class Bio::Blast::Default::Report::HSP

Bio::Blast::Default::Report::HSP holds information about the hsp (high-scoring segment pair).

Attributes

align_len[R]

aligned length

bit_score[R]

bit score

evalue[R]

e-value

gaps[R]

Gaps (number of gaps)

hit_frame[R]

frame of the hit

hit_from[R]

start position of the hit (the first position is 1)

hit_strand[R]

strand of the hit (“Plus” or “Minus” or nil)

hit_to[R]

end position of the hit (including its position)

hseq[R]

hit sequence (with gaps) of the alignment of the hsp

identity[R]

Identity (number of identical nucleotides or amino acids)

midline[R]

middle line of the alignment of the hsp

percent_gaps[R]

percent of gaps

percent_identity[R]

percent of identical nucleotides or amino acids

percent_positive[R]

percent of positive hit amino acids or nucleotides

positive[R]

Positives (number of positive hit amino acids or nucleotides)

qseq[R]

query sequence (with gaps) of the alignment of the hsp

query_frame[R]

frame of the query

query_from[R]

start position of the query (the first position is 1)

query_strand[R]

strand of the query (“Plus” or “Minus” or nil)

query_to[R]

end position of the query (including its position)

score[R]

score

stat_method[R]

statistical method for calculating evalue and/or score (nil or a string) (note that composition-based statistics for blastp or tblastn were enabled by default after NCBI BLAST 2.2.17)

Public Class Methods

new(data) click to toggle source

Creates new HSP object. It is designed to be called only internally from the Bio::Blast::Default::Report::Hit class. Users should not call the method directly.

# File lib/bio/appl/blast/format0.rb, line 960
def initialize(data)
  @f0score = data.shift
  @f0alignment = []
  while r = data[0] and /^(Query|Sbjct)\:/ =~ r
    @f0alignment << data.shift
  end
end