Class | Bio::Blast::Default::Report::HSP |
In: |
lib/bio/appl/blast/format0.rb
|
Parent: | Object |
Bio::Blast::Default::Report::HSP holds information about the hsp (high-scoring segment pair).
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) |
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 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