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 of gaps
percent of identical nucleotides or amino acids
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
frame of the query
start position of the query (the first position is 1)
strand of the query (“Plus” or “Minus” or nil)
end position of the query (including its position)
score
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
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 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