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

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

Attributes

aligned length

bit score

e-value

Gaps (number of gaps)

frame of the hit

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

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

end position of the hit (including its position)

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

Identity (number of identical nucleotides or amino acids)

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

Positives (number of positive hit amino acids or nucleotides)

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

query_frame [R]

frame of the query

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

query_strand [R]

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

end position of the query (including its position)

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

Source

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

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.