Class Bio::Blat::Report::SeqDesc
In: lib/bio/appl/blat/report.rb
Parent: Object

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

Methods

new  

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)

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

[Source]

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

[Validate]