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[R]

end position of the final segment

gap_bases[R]

gap bases

gap_count[R]

gap count

name[R]

name of the sequence

seqs[R]

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

size[R]

length of the sequence

start[R]

start position of the first segment

starts[R]

start positions of segments. Returns an array of numbers.

Public Class Methods

new(gap_count, gap_bases, name, size, st, ed, starts, seqs) click to toggle source

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

# 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