Class Bio::Blast::Report::Hit
In: lib/bio/appl/blast/report.rb  (CVS)
Parent: Object

Methods

bit_score   each   evalue   identity   lap_at   midline   new   overlap   percent_identity   query_end   query_seq   query_start   target_end   target_seq   target_start  

External Aliases

accession -> target_id
  Compatible method with Bio::Fasta::Report::Hit class.
definition -> target_def
  Compatible method with Bio::Fasta::Report::Hit class.
len -> target_len
  Compatible method with Bio::Fasta::Report::Hit class.

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.

Public Class methods

new()

[Source]

# File lib/bio/appl/blast/report.rb, line 212
    def initialize
      @hsps = []
    end

Public Instance methods

bit_score()

[Source]

# File lib/bio/appl/blast/report.rb, line 254
    def bit_score;        @hsps.first.bit_score;        end
each() {|x| ...}

Iterates on each Hsp object.

[Source]

# File lib/bio/appl/blast/report.rb, line 231
    def each
      @hsps.each do |x|
        yield x
      end
    end
evalue()

Shortcut methods for the best Hsp, some are also compatible with Bio::Fasta::Report::Hit class.

[Source]

# File lib/bio/appl/blast/report.rb, line 253
    def evalue;           @hsps.first.evalue;           end
identity()

[Source]

# File lib/bio/appl/blast/report.rb, line 255
    def identity;         @hsps.first.identity;         end
lap_at()

[Source]

# File lib/bio/appl/blast/report.rb, line 267
    def lap_at
      [ query_start, query_end, target_start, target_end ]
    end
midline()

[Source]

# File lib/bio/appl/blast/report.rb, line 261
    def midline;          @hsps.first.midline;          end
overlap()

[Source]

# File lib/bio/appl/blast/report.rb, line 257
    def overlap;          @hsps.first.align_len;        end
percent_identity()

[Source]

# File lib/bio/appl/blast/report.rb, line 256
    def percent_identity; @hsps.first.percent_identity; end
query_end()

[Source]

# File lib/bio/appl/blast/report.rb, line 264
    def query_end;        @hsps.first.query_to;         end
query_seq()

[Source]

# File lib/bio/appl/blast/report.rb, line 259
    def query_seq;        @hsps.first.qseq;             end
query_start()

[Source]

# File lib/bio/appl/blast/report.rb, line 263
    def query_start;      @hsps.first.query_from;       end
target_end()

[Source]

# File lib/bio/appl/blast/report.rb, line 266
    def target_end;       @hsps.first.hit_to;           end
target_seq()

[Source]

# File lib/bio/appl/blast/report.rb, line 260
    def target_seq;       @hsps.first.hseq;             end
target_start()

[Source]

# File lib/bio/appl/blast/report.rb, line 265
    def target_start;     @hsps.first.hit_from;         end

[Validate]