Method: Bio::Blat::Report::SegmentPair#initialize

Defined in:

lib/bio/appl/blat/report.rb

#initialize(query_len, target_len, strand, blksize, qstart, tstart, qseq, tseq, protein_flag) ⇒ SegmentPair

Creates a new SegmentPair 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 199

def initialize(query_len, target_len, strand,
               blksize, qstart, tstart, qseq, tseq,
               protein_flag)
  @blocksize  = blksize
  @qseq       = qseq
  @hseq       = hseq
  @hit_strand   = 'plus'
  w = (protein_flag ? 3 : 1) # 3 means query=protein target=dna
  case strand
  when '-'
    # query is minus strand
    @query_strand = 'minus'
    # convert positions
    @query_from = query_len - qstart
    @query_to   = query_len - qstart - blksize + 1
    # To keep compatibility, with other homology search programs,
    # we add 1 to each position number.
    @hit_from   = tstart + 1
    @hit_to     = tstart + blksize * w # - 1 + 1
  when '+-'
    # hit is minus strand
    @query_strand = 'plus'
    @hit_strand = 'minus'
    # To keep compatibility, with other homology search programs,
    # we add 1 to each position number.
    @query_from   = qstart + 1
    @query_to     = qstart + blksize # - 1 + 1
    # convert positions
    @hit_from     = target_len - tstart
    @hit_to       = target_len - tstart - blksize * w + 1
  else #when '+', '++'
    @query_strand = 'plus'
    # To keep compatibility with other homology search programs,
    # we add 1 to each position number.
    @query_from = qstart + 1
    @query_to   = qstart + blksize # - 1 + 1
    @hit_from   = tstart + 1
    @hit_to     = tstart + blksize * w # - 1 + 1
  end
end