line 36 def to_s() "#:>#{self.id}\n#:#{self.aln}\n" end
to_seq_s()
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# File lib/rocker/sequence.rb, line 35 def to_seq_s() ">#{self.id}\n#{self.seq}\n" end