class Bio::Blast::Report::Hit

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