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

Inherits:
Default::Report::Hit show all
Defined in:
lib/bio/appl/blast/wublast.rb

Overview

Bio::Blast::WU::Report::Hit contains information about a hit. It may contain some Bio::Blast::WU::Report::HSP objects.

Because it inherits Bio::Blast::Default::Report::Hit, please also refer Bio::Blast::Default::Report::Hit.

Instance Attribute Summary collapse

Attributes inherited from Default::Report::Hit

#hsps

Instance Method Summary collapse

Methods inherited from Default::Report::Hit

#bit_score, #definition, #each, #evalue, #found_again?, #identity, #lap_at, #len, #midline, #overlap, #query_end, #query_seq, #query_start, #target_end, #target_id, #target_seq, #target_start

Constructor Details

#initialize(data) ⇒ Hit

Creates a new Hit object. It is designed to be called only internally from the Bio::Blast::WU::Report::Iteration class. Users should not call the method directly.



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# File 'lib/bio/appl/blast/wublast.rb', line 406

def initialize(data)
  @f0hitname = data.shift
  @hsps = []
  while r = data.first
    if r =~ /^\s*(?:Plus|Minus) +Strand +HSPs\:/ then
      data.shift
      r = data.first
    end
    if /\A\s+Score/ =~ r then
      @hsps << HSP.new(data)
    else
      break
    end
  end
  @again = false
end

Instance Attribute Details

#n_number ⇒ Object (readonly)

n-number (???)



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# File 'lib/bio/appl/blast/wublast.rb', line 430

def n_number
  @n_number
end

#pvalue ⇒ Object (readonly)

p-value



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# File 'lib/bio/appl/blast/wublast.rb', line 428

def pvalue
  @pvalue
end

Instance Method Details

#score ⇒ Object

Returns score.



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# File 'lib/bio/appl/blast/wublast.rb', line 424

def score
  @score
end