class SequenceGroup
Attributes
output_files[RW]
output_text[RW]
stats[RW]
Public Class Methods
new(seqs)
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# File lib/seqtrimnext/classes/sequence_group.rb, line 8 def initialize(seqs) @stats={} @seqs=seqs @output_text={} @output_files={} end
Public Instance Methods
add(array)
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# File lib/seqtrimnext/classes/sequence_group.rb, line 56 def add(array) @seqs = @seqs + array # sort by tuple_id and order in tuple @seqs.sort! do |a,b| comp = (a.tuple_id <=> b.tuple_id) comp.zero? ? (a.order_in_tuple <=> b.order_in_tuple) : comp end # print # @seqs.each do |s| # puts "TID:#{s.tuple_id}, OIT: #{s.order_in_tuple}" # end end
count()
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# File lib/seqtrimnext/classes/sequence_group.rb, line 72 def count return @seqs.count end
delete(seq)
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# File lib/seqtrimnext/classes/sequence_group.rb, line 21 def delete(seq) @seqs.delete(seq) end
each() { |seq| ... }
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# File lib/seqtrimnext/classes/sequence_group.rb, line 30 def each @seqs.each do |seq| yield seq end end
each_slice(n) { |seqs| ... }
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# File lib/seqtrimnext/classes/sequence_group.rb, line 36 def each_slice(n) @seqs.each_slice(n) do |seqs| yield seqs end end
each_with_index() { |seq,i| ... }
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# File lib/seqtrimnext/classes/sequence_group.rb, line 43 def each_with_index @seqs.each_with_index do |seq,i| yield seq,i end end
empty?()
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# File lib/seqtrimnext/classes/sequence_group.rb, line 25 def empty? return @seqs.empty? end
include?(s)
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# File lib/seqtrimnext/classes/sequence_group.rb, line 76 def include?(s) return @seqs.include?(s) end
inspect()
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def job_identifier
return @seqs[0].seq_name
end
# File lib/seqtrimnext/classes/sequence_group.rb, line 88 def inspect return "Group with #{@seqs.count} sequences" end
push(seq)
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# File lib/seqtrimnext/classes/sequence_group.rb, line 17 def push(seq) @seqs.push seq end
remove_all_seqs()
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# File lib/seqtrimnext/classes/sequence_group.rb, line 80 def remove_all_seqs @seqs=[] end
reverse_each() { |seq| ... }
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# File lib/seqtrimnext/classes/sequence_group.rb, line 50 def reverse_each @seqs.reverse_each do |seq| yield seq end end