Method run has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

Method create_file_description has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def create_file_description(source_files, config)
      Mspire::Mzml::FileDescription.new  do |fd|

        fd.file_content = Mspire::Mzml::FileContent.new.describe_many!( [
          'MS:1000579', # MS1 Spectrum

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Method from_xml has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

      def self.from_xml(xml, link)
        obj = self.new(xml[:id])
        obj.spot_id = xml[:spotID]

        obj.data_processing = link[:data_processing_hash][xml[:dataProcessingRef]] || link[:spectrum_default_data_processing]

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Method to_xml has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

      def to_xml(builder, default_ids)
        io = builder.target!

        atts = data_array_xml_atts
        if @data_processing && default_ids[:spectrum_data_processing] != @data_processing.id 

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Method inverse has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def inverse
    i = Hash.new
    self.each_pair do |k,v|
      if (Array === v) ; v.each{ |x| i[x] = ( i.has_key?(x) ? [k,i[x]].flatten : k ) }
      else ; i[v] = ( i.has_key?(v) ? [k,i[v]].flatten : k ) end

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Method peak_boundaries has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def peak_boundaries(gt=0.0)
      in_peak = false
      prev_y = gt
      prev_prev_y = gt
      peak_inds = []

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Method cmdline has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def self.cmdline(argv)
    opt = DEFAULT_PEPTIDE_CENTRIC_DB.dup

    opts = OptionParser.new do |op|
      op.banner = "usage: #{File.basename($0)} <file>.fasta ..."

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

Open

    def split_contiguous(methd=:greedy_y, local_min_indices=nil)
      local_min_indices ||= ((pb=peak_boundaries.first) && pb.shift && pb.pop && pb)

      if local_min_indices.size == 0
        self

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Method peptide_hits_to_protein_groups has a Cognitive Complexity of 11 (exceeds 5 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 }

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

Open

      def create_scan_to_index
        scan_re = /scan=(\d+)/
          scan_to_index = {}
        ids.each_with_index do |id, index|
          md = id.match(scan_re)

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

Open

      def describe_from_xml!(xml_node, ref_hash=nil)
        # TODO: this was merely cleaned up from Paramable and should be
        # re-factored
        return nil unless (child_n = xml_node.child) 
        loop do

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

Open

  def to_xml(opts={})
    opts ||= {}
    if opts.is_a?(String) 
      opts = ( opts.match(/\.xml$/) ?  {:outfile => opts} : {:outdir => opts } )
    end

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

Open

    def describe_from_xml!(xml_node, ref_hash=nil)
      return nil unless (child_n = xml_node.child) 
      loop do
        array = 
          case child_n.name

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Method to_xml has 31 lines of code (exceeds 25 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!

Method to_binary has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

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

Open

  def db_from_fasta_digestion_file(digestion_file, opts={})
    opts = DEFAULT_PEPTIDE_CENTRIC_DB.merge(opts)

    start_time = Time.now
    puts "Organizing raw digestion #{digestion_file} ..." if $VERBOSE

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

Open

      def self.from_xml(xml, link)
        obj = self.new(xml[:id])
        obj.spot_id = xml[:spotID]

        obj.data_processing = link[:data_processing_hash][xml[:dataProcessingRef]] || link[:spectrum_default_data_processing]

Method simple_search_hits has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def self.simple_search_hits(file, &block)
    hit_values = File.open(file) do |io|
      doc = Nokogiri::XML.parse(io, nil, nil, Nokogiri::XML::ParseOptions::DEFAULT_XML | Nokogiri::XML::ParseOptions::NOBLANKS | Nokogiri::XML::ParseOptions::STRICT)
      # we can work with namespaces, or just remove them ...
      doc.remove_namespaces!

Method peak_boundaries has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def peak_boundaries(gt=0.0)
      in_peak = false
      prev_y = gt
      prev_prev_y = gt
      peak_inds = []

Method split_contiguous has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def split_contiguous(methd=:greedy_y, local_min_indices=nil)
      local_min_indices ||= ((pb=peak_boundaries.first) && pb.shift && pb.pop && pb)

      if local_min_indices.size == 0
        self