Class: Bio::Blast::Report::Iteration

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

Overview

Bio::Blast::Report::Iteration

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initializeIteration


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# File 'lib/bio/appl/blast/report.rb', line 213

def initialize
  @message = nil
  @statistics = {}
  @num = 1
  @hits = []
end

Instance Attribute Details

#hitsObject (readonly)

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


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

def hits
  @hits
end

#messageObject

Returns a String (or nil) containing execution message (typically “CONVERGED”).


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# File 'lib/bio/appl/blast/report.rb', line 232

def message
  @message
end

#numObject

Returns the number of iteration counts.


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

def num
  @num
end

#query_defObject

query definition, only available for new BLAST XML format


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# File 'lib/bio/appl/blast/report.rb', line 245

def query_def
  @query_def
end

#query_idObject

query ID, only available for new BLAST XML format


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

def query_id
  @query_id
end

#query_lenObject

query length, only available for new BLAST XML format


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# File 'lib/bio/appl/blast/report.rb', line 248

def query_len
  @query_len
end

#statisticsObject (readonly)

Returns a Hash containing execution statistics. Valid keys are: 'db-len', 'db-num', 'eff-space', 'entropy', 'hsp-len', 'kappa', 'lambda'


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# File 'lib/bio/appl/blast/report.rb', line 225

def statistics
  @statistics
end

Instance Method Details

#eachObject

Iterates on each Bio::Blast::Report::Hit object.


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# File 'lib/bio/appl/blast/report.rb', line 235

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