mspire 0.4.9 → 0.5.0

data/lib/spec_id/sequest/pepxml.rb

@@ -1,1458 +0,0 @@
-
-require 'sample_enzyme'
-require 'ms/parser/mzxml'
-require 'hash_by'
-require 'set_from_hash'
-require 'spec_id/bioworks'
-require 'instance_var_set_from_hash'
-require 'ms/msrun'
-require 'spec_id/srf'
-require 'spec_id/sequest/params'
-require 'fileutils'
-
-class Numeric
-  # returns a string with a + or - on the front
-  def to_plus_minus_string
-    if self >= 0
-      '+' << self.to_s
-    else
-      self.to_s
-    end
-  end
-end
-
-
-module Sequest ; end
-class Sequest::PepXML; end
-
-class Sequest::PepXML::MSMSPipelineAnalysis
-  include SpecIDXML
-  # Version 1.2.3
-  attr_writer :date
-  attr_writer :xmlns, :xmlns_xsi, :xsi_schemaLocation
-  attr_accessor :summary_xml 
-  # Version 2.3.4
-  attr_writer :xmlns, :xmlns_xsi, :xsi_schema_location
-  attr_accessor :pepxml_version
-  attr_accessor :msms_run_summary
-
-  # if block given, sets msms_run_summary to block
-  def initialize(hash=nil)
-    @xmlns = nil
-    @xmlns_xsi = nil
-    @xsi_schema_location = nil
-    if hash
-      self.set_from_hash(hash)
-    end
-    if block_given?
-      @msms_run_summary = yield
-    end
-  end
-
-  # if no date string given, then it will set to Time.now
-  def date
-    if @date ; @date 
-    else
-      case Sequest::PepXML.pepxml_version
-      when 18 ;  tarr = Time.now.to_a ; tarr[3..5].reverse.join('-') + "T#{tarr[0..2].reverse.join(':')}"
-      end
-    end
-  end
-
-  def xmlns
-    if @xmlns ; @xmlns
-    else ; "http://regis-web.systemsbiology.net/pepXML"
-    end
-  end
-
-  def xmlns_xsi
-    if @xmlns_xsi ; @xmlns_xsi
-    else ; "http://www.w3.org/2001/XMLSchema-instance"
-    end
-  end
-
-  def xsi_schema_location
-    if @xsi_schema_location ; @xsi_schema_location 
-    else ; "http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v18.xsd"
-    end
-  end
-
-  def to_pepxml
-    case Sequest::PepXML.pepxml_version
-    when 18
-      element_xml_and_att_string(:msms_pipeline_analysis, "date=\"#{date}\" xmlns=\"#{xmlns}\" xmlns:xsi=\"#{xmlns_xsi}\" xsi:schemaLocation=\"#{xsi_schema_location}\" summary_xml=\"#{summary_xml}\"") do
-        @msms_run_summary.to_pepxml
-      end
-    else
-      abort "Don't know how to deal with version: #{Sequest::PepXML.pepxml_version}"
-    end
-  end
-
-end
-
-class Sequest::PepXML::MSMSRunSummary
-  include SpecID
-  include SpecIDXML
-
-  # the version of TPP you are using (determines xml output)
-  # The name of the pep xml file (without extension) (but this is a long
-  # filename!!!)
