class SequenceServer::BLAST::HSP::BLASTN

HSP subclass for BLASTN algorithm.

Public Instance Methods

nqseq() click to toggle source

BLASTN is a bit weird in that, no matter which direction the query sequence aligned in, qstart is taken as alignment start coordinate for query.

NOTE:

Because BLAST reverses the qstart and qend for BLASTN?
# File lib/sequenceserver/blast/hsp.rb, line 219
def nqseq
  qstart
end
nsseq() click to toggle source

BLASTN is a bit weird in that, no matter which direction the subject sequence aligned in, sstart is taken as alignment start coordinate for subject.

NOTE:

Because BLAST reverses the sstart and send for BLASTN?
# File lib/sequenceserver/blast/hsp.rb, line 229
def nsseq
  sstart
end
stats() click to toggle source
Calls superclass method
# File lib/sequenceserver/blast/hsp.rb, line 208
def stats
  super.update('Strand' =>
               "#{qframe > 0 ? '+' : '-'}/#{sframe > 0 ? '+' : '-'}")
end