class Bio::Blat::Report::SeqDesc

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

Attributes

end position of the final segment

gap bases

gap count

name of the sequence

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

length of the sequence

start position of the first segment

start positions of segments. Returns an array of numbers.

Public Class Methods

new (gap_count, gap_bases, name, size, st, ed, starts, seqs)

Source

    # File lib/bio/appl/blat/report.rb
161 def initialize(gap_count, gap_bases, name, size,
162                st, ed, starts, seqs)
163   @gap_count = gap_count.to_i
164   @gap_bases = gap_bases.to_i
165   @name = name
166   @size = size.to_i
167   @start = st.to_i
168   @end = ed.to_i
169   @starts = starts.collect { |x| x.to_i }
170   @seqs = seqs
171 end

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