-  attr_accessor :base_name
-  # The name of the mass spec manufacturer 
-  attr_accessor :ms_manufacturer
-  attr_accessor :ms_model
-  attr_accessor :ms_mass_analyzer
-  attr_accessor :ms_detector
-  attr_accessor :raw_data_type
-  attr_accessor :raw_data
-  attr_accessor :ms_ionization
-  attr_accessor :pepxml_version
-
-  # A SampleEnzyme object (responds to: name, cut, no_cut, sense)
-  attr_accessor :sample_enzyme
-  # A SearchSummary object
-  attr_accessor :search_summary
-  # An array of spectrum_queries
-  attr_accessor :spectrum_queries
-
-  # takes a hash of name, value pairs
-  # if block given, spectrum_queries (should be array of spectrum queries) is
-  # set to the return value of the block
-  def initialize(hash=nil)
-    @spectrum_queries = []
-    if hash
-      instance_var_set_from_hash(hash)
-    end
-    if block_given? ; @spectrum_queries = yield end
-  end
-
-  def to_pepxml
-    case Sequest::PepXML.pepxml_version
-    when 18
-      element_xml_and_att_string(:msms_run_summary, "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}\"") do
-        sample_enzyme.to_pepxml +
-          search_summary.to_pepxml +
-          spectrum_queries.map {|sq| sq.to_pepxml }.join
-      end
-    end
-  end
-
-  def search_hit_class
-    Sequest::PepXML::SearchHit
-  end
-
-  def self.from_pepxml_node(node)
-    self.new.from_pepxml_node(node)
-  end
-
-  # peps correspond to search_results
-  def from_pepxml_node(node)
-    @base_name = node['base_name']
-    @ms_manufacturer = node['msManufacturer']
-    @ms_model = node['msModel']
-    @ms_manufacturer = node['msIonization']
-    @ms_mass_analyzer = node['msMassAnalyzer']
-    @ms_detector = node['msDetector']
-    @raw_data_type = node['raw_data_type']
-    @raw_data = node['raw_data']
-    self
-  end
-end
-
-
-
-class Sequest::PepXML
-  include SpecIDXML
-
-  ## CREATE a default version for the entire class
-  class << self
-    attr_accessor :pepxml_version
-  end
-  DEF_VERSION = 18
-  self.pepxml_version = DEF_VERSION # default version
-
-  attr_accessor :pepxml_version, :msms_pipeline_analysis
-  ## the full path name (no extension)
-  attr_accessor :base_name
-  attr_accessor :h_plus
-  attr_accessor :avg_parent
-
-  #attr_accessor :spectrum_queries, :params, :base_name, :search_engine, :database, :raw_data_type, :raw_data, :out_data_type, :out_data, :sample_enzyme, :pepxml_version
-
-  # returns an array of spectrum queries
-  def spectrum_queries
-    msms_pipeline_analysis.msms_run_summary.spectrum_queries
-  end
-
-  # msms_pipeline_analysis is set to the result of the yielded block
-  # and set_mono_or_avg is called with params if given
-  def initialize(pepxml_version=DEF_VERSION, sequest_params_obj=nil)
-    self.class.pepxml_version = pepxml_version
-    if sequest_params_obj
-      set_mono_or_avg(sequest_params_obj)
-    end
-    if block_given?
-      @msms_pipeline_analysis = yield
-      @base_name = @msms_pipeline_analysis.msms_run_summary.base_name
-    end
-  end
-
-  # sets @h_plus and @avg_parent from the sequest params object
-  def set_mono_or_avg(sequest_params_obj)
-    case sequest_params_obj.precursor_mass_type
-    when "monoisotopic" ; @avg_parent = false
-    else ; @avg_parent = true
-    end
-
-    case @avg_parent
-    when true ; @h_plus = SpecID::AVG[:h_plus]
-    when false ; @h_plus = SpecID::MONO[:h_plus]
-    end
-  end
-
-  def date
-    Time.new.to_s
-  end
-
-  def xml_version 
-    '<?xml version="1.0" encoding="UTF-8"?>' + "\n"
-  end
-
-  # for pepxml_version == 0
-  def doctype
-    '<!DOCTYPE msms_pipeline_analysis SYSTEM "/usr/bin/msms_analysis3.dtd">' + "\n"
-  end
-
-  def style_sheet
-    case self.class.pepxml_version
-    when 18
-    '<?xml-stylesheet type="text/xsl" href="/tools/bin/TPP/tpp/schema/pepXML_std.xsl"?>'
-    end
-  end
-
-  def header
-    case self.class.pepxml_version
-    when 18 ; xml_version + style_sheet
-    end
-  end
-
-  # updates the private attrs _num_prots and _first_prot on bioworks pep
-  # objects.  Ideally, we'd like these attributes to reside elsewhere, but for
-  # memory concerns, this is best for now.
-  def self._prot_num_and_first_prot_by_pep(pep_array)
-    pep_array.hash_by(:aaseq).each do |aasq, pep_arr|
-      prts = []
-      pep_arr.each { |pep| prts.push( *(pep.prots) ) }
-      prts.uniq!
