Method run has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def run(lst = @hits)
      if type.to_s != 'nucleotide'
        @validation_report = ValidationReport.new('', :unapplicable)
        return @validation_report
      end

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Method check_multiple_coverage has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def check_multiple_coverage(hit_alignment, query_alignment, hsp, coverage,
                                ranges_prediction)
      # for each hsp of the curent hit
      # iterate through the alignment and count the matching residues
      [*(0..hit_alignment.length - 1)].each do |i|

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Method calculate_run_time has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

      def calculate_run_time(json_data)
        run_time = Hash.new(Pair1.new(0, 0))
        json_data.map do |row|
          row[:validations].each do |short_header, v|
            next if v[:run_time].nil? || v[:run_time].zero?

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Function plot_bars has 7 arguments (exceeds 4 allowed). Consider refactoring.

Open

  GV.plot_bars = function (alldata, target, title, footer, xTitle, yTitle, bar) {

Method initialize has 7 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def initialize(short_header, header, description, pvalue, averages,
                   threshold = 0.05, expected = :yes)

Method iterate_xml has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

      def iterate_xml(file, db_type)
        n = Bio::BlastXMLParser::XmlIterator.new(opt[:blast_xml_file]).to_enum
        n.each do |iter|
          iter.each do |hit|
            raise BLASTDBError if hit.hit_id =~ /\|BL_ORD_ID\|/

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Method initialize has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def initialize(short_header, header, description, splice_sites, exons,
                   expected = :yes)

Method initialize has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def initialize(short_header, header, description, query_length, limits,
                   expected = :yes)

Method conclude has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def conclude
      if @result == :yes
        'There is no evidence based on the top 10 BLAST hits to suggest any' \
        ' problems with the query sequence.'
      else

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Method check_validations has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def check_validations(vals)
      # check the class type of the elements in the list
      vals.each { |v| raise ValidationClassError unless v.is_a? ValidationTest }
      # check alias duplication
      aliases = vals.map(&:cli_name)

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Method conclude has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def conclude
      if @unimodality
        'This suggest that the query sequence represents a single gene.'
      else
        diff = @result == :yes ? ' within' : ' outside'

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Function plot_simple_bars has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

  GV.plot_simple_bars = function (alldata, target, title, footer, xTitle, yTitle) {

Method initialize has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def initialize(short_header, header, description, slope, unimodality,
                   expected = :no)

Method general_overview has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

      def general_overview(o)
        good_pred = o[:good_scores] == 1 ? 'One' : "#{o[:good_scores]} are"
        bad_pred  = o[:bad_scores] == 1 ? 'One' : "#{o[:bad_scores]} are"

        plural = 'prediction was' if o[:insufficient_BLAST_hits] == 1

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Method run has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def run
      # Run BLAST on all sequences (generates @opt[:blast_xml_file])
      # if no BLAST OUTPUT file provided...
      unless @opt[:blast_xml_file] || @opt[:blast_tabular_file]
        blast_xml_fname = "#{dirs[:filename]}.blast_xml"

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Consider simplifying this complex logical expression.

Open

      if cond1_x && cond2_x && cond3_x && cond1_y && cond2_y && cond3_y
        true
      else
        false
      end

Method check_multiple_coverage has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def check_multiple_coverage(hit_alignment, query_alignment, hsp, coverage,
                                ranges_prediction)

Method initialize has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def initialize(short_header, header, description, frames,
                   expected = :yes)

Method run has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def run
      raise NotEnoughHitsError if hits.length < opt[:min_blast_hits]
      raise unless prediction.is_a?(Query) && hits[0].is_a?(Query)

      start = Time.now

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Method get_orfs has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def get_orfs(_orf_length = 100, prediction = @prediction)
      '-' if prediction.type != 'nucleotide'

      seq = Bio::Sequence::NA.new(prediction.raw_sequence)

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