Method bin has a Cognitive Complexity of 40 (exceeds 5 allowed). Consider refactoring.

Open

    def self.bin(bins, objects, *data_capture_obj, &block)
      data_capture = data_capture_obj.first || bins

      if objects.size > 0
        obj_e = objects.each ; obj = obj_e.next  

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Method create_digestion_file has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.

Open

  def create_digestion_file(fasta_file, opts={})
    opts = DEFAULT_PEPTIDE_CENTRIC_DB.merge(opts)

    (missed_cleavages, enzyme, cleave_initiator_methionine, expand_aa) = opts.values_at(:missed_cleavages, :enzyme, :cleave_initiator_methionine, :expand_aa) 
    start_time = Time.now

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Method write has 99 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def write(mzml_filenames, config={})

      base = config[:combine] || mzml_filenames.first.chomp(File.extname(mzml_filenames.first))
      config[:imzml_filename] = base + ".imzML"
      config[:ibd_filename] = base + ".ibd"

Method merge_centroids has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

      def merge_centroids(peaklists, opts={})
        opts[:return_data] = true if opts[:only_data]

        # Create Mspire::Bin objects
        bins = opts[:bins] ? opts[:bins] : create_bins(peaklists, opts)

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Method write has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.

Open

    def write(mzml_filenames, config={})

      base = config[:combine] || mzml_filenames.first.chomp(File.extname(mzml_filenames.first))
      config[:imzml_filename] = base + ".imzML"
      config[:ibd_filename] = base + ".ibd"

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File writer.rb has 304 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'nokogiri'
require 'securerandom'
require 'cv'
require 'mspire/mzml'
require 'mspire/mzml/spectrum'

Method hash_like_from_digestion_file has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

  def hash_like_from_digestion_file(digestion_file, min_length, data_type=:hash)
    case data_type
    when :trie
      trie = get_a_trie
      ::IO.foreach(digestion_file) do |line|

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Method from_xml has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

  def self.from_xml(xml, link)
    da = self.new 
    binary_n = da.describe_from_xml!(xml, link[:ref_hash])

    if (dp_id = xml[:dataProcessingRef])

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Method read_header! has 57 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def read_header!(list_type_to_default_data_processing_id)
    @io.rewind

    string = get_header_string(@io)
    doc = Nokogiri::XML.parse(string, nil, @encoding, Mspire::Mzml::Parser::NOBLANKS)

Method to_xml has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

    def to_xml(filename=nil)
      # TODO: support indexed mzml files
      io = filename ? File.open(filename, 'w') : StringIO.new
      xml = Builder::XmlMarkup.new(:target => io, :indent => 2)
      xml.instruct!

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Method parser has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def self.parser
    return @parser if @parser

    default_config = "config.yaml"
    scan_patterns = %w(flyback meandering random)

Method run has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

  def run(normalize=true, opts={})
    exe = executable
    puts "using #{exe}" if $VERBOSE
    executable_base = exe.split('-')[0]

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Method hash_like_from_digestion_file has 44 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def hash_like_from_digestion_file(digestion_file, min_length, data_type=:hash)
    case data_type
    when :trie
      trie = get_a_trie
      ::IO.foreach(digestion_file) do |line|

Method to_binary has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

  def to_binary
    # single pass over params for speed
    pack_code = nil
    compression = nil
    each_accessionable_param do |param|

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Method x_y_positions has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def x_y_positions(config)
      (scan_pattern, scan_type, scan_direction, scan_sequence, shots_per_pos) = config.values_at(:scan_pattern, :scan_type, :linescan_direction, :linescan_sequence, :shots_per_position).map(&:to_s)
      shots_per_pos = shots_per_pos.to_i
      #puts "EXAMIN ARGS: "
      #p [ scan_pattern, scan_type, scan_direction, scan_sequence, shots_per_pos, shots_per_pos]

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

Open

  def to_xml(builder=nil)
    xmlb = builder || Nokogiri::XML::Builder.new
    hash = {:base_name => base_name, :msManufacturer => ms_manufacturer, :msModel => ms_model, :msIonization => ms_ionization, :msMassAnalyzer => ms_mass_analyzer, :msDetector => ms_detector, :raw_data_type => raw_data_type, :raw_data => raw_data}
    hash.each {|k,v| hash.delete(k) unless v }
    xmlb.msms_run_summary(hash) do |xmlb|

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Method image_hash_to_cvs has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def image_hash_to_cvs(hash)
      cvs = []
      cvs << case hash[:data_structure].to_sym
      when :processed ; 'IMS:1000031'
      when :continuous ; 'IMS:1000030'

Method merge_centroids has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def merge_centroids(peaklists, opts={})
        opts[:return_data] = true if opts[:only_data]

        # Create Mspire::Bin objects
        bins = opts[:bins] ? opts[:bins] : create_bins(peaklists, opts)

Method create_digestion_file has 37 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create_digestion_file(fasta_file, opts={})
    opts = DEFAULT_PEPTIDE_CENTRIC_DB.merge(opts)

    (missed_cleavages, enzyme, cleave_initiator_methionine, expand_aa) = opts.values_at(:missed_cleavages, :enzyme, :cleave_initiator_methionine, :expand_aa) 
    start_time = Time.now

Method peptide_hits_to_protein_groups has 37 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def self.peptide_hits_to_protein_groups(peptide_hits, update_peptide_hits=false, &sort_by)
        update_peptide_hits = 'protein_groups='.to_sym if (update_peptide_hits==true)
        sort_by ||= PRIORITIZE_PROTEINS
        # note to self: I wrote this in 2011, so I think I know what I'm doing now
        protein_to_peptides = Hash.new {|h,k| h[k] = Set.new }