-      _size = prts.size 
-      pep_arr.each do |pep|
-        pep._num_prots = _size
-        pep._first_prot = prts.first
-      end
-    end
-  end
-
-
-Default_Options = {
-    :out_path => '.',
-    #:backup_db_path => '.',
-    # a PepXML option
-    :pepxml_version => DEF_VERSION,  
-    ## MSMSRunSummary options:
-    # string must be recognized in sample_enzyme.rb 
-    # or create your own SampleEnzyme object
-    :ms_manufacturer => 'ThermoFinnigan',
-    :ms_model => 'LCQ Deca XP Plus',
-    :ms_ionization => 'ESI',
-    :ms_mass_analyzer => 'Ion Trap',
-    :ms_detector => 'UNKNOWN',
-    :ms_data => '.',      # path to ms data files (raw or mzxml)
-    :raw_data_type => "raw",
-    :raw_data => ".mzXML", ## even if you don't have it?
-    ## SearchSummary options:
-    :out_data_type => "out", ## may be srf?? don't think pepxml recognizes this yet
-    :out_data => ".tgz", ## may be srf??
-    :copy_mzxml => false, # copy the mzxml file to the out_path (create it if necessary)
-    :print => false, # print the objects to file
-  }
-
-  # will dynamically set :ms_model and :ms_mass_analyzer from srf info
-  # (ignoring defaults or anything passed in) for LTQ Orbitrap
-  # and LCQ Deca XP
-  # See SRF::Sequest::PepXML::Default_Options hash for defaults
-  # unless given, the out_path will be given as the path of the srf_file
-  # srf may be an object or a filename
-  def self.new_from_srf(srf, opts={})
-    opts = Default_Options.merge(opts)
-
-    ## read the srf file
-    if srf.is_a? String
-      srf = SRF.new(srf)
-    end
-
-    ## set the outpath
-    out_path = opts.delete(:out_path)
-
-    params = srf.params
-
-    ## check to see if we need backup_db
-    backup_db_path = opts.delete(:backup_db_path)
-    if !File.exist?(params.database) && backup_db_path
-      params.database_path = backup_db_path
-    end
-
-    #######################################################################
-    # PREPARE THE OPTIONS:
-    #######################################################################
-    ## remove items from the options hash that don't belong to 
-    ppxml_version = opts.delete(:pepxml_version)
-    out_data_type = opts.delete(:out_data_type)
-    out_data = opts.delete(:out_data)
-
-    ## Extract meta info from srf
-    bn_noext = base_name_noext(srf.header.raw_filename)
-    opts[:ms_model] = srf.header.model
-    case opts[:ms_model]
-    when /Orbitrap/
-      opts[:ms_mass_analyzer] = 'Orbitrap'
-    when /LCQ Deca XP/
-      opts[:ms_mass_analyzer] = 'Ion Trap'
-    end
-
-    ## Create the base name
-    full_base_name_no_ext = make_base_name( File.expand_path(out_path), bn_noext)
-    opts[:base_name] = full_base_name_no_ext
-
-    ## Create the search summary:
-    search_summary_options = {
-      :search_database => Sequest::PepXML::SearchDatabase.new(params),
-      :base_name => full_base_name_no_ext,
-      :out_data_type => out_data_type,
-      :out_data => out_data
-    }
-    modifications_string = srf.header.modifications
-    search_summary = Sequest::PepXML::SearchSummary.new( params, modifications_string, search_summary_options)
-
-    # create the sample enzyme from the params object:
-    sample_enzyme_obj = 
-      if opts[:sample_enzyme]
-        opts[:sample_enzyme]
-      else
-        params.sample_enzyme
-      end
-    opts[:sample_enzyme] = sample_enzyme_obj
-
-    ## Create the pepxml obj and top level objects
-    pepxml_obj = Sequest::PepXML.new(ppxml_version, params) 
-    pipeline = Sequest::PepXML::MSMSPipelineAnalysis.new({:date=>nil,:summary_xml=> bn_noext +'.xml'})
-    pepxml_obj.msms_pipeline_analysis = pipeline
-    pipeline.msms_run_summary = Sequest::PepXML::MSMSRunSummary.new(opts)
-    pipeline.msms_run_summary.search_summary = search_summary
-    modifications_obj = search_summary.modifications
-
-    ## name some common variables we'll need
-    h_plus = pepxml_obj.h_plus
-    avg_parent = pepxml_obj.avg_parent
-
-
-    ## COPY MZXML FILES IF NECESSARY
-    if opts[:copy_mzxml]
-      mzxml_pathname_noext = File.join(opts[:ms_data], bn_noext)
-      to_copy = MS::Converter::MzXML.file_to_mzxml(mzxml_pathname_noext)
-      if to_copy
-        FileUtils.cp to_copy, out_path
