Class: Bio::Blast::Default::Report::HSP

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)

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.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 967
967:           def initialize(data)
968:             @f0score = data.shift
969:             @f0alignment = []
970:             while r = data[0] and /^(Query|Sbjct)\:/ =~ r
971:               @f0alignment << data.shift
972:             end
973:           end

Methods

Attributes

Public Class methods