Method run_validations has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def run_validations(iterator)
      p = Pool.new(@opt[:num_threads]) if @opt[:num_threads] > 1

      check_if_maker_input?

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Method run has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def run(hits = @hits, prediction = @prediction)
      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 initialize has 12 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def initialize(short_header, header, description, msg, query_length,
                   no_of_hits, median, mean, smallest_hit, largest_hit,
                   extreme_hits, percentage)

Method multiple_align_mafft has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

    def multiple_align_mafft(prediction, hits)
      raise unless prediction.is_a?(Query) && hits[0].is_a?(Query)

      opt = ['--maxiterate', '1000', '--localpair', '--anysymbol', '--quiet',
             '--thread', @num_threads.to_s]

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Function addPlot has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  GV.addPlot = function (jsonData, target, type, title, footer, xtitle, ytitle, aux1, aux2) {
    var legend;
    if (footer === '') {
      legend = [];
    } else {

Method unimodality_test has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def unimodality_test(xx, yy)
      mean_x = xx.mean
      median_x = xx.median
      mode_x = xx.mode
      sd_x = xx.standard_deviation

Method plot_alignment has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def plot_alignment(freq, ma = @multiple_alignment)
      # get indeces of consensus in the multiple alignment
      consensus = get_consensus(ma[0..ma.length - 2])
      consensus_idxs = consensus.split(//).each_index.select { |j| isalpha(consensus[j]) }
      consensus_ranges = array_to_ranges(consensus_idxs)

Function addPlot has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

  GV.addPlot = function (jsonData, target, type, title, footer, xtitle, ytitle, aux1, aux2) {

Method clusterization_by_length has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def clusterization_by_length(_debug = false,
                                 lst = @hits,
                                 predicted_seq = @prediction)
      raise TypeError unless lst[0].is_a?(Query) && predicted_seq.is_a?(Query)

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Method get_sm_pssm has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def get_sm_pssm(ma, threshold = 0.7)
      sm = ''
      freq = []
      (0..ma[0].length - 1).each do |i|
        freqs = Hash.new(0)

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Method conclude has 26 lines of code (exceeds 25 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

Method run has 26 lines of code (exceeds 25 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

Method initialize has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def initialize(message = 'Not enough evidence', validation_result = :no,
                   short_header = '', header = '', description = '',
                   approach = '', explanation = '', conclusion = '')

Method initialize has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def initialize(short_header, header, description, orfs, coverage,
                   longest_orf_frame, threshold = 80, expected = :yes)

Method initialize has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def initialize(short_header, header, description, gaps = 0, extra_seq = 0,
                   consensus = 1, threshold = 20, expected = :yes)

Function plot_align has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

  GV.plot_align = function (data, target, title, footer, xTitle, yTitle, no_lines, yValues) {

Function plot_scatter has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

  GV.plot_scatter = function (data, target, title, footer, xTitle, yTitle, yLine, slope) {

Method overview_hash has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

      def overview_hash(scores_from_json, quartiles, nee, no_mafft, no_internet,
                        map_errors, run_time, insufficient_BLAST_hits)

Function plot_lines has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

  GV.plot_lines = function (data, target, title, footer, xTitle, yTitle, no_lines, yValues) {

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

Open

      def run(identifier, accession)
        # first try to extract from previously created raw_sequences HASH
        raw_seq = extract_from_index(accession) if opt[:raw_sequences]
        # then try to just extract that sequence based on accession.
        if opt[:db] !~ /remote/ && (raw_seq.nil? || raw_seq =~ /Error/i)

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