-      else
-        puts "Couldn't file mzXML file with base: #{mzxml_pathname_noext}"
-        puts "Perhaps you need to specifiy the location of the raw data"
-        puts "or need an mzXML converter (readw or t2x)"
-        exit
-      end
-    end
-
-
-    #######################################################################
-    # CREATE the spectrum_queries_ar
-    #######################################################################
-    srf_index = srf.index
-    out_files = srf.out_files
-    spectrum_queries_arr = Array.new(srf.dta_files.size)
-    files_with_hits_index = 0  ## will end up being 1 indexed
-
-    deltacn_orig = opts[:deltacn_orig]
-    deltacn_index = 
-      if deltacn_orig ; 20
-      else 19
-      end
-
-    srf.dta_files.each_with_index do |dta_file,dta_i|
-      next if out_files[dta_i].num_hits == 0
-      files_with_hits_index += 1
-
-      precursor_neutral_mass = dta_file.mh - h_plus
-
-      (start_scan, end_scan, charge) = srf_index[dta_i]
-      sq_hash = {
-        :spectrum => [bn_noext, start_scan, end_scan, charge].join('.'),
-        :start_scan => start_scan,
-        :end_scan => end_scan,
-        :precursor_neutral_mass => precursor_neutral_mass,
-        :assumed_charge => charge.to_i,
-        :pepxml_version => ppxml_version,
-        :index => files_with_hits_index,
-      }
-
-      spectrum_query = Sequest::PepXML::SpectrumQuery.new(sq_hash)
-
-
-      hits = out_files[dta_i].hits
-
-      search_hits = 
-        if opts[:all_hits]
-          Array.new(out_files[dta_i].num_hits)  # all hits
-        else
-          Array.new(1)  # top hit only
-        end
-
-      (0...(search_hits.size)).each do |hit_i|
-        hit = hits[hit_i]
-        # under the modified deltacn schema (like bioworks)
-        # Get proper deltacn and deltacnstar
-        # under new srf, deltacn is already corrected for what prophet wants,
-        # deltacn_orig_updated is how to access the old one
-        # Prophet deltacn is not the same as the native Sequest deltacn
-        # It is the deltacn of the second best hit!
-
-        ## mass calculations:
-        calc_neutral_pep_mass = hit[0] - h_plus
-
-
-        sequence = hit.sequence
-
-        #  NEED TO MODIFY SPLIT SEQUENCE TO DO MODS!
-        ## THIS IS ALL INNER LOOP, so we make every effort at speed here:
-        (prevaa, pepseq, nextaa) = SpecID::Pep.prepare_sequence(sequence)
-        # 0=mh 1=deltacn_orig 2=sp 3=xcorr 4=id 5=num_other_loci 6=rsp 7=ions_matched 8=ions_total 9=sequence 10=prots 11=deltamass 12=ppm 13=aaseq 14=base_name 15=first_scan 16=last_scan 17=charge 18=srf 19=deltacn 20=deltacn_orig_updated
-
-        sh_hash = {
-          :hit_rank => hit_i+1,
-          :peptide => pepseq,
-          :peptide_prev_aa => prevaa,
-          :peptide_next_aa => nextaa,
-          :protein => hit[10].first.reference.split(" ").first, 
-          :num_tot_proteins => hit[10].size,
-          :num_matched_ions => hit[7],
-          :tot_num_ions => hit[8],
-          :calc_neutral_pep_mass => calc_neutral_pep_mass,
-          :massdiff => precursor_neutral_mass - calc_neutral_pep_mass, 
-          :num_tol_term => sample_enzyme_obj.num_tol_term(sequence),
-          :num_missed_cleavages => sample_enzyme_obj.num_missed_cleavages(pepseq),
-          :is_rejected => 0,
-          # These are search score attributes:
-          :xcorr => hit[3],
-          :deltacn => hit[deltacn_index],
-          :spscore => hit[2],
-          :sprank => hit[6],
-          :modification_info => modifications_obj.modification_info(SpecID::Pep.split_sequence(sequence)[1]),
-        }
-        unless deltacn_orig
-          sh_hash[:deltacnstar] = 
-            if hits[hit_i+1].nil?  # no next hit? then its deltacnstar == 1
-            '1'
-            else
-            '0'
-            end
-        end
-        search_hits[hit_i] = Sequest::PepXML::SearchHit.new(sh_hash) # there can be multiple hits
-      end
-
-      search_result = Sequest::PepXML::SearchResult.new
-      search_result.search_hits = search_hits
-      spectrum_query.search_results = [search_result]
-      spectrum_queries_arr[files_with_hits_index] = spectrum_query
-    end
-    spectrum_queries_arr.compact!
