Class: Bio::Blat::Report::SeqDesc

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/blat/report.rb

Overview

Bio::Blat::Report::SeqDesc stores sequence information of query or subject of the BLAT report. It also includes some hit information.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(gap_count, gap_bases, name, size, st, ed, starts, seqs) ⇒ SeqDesc

Creates a new SeqDesc object. It is designed to be called internally from Bio::Blat::Report class. Users shall not use it directly.



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# File 'lib/bio/appl/blat/report.rb', line 161

def initialize(gap_count, gap_bases, name, size,
               st, ed, starts, seqs)
  @gap_count = gap_count.to_i
  @gap_bases = gap_bases.to_i
  @name = name
  @size = size.to_i
  @start = st.to_i
  @end = ed.to_i
  @starts = starts.collect { |x| x.to_i }
  @seqs = seqs
end

Instance Attribute Details

#end ⇒ Object (readonly)

end position of the final segment



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# File 'lib/bio/appl/blat/report.rb', line 183

def end
  @end
end

#gap_bases ⇒ Object (readonly)

gap bases



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# File 'lib/bio/appl/blat/report.rb', line 175

def gap_bases
  @gap_bases
end

#gap_count ⇒ Object (readonly)

gap count



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# File 'lib/bio/appl/blat/report.rb', line 173

def gap_count
  @gap_count
end

#name ⇒ Object (readonly)

name of the sequence



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# File 'lib/bio/appl/blat/report.rb', line 177

def name
  @name
end

#seqs ⇒ Object (readonly)

sequences of segments. Returns an array of String. Returns nil if there are no sequence data.



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# File 'lib/bio/appl/blat/report.rb', line 190

def seqs
  @seqs
end

#size ⇒ Object (readonly)

length of the sequence



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# File 'lib/bio/appl/blat/report.rb', line 179

def size
  @size
end

#start ⇒ Object (readonly)

start position of the first segment



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# File 'lib/bio/appl/blat/report.rb', line 181

def start
  @start
end

#starts ⇒ Object (readonly)

start positions of segments. Returns an array of numbers.



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# File 'lib/bio/appl/blat/report.rb', line 186

def starts
  @starts
end