Class: AlignmentValidationOutput

Inherits:

ValidationReport

• Object
• ValidationReport
• AlignmentValidationOutput

show all

Defined in:

lib/genevalidator/validation_alignment.rb

Overview

Instance Attribute Summary (collapse)

• - (Object) consensus readonly

  Returns the value of attribute consensus.

• - (Object) extra_seq readonly

  Returns the value of attribute extra_seq.

• - (Object) gaps readonly

  Returns the value of attribute gaps.

• - (Object) threahsold readonly

  Returns the value of attribute threahsold.

Attributes inherited from ValidationReport

#bg_color, #errors, #expected, #message, #plot_files, #result, #validation_result

Instance Method Summary (collapse)

• - (AlignmentValidationOutput) initialize(gaps = 0, extra_seq = 0, consensus = 1, threshold = 0.2, expected = :yes) constructor

  A new instance of AlignmentValidationOutput.

• - (Object) print
• - (Object) validation

Methods inherited from ValidationReport

#color

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# File 'lib/genevalidator/validation_alignment.rb', line 13

def initialize (gaps = 0, extra_seq = 0, consensus = 1, threshold = 0.2, expected = :yes)
  @gaps       = gaps
  @extra_seq  = extra_seq
  @consensus  = consensus
  @threshold  = threshold
  @result     = validation
  @expected   = expected
  @plot_files = []
end

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# File 'lib/genevalidator/validation_alignment.rb', line 10

def consensus
  @consensus
end

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# File 'lib/genevalidator/validation_alignment.rb', line 9

def extra_seq
  @extra_seq
end

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# File 'lib/genevalidator/validation_alignment.rb', line 8

def gaps
  @gaps
end

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# File 'lib/genevalidator/validation_alignment.rb', line 11

def threahsold
  @threahsold
end

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# File 'lib/genevalidator/validation_alignment.rb', line 23

def print
  "#{(gaps*100).round(0)}% missing, #{(extra_seq*100).round(0)}% extra, #{(consensus*100).round(0)}% conserved"
end

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# File 'lib/genevalidator/validation_alignment.rb', line 27

def validation
  if gaps < @threshold and extra_seq < @threshold #and consensus < @threshold
    :yes
  else
    :no
  end
end