-
-    pipeline.msms_run_summary.spectrum_queries = spectrum_queries_arr 
-    pepxml_obj.base_name = pipeline.msms_run_summary.base_name
-    pipeline.msms_run_summary.spectrum_queries =  spectrum_queries_arr 
-
-    pepxml_obj
-  end
-
-  # takes an .srg or bioworks.xml file
-  # if possible, ensures that an mzXML file is present for each pepxml file
-  # :print => true, will print files
-  # NOTES: num_tol_term and num_missing_cleavages are both calculated from the
-  # sample_enzyme.  Thus, a No_Enzyme search may still pass in a
-  # :sample_enzyme option to get these calculated.
-  def self.set_from_bioworks(bioworks_file, opts={})
-    opts = Default_Options.merge(opts)
-    ## Create the out_path directory if necessary
-
-      unless File.exist? opts[:out_path]
-        FileUtils.mkpath(opts[:out_path])
-      end
-      unless File.directory? opts[:out_path]
-        abort "#{opts[:out_path]} must be a directory!"
-      end
-
-      spec_id = SpecID.new(bioworks_file)
-      pepxml_objs = 
-        if spec_id.is_a? Bioworks
-          abort("must have opts[:params] set!") unless opts[:params]
-          set_from_bioworks_xml(bioworks_file, opts[:params], opts)
-        elsif spec_id.is_a? SRFGroup
-          spec_id.srfs.map do |srf|
-            new_from_srf(srf, opts) 
-          end
-        else
-          abort "invalid object"
-        end
-
-      if opts[:print]
-        pepxml_objs.each do |obj|
-          obj.to_pepxml(obj.base_name + ".xml")
-        end
-      end
-      pepxml_objs
-    end
-
-
-    # Takes bioworks 3.2/3.3 xml output (with no filters)
-    # Returns a list of PepXML objects
-    # params = sequest.params file
-    # bioworks = bioworks.xml exported multi-consensus view file
-    # pepxml_version = 0 for tpp 1.2.3
-    # pepxml_version = 18 for tpp 2.8.2, 2.8.3, 2.9.2
-  def self.set_from_bioworks_xml(bioworks, params, opts={})
-    opts = Default_Options.merge(opts)
-    pepxml_version, ms_manufacturer, ms_model, ms_ionization, ms_mass_analyzer, ms_detector, raw_data_type, raw_data, out_data_type, out_data, ms_data, out_path = opts.values_at(:pepxml_version, :ms_manufacturer, :ms_model, :ms_ionization, :ms_mass_analyzer, :ms_detector, :raw_data_type, :raw_data, :out_data_type, :out_data, :ms_data, :out_path)
-
-
-
-    unless out_path
-      out_path = '.'
-    end
-
-    supported_versions = [18]
-
-    unless supported_versions.include?(opts[:pepxml_version]) 
-      abort "pepxml_version: #{pepxml_version} not currently supported.  Current support is for versions #{supported_versions.join(', ')}"
-    end
-
-    ## Turn params and bioworks_obj into objects if necessary:
-    # Params:
-    if params.class == Sequest::Params  # OK!
-    elsif params.class == String ; params = Sequest::Params.new(params)
-    else                         ; abort "Don't recognize #{params} as object or string!"
-    end
-    # Bioworks:
-    if bioworks.class == Bioworks  # OK!
-    elsif bioworks.class == String ; bioworks = SpecID.new(bioworks)
-    else                           ; abort "Don't recognize #{bioworks} as object or string!"
