Class: SequenceServer::BLAST::HSP::BLASTN

Inherits:
SequenceServer::BLAST::HSP show all
Defined in:
lib/sequenceserver/blast/hsp.rb

Overview

HSP subclass for BLASTN algorithm.

Instance Attribute Summary

Attributes inherited from SequenceServer::BLAST::HSP

#bit_score, #evalue, #gaps, #hit, #identity, #length, #midline, #number, #positives, #qend, #qframe, #qseq, #qstart, #score, #send, #sframe, #sseq, #sstart

Instance Method Summary collapse

Instance Method Details

#nqseqObject

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?

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# File 'lib/sequenceserver/blast/hsp.rb', line 204

def nqseq
  qstart
end

#nsseqObject

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?

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# File 'lib/sequenceserver/blast/hsp.rb', line 214

def nsseq
  sstart
end

#statsObject


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# File 'lib/sequenceserver/blast/hsp.rb', line 193

def stats
  super.update('Strand' =>
               "#{qframe > 0 ? '+' : '-'}/#{sframe > 0 ? '+' : '-'}")
end