Avoid deeply nested control flow statements.

Open

              value = (block.nil? ? obj : block.call(obj))

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

Open

  def num_tol_term(prev_aa, middle, next_aa)
    raise NotImplementedError, 'need to implement for N terminal sense'  if sense == 'N'
    no_cut = @no_cut || ''
    num_tol = 0
    last_of_middle = middle[-1,1]

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Consider simplifying this complex logical expression.

Open

          if cbin.begin <= value
            until cbin === value && data_capture[bin_i] << obj
              bin_i += 1
              cbin=bins[bin_i] || (done=true && break)
            end

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

Open

    def site_digest(seq, max_misses=0, offset=0, length=seq.length-offset, &block) # :yields: start_index, end_index

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

Open

      def self.[](*args)
        #puts "param args #{args.inspect}"
        unit = 
          case args.size
          when 1

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

Open

      def to_xml(builder)
        atts = { id: @id,
          defaultInstrumentConfigurationRef: @default_instrument_configuration.id
        }
        atts[:defaultSourceFileRef] = @default_source_file.id if @default_source_file

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

Open

    def cleavage_sites(seq, offset=0, length=seq.length-offset)
      return [0, 1] if seq.size == 1  # adding exceptions is lame--algorithm should just work

      adjustment = cterm_cleavage ? 0 : 1
      limit = offset + length

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

Open

  def self.args_to_hashes(args, replicate_postfix="-rep")
    # groupname => files
    condition_to_samplenames = {}
    samplename_to_filename = {}
    args.each do |arg|

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

Open

  def get_header_string(io)
    chunk_size = 2**12
    loc = 0
    string = ''
    while chunk = @io.read(chunk_size)

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

Open

  def num_missed_cleavages(aaseq)
    seq_to_scan = '  ' + aaseq + '  ' 
    raise NotImplementedError, 'need to implement for N terminal sense'  if sense == 'N'
    @num_missed_cleavages_regex = 
      if @num_missed_cleavages_regex ; @num_missed_cleavages_regex

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

Open

    def write_binary(filename, spectra_iterator, config)
      config = DEFAULTS.merge(config)
      raise ":data_structure must be :continuous or :processed" unless [:processed, :continuous].include?(config[:data_structure])
      (mz_dtype, mz_prec, int_dtype, int_prec) = config.values_at(:mz_data_type, :mz_precision, :intensity_data_type, :intensity_precision)
      mz_prec_in_bytes = mz_prec / 8

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Method from_xml has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

      def self.from_xml(xml, link)
        scan_list = self.new
        scan_n = scan_list.describe_from_xml!(xml, link[:ref_hash])
        if scan_n
          loop do

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Method from_xml has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

      def self.from_xml(io, xml, link)

        # expects that the DataProcessing objects to link to have *already* been
        # parsed (parse the defaultDataProcessingRef's after grabbing the
        # index, then grab the DataProcessing object associated with that id).

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Method initialize has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def initialize(*args)
      self.unit = 
        if args.size > 1 && ((args.last.is_a?(::CV::Param) || args.last =~ /^[A-Za-z]+:\d+$/))
          unit_arg = args.pop
          unit_arg.is_a?(::CV::Param) ? unit_arg : Mspire::CV::Param[unit_arg]

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Method run has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def self.run(argv)

      parser = Trollop::Parser.new do
        banner "usage: mspire <subcommand> [OPTIONS]"
        text ""

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Method split has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def split(split_multipeaks_mthd=:zero)
      if split_multipeaks_mthd == :zero
        split_on_zeros
      else
        boundaries = peak_boundaries(0.0)

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Method cast_method has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def cast_method
      xref = @tagvalues['xref'].first
      @cast_method = 
        if xref.nil? || (@cast_method == false)
          false

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Method write_data_array has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def write_data_array(fh, values, dtype=:float, precision=32)
      pack_code = 
        case dtype
        when :float
          precision == 64 ? 'E*' : 'e*'

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Method experiment_hash_to_cvs has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def experiment_hash_to_cvs(hash)
      cvs = { 
        :matrix_solution_concentration => "MS:1000835",
        :matrix_solution => "MS:1000834",
        :solvent => 'IMS:1001211',

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Method write has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def write(filename=nil, ascii=false)
      if ascii
        write_ascii(filename)
      else
        write_file_or_string(filename) do |out|

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