-    end
-
-    sample_enzyme_obj = 
-      if opts[:sample_enzyme]
-        opts[:sample_enzyme]
-      else
-        params.sample_enzyme
-      end
-
-    #puts "bioworks.peps.size: #{bioworks.peps.size}"; #puts "bioworks.prots.size: #{bioworks.prots.size}"; #puts "Bioworks.version: #{bioworks.version}"
-
-    ## TURN THIS ON IF YOU THINK YOU MIGHT NOT BE GETTING PEPTIDES from
-    ## bioworks
-    #bioworks.peps.each { |pep| if pep.class != Bioworks::Pep ; puts "trying to pass as pep: "; p pep; abort "NOT a pep!" end }
-
-    ## check to see if we need backup_db
-
-    backup_db_path = opts.delete(:backup_db_path)
-    if !File.exist?(params.database) && backup_db_path
-      params.database_path = backup_db_path
-    end
-
-    ## Start
-    split_bio_objs = []
-
-    ## (num_prots_by_pep, prot_by_pep) = 
-    #num_prots_by_pep.each do |k,v| puts "k: #{k} v: #{v}\n"; break end ; prot_by_pep.each do |k,v| puts "k: #{k} v: #{v}" ; break end ; abort "HERE"
-
-    modifications_string = bioworks.modifications
-
-    ## Create a hash of spectrum_query arrays by filename (this very big block):
-    spectrum_queries_by_base_name = {}
-    # Hash by the filenames to split into filenames:
-    pepxml_objects = bioworks.peps.hash_by(:base_name).map do |base_name, pep_arr|
-
-      search_summary = Sequest::PepXML::SearchSummary.new(params, modifications_string, {:search_database => Sequest::PepXML::SearchDatabase.new(params), :out_data_type => out_data_type, :out_data => out_data})
-      modifications_obj = search_summary.modifications
-
-      pepxml_obj = Sequest::PepXML.new(pepxml_version, params)
-      full_base_name_no_ext = self.make_base_name( File.expand_path(out_path), base_name)
-
-      case pepxml_version
-      when 18
-        pipeline =  Sequest::PepXML::MSMSPipelineAnalysis.new({:date=>nil,:summary_xml=>base_name+'.xml'})
-        msms_run_summary = Sequest::PepXML::MSMSRunSummary.new({
-          :base_name => full_base_name_no_ext,
-          :ms_manufacturer => ms_manufacturer,
-          :ms_model => ms_model,
-          :ms_ionization => ms_ionization,
-          :ms_mass_analyzer => ms_mass_analyzer,
-          :ms_detector => ms_detector,
-          :raw_data_type => raw_data_type,
-          :raw_data => raw_data,
-          :sample_enzyme => sample_enzyme_obj, # usually, params.sample_enzyme,
-          :search_summary => search_summary,
-        }) 
-        pipeline.msms_run_summary = msms_run_summary
-        pepxml_obj.msms_pipeline_analysis = pipeline
-        pepxml_obj.msms_pipeline_analysis.msms_run_summary.search_summary.base_name =  full_base_name_no_ext
-        pepxml_obj.base_name = full_base_name_no_ext
-        pepxml_obj 
-      end
-
-      # Create a hash by pep object containing num_tot_proteins
-      # This is only valid if all hits are present (no previous thresholding)
-      # Since out2summary only acts on one folder at a time,
-      # we should only do it for one folder at a time! (that's why we do this
-      # here instead of globally)
-      self._prot_num_and_first_prot_by_pep(pep_arr)
-      prec_mz_arr = nil
-      case x = bioworks.version
-      when /3.2/ 
-        calc_prec_by = :prec_mz_arr
-        # get the precursor_mz array for this filename
-        mzxml_file = MS::Converter::MzXML.file_to_mzxml(File.join(ms_data, base_name))
-        prec_mz_arr = MS::MSRun.precursor_mz_by_scan_num(mzxml_file)
-      when /3.3/
-        calc_prec_by = :deltamass
-      else
-        abort "invalid BioworksBrowser version: #{x}"
-      end
-
-      if opts[:copy_mzxml]
-        to_copy = MS::Converter::MzXML.file_to_mzxml(File.join(ms_data, base_name))
-        if to_copy
-          FileUtils.cp to_copy, out_path
-        end
-      end
-
-
-      spectrum_queries_ar = pep_arr.hash_by(:first_scan, :last_scan, :charge).map do |key,arr|
-
-
-        # Sort_by_rank and take the top hit (to mimick out2summary):
-
-        arr = arr.sort_by {|pep| pep.xcorr.to_f } # ascending
-        top_pep = arr.pop
-        second_hit = arr.last # needed for deltacnstar
-
-
-        case calc_prec_by
-        when :prec_mz_arr
-          precursor_neutral_mass = Sequest::PepXML::SpectrumQuery.calc_precursor_neutral_mass(calc_prec_by, top_pep.first_scan.to_i, top_pep.last_scan.to_i, prec_mz_arr, top_pep.charge, pepxml_obj.avg_parent)
-        when :deltamass
-          precursor_neutral_mass = Sequest::PepXML::SpectrumQuery.calc_precursor_neutral_mass(calc_prec_by, top_pep.mass.to_f, top_pep.deltamass.to_f, pepxml_obj.avg_parent)
-        end
-
-        calc_neutral_pep_mass = (top_pep.mass.to_f - pepxml_obj.h_plus)
-
-        # deltacn & star:
-        # (NOTE: OLD?? out2summary wants the deltacn of the 2nd best hit.)
