class Bio::Blast::Report::Hit
Attributes
accession[RW]
Accession
definition[RW]
Definition line of subject
hit_id[RW]
SeqId of subject
hsps[R]
Returns an Array of Bio::Blast::Report::Hsp objects.
len[RW]
Length of subject
num[RW]
Hit number
query_def[RW]
Compatible method with Bio::Fasta::Report::Hit class.
query_id[RW]
Compatible method with Bio::Fasta::Report::Hit class.
query_len[RW]
Compatible method with Bio::Fasta::Report::Hit class.
target_def[RW]
Definition line of subject
target_id[RW]
Accession
target_len[RW]
Length of subject
Public Class Methods
new()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 255 def initialize @hsps = [] end
Public Instance Methods
bit_score()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 297 def bit_score; @hsps.first.bit_score; end
each() { |x| ... }
click to toggle source
Iterates on each Hsp object.
# File lib/bio/appl/blast/report.rb, line 274 def each @hsps.each do |x| yield x end end
evalue()
click to toggle source
Shortcut methods for the best Hsp, some are also compatible with Bio::Fasta::Report::Hit class.
# File lib/bio/appl/blast/report.rb, line 296 def evalue; @hsps.first.evalue; end
identity()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 298 def identity; @hsps.first.identity; end
lap_at()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 310 def lap_at [ query_start, query_end, target_start, target_end ] end
midline()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 304 def midline; @hsps.first.midline; end
overlap()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 300 def overlap; @hsps.first.align_len; end
percent_identity()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 299 def percent_identity; @hsps.first.percent_identity; end
query_end()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 307 def query_end; @hsps.first.query_to; end
query_seq()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 302 def query_seq; @hsps.first.qseq; end
query_start()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 306 def query_start; @hsps.first.query_from; end
target_end()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 309 def target_end; @hsps.first.hit_to; end
target_seq()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 303 def target_seq; @hsps.first.hseq; end
target_start()
click to toggle source
# File lib/bio/appl/blast/report.rb, line 308 def target_start; @hsps.first.hit_from; end