Class: Bio::Blast::Report::Hit

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/blast/report.rb

Overview

Bio::Blast::Report::Hit

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Hit

Returns a new instance of Hit.



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# File 'lib/bio/appl/blast/report.rb', line 212

def initialize
  @hsps = []
end

Instance Attribute Details

#accession ⇒ Object Also known as: target_id

Accession



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# File 'lib/bio/appl/blast/report.rb', line 228

def accession
  @accession
end

#definition ⇒ Object Also known as: target_def

Definition line of subject



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# File 'lib/bio/appl/blast/report.rb', line 226

def definition
  @definition
end

#hit_id ⇒ Object

SeqId of subject



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# File 'lib/bio/appl/blast/report.rb', line 222

def hit_id
  @hit_id
end

#hsps ⇒ Object (readonly)

Returns an Array of Bio::Blast::Report::Hsp objects.



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# File 'lib/bio/appl/blast/report.rb', line 217

def hsps
  @hsps
end

#len ⇒ Object Also known as: target_len

Length of subject



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# File 'lib/bio/appl/blast/report.rb', line 224

def len
  @len
end

#num ⇒ Object

Hit number



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# File 'lib/bio/appl/blast/report.rb', line 220

def num
  @num
end

#query_def ⇒ Object

Compatible method with Bio::Fasta::Report::Hit class.



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# File 'lib/bio/appl/blast/report.rb', line 240

def query_def
  @query_def
end

#query_id ⇒ Object

Compatible method with Bio::Fasta::Report::Hit class.



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# File 'lib/bio/appl/blast/report.rb', line 238

def query_id
  @query_id
end

#query_len ⇒ Object

Compatible method with Bio::Fasta::Report::Hit class.



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# File 'lib/bio/appl/blast/report.rb', line 242

def query_len
  @query_len
end

Instance Method Details

#bit_score ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 254

def bit_score;        @hsps.first.bit_score;        end

#each ⇒ Object

Iterates on each Hsp object.



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# File 'lib/bio/appl/blast/report.rb', line 231

def each
  @hsps.each do |x|
    yield x
  end
end

#evalue ⇒ Object

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



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# File 'lib/bio/appl/blast/report.rb', line 253

def evalue;           @hsps.first.evalue;           end

#identity ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 255

def identity;         @hsps.first.identity;         end

#lap_at ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 267

def lap_at
  [ query_start, query_end, target_start, target_end ]
end

#midline ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 261

def midline;          @hsps.first.midline;          end

#overlap ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 257

def overlap;          @hsps.first.align_len;        end

#percent_identity ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 256

def percent_identity; @hsps.first.percent_identity; end

#query_end ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 264

def query_end;        @hsps.first.query_to;         end

#query_seq ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 259

def query_seq;        @hsps.first.qseq;             end

#query_start ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 263

def query_start;      @hsps.first.query_from;       end

#target_end ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 266

def target_end;       @hsps.first.hit_to;           end

#target_seq ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 260

def target_seq;       @hsps.first.hseq;             end

#target_start ⇒ Object 



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# File 'lib/bio/appl/blast/report.rb', line 265

def target_start;     @hsps.first.hit_from;         end