-        if second_hit 
-          #top_pep.deltacn = second_hit.deltacn 
-          deltacnstar = '0'
-        else 
-          top_pep.deltacn = '1.0'
-          deltacnstar = '1'
-        end
-        # Create the nested structure of queries{results{hits}}
-        # (Ruby's blocks work beautifully for things like this)
-        spec_query = Sequest::PepXML::SpectrumQuery.new({
-          :spectrum => [top_pep.base_name, top_pep.first_scan, top_pep.last_scan, top_pep.charge].join("."),
-          :start_scan => top_pep.first_scan,
-          :end_scan => top_pep.last_scan,
-          :precursor_neutral_mass => precursor_neutral_mass,
-          :assumed_charge => top_pep.charge,
-          :pepxml_version => pepxml_version,
-        }) 
-
-
-        search_result = Sequest::PepXML::SearchResult.new 
-        #puts "set MASSDIFF: "
-        #p precursor_neutral_mass - calc_neutral_pep_mass
-        ## Calculate some interdependent values;
-        # NOTE: the bioworks mass is reallyf M+H if two or more scans went
-        # into the search_hit; calc_neutral_pep_mass is simply the avg of
-        # precursor masses adjusted to be neutral
-        (prevaa, pepseq, nextaa) = SpecID::Pep.prepare_sequence(top_pep.sequence)
-        (num_matched_ions, tot_num_ions) = Sequest::PepXML::SearchHit.split_ions(top_pep.ions)
-        search_hit = Sequest::PepXML::SearchHit.new({
-          :hit_rank => 1,
-          :peptide => pepseq,
-          :peptide_prev_aa => prevaa,
-          :peptide_next_aa => nextaa,
-          :protein => top_pep._first_prot.reference.split(" ").first, 
-          :num_tot_proteins => top_pep._num_prots,
-          :num_matched_ions => num_matched_ions,
-          :tot_num_ions => tot_num_ions,
-          :calc_neutral_pep_mass => calc_neutral_pep_mass,
-          :massdiff => precursor_neutral_mass - calc_neutral_pep_mass,
-          :num_tol_term => sample_enzyme_obj.num_tol_term(top_pep.sequence),
-          :num_missed_cleavages => sample_enzyme_obj.num_missed_cleavages(pepseq),
-          :is_rejected => 0,
-          # These are search score attributes:
-          :xcorr => top_pep.xcorr,
-          :deltacn => top_pep.deltacn,
-          :deltacnstar => deltacnstar,
-          :spscore => top_pep.sp,
-          :sprank => top_pep.rsp,
-          :modification_info => modifications_obj.modification_info(SpecID::Pep.split_sequence(top_pep.sequence)[1]),
-          :spectrum_query => spec_query,
-        })
-        search_result.search_hits = [search_hit] # there can be multiple search hits
-        spec_query.search_results = [search_result]  # can be multiple search_results
-        spec_query
-      end
-
-      # create an index by spectrum as results end up typically in out2summary
-      # (I really dislike this order, however)
-      spectrum_queries_ar = spectrum_queries_ar.sort_by {|pep| pep.spectrum }
-      spectrum_queries_ar.each_with_index {|res,index| res.index = "#{index + 1}" }
-      pipeline.msms_run_summary.spectrum_queries = spectrum_queries_ar
-      pepxml_obj
-    end ## collects pepxml_objs
-    # summary_xml is the short basename of the pepxml file (e.g., "020.xml")
-    pepxml_objects.sort_by {|obj| obj.summary_xml }
-  end
-
-  def summary_xml
-    base_name + ".xml"
-  end
-
-  def precursor_mass_type
-    @params.precursor_mass_type
-  end
-
-  def fragment_mass_type
-    @params.fragment_mass_type
-  end
-
-  # combines filename in a manner consistent with the path
-  def self.make_base_name(path, filename)
-    sep = '/'
-    if path.split('/').size < path.split("\\").size
-      sep = "\\"
-    end
-    if path.split('').last == sep
-      path + File.basename(filename)
-    else
-      path + sep + File.basename(filename)
-    end
-  end
-
-  # outputs pepxml, (to file if given)
-  def to_pepxml(file=nil)
-    string = header
-    string << @msms_pipeline_analysis.to_pepxml
-
-    if file
-      File.open(file, "w") do |fh| fh.print string end
-    end
-    string
-  end
-
-  # given any kind of filename (from windows or whatever)
-  # returns the base of the filename with no file extension
-  def self.base_name_noext(file)
-    basename = file.split(/[\/\\]/).last
-    basename.chomp(File.extname(basename))
-  end
-
-
-end # PepXML
-
-
-class Sequest::PepXML::SearchResult
-  include SpecIDXML
-  # an array of search_hits
-  attr_accessor :search_hits
-
-  # if block given, then search_hits set to return value
-  def initialize(search_hits = [])
-    @search_hits = search_hits
-  end
-
-  def to_pepxml
-    element_xml_no_atts(:search_result) do
-      @search_hits.map {|sh| sh.to_pepxml }.join
-    end
-  end
-
-end
-
-class Sequest::PepXML::SearchSummary
-  include SpecIDXML
-  attr_accessor :params
-  attr_accessor :base_name
-  attr_accessor :out_data_type
-  attr_accessor :out_data
-  # by default, "1"
-  attr_accessor :search_id
-  attr_accessor :modifications
-  # A SearchDatabase object (responds to :local_path and :type)
-  attr_accessor :search_database
-  # if given a sequest params object, then will set the following attributes:
-  # args is a hash of parameters
-  # modifications_string -> See Modifications
-  def initialize(prms=nil, modifications_string='', args=nil)
-    @search_id = "1"
-    if prms
-      @params = prms
-      @modifications = Sequest::PepXML::Modifications.new(prms, modifications_string)
-    end
-    if args ; set_from_hash(args) end
-  end
-
-  def method_missing(symbol, *args)
-    if @params ; @params.send(symbol, *args) end
-  end
-
-  def to_pepxml
-    element_xml(:search_summary, [:base_name, :search_engine, :precursor_mass_type, :fragment_mass_type, :out_data_type, :out_data, :search_id]) do
-      search_database.to_pepxml +
-        if @params.enzyme =~ /^No_Enzyme/
-          ''
-        else
-          short_element_xml(:enzymatic_search_constraint, [:enzyme, :max_num_internal_cleavages, :min_number_termini])
-        end +
-        @modifications.to_pepxml +
-        Sequest::PepXML::Parameters.new(@params).to_pepxml
-    end
-  end
-
-  def self.from_pepxml_node(node)
-    self.new.from_pepxml_node(node)
-  end
-
-  def from_pepxml_node(node)
-    raise NotImplementedError, "right now we just have the xml node at your disposal"
-  end
-
-end
-
-class Sequest::PepXML::Parameters
-  include SpecIDXML
-
-  attr_accessor :params
-  
-  def initialize(obj=nil)
-    @params = obj
-  end
-  #  (used to be called pepxml_parameters)
-  # Returns xml in the form <parameter name="#{method_name}"
-  # value="#{method_value}"/> for list of symbols
-  def to_pepxml
-    keys_as_symbols = @params.opts.sort.map do |k,v| k.to_s end
-    params_xml(@params, *keys_as_symbols)
-    # (:peptide_mass_tol, :peptide_mass_units, :fragment_ion_tol, :ion_series, :max_num_differential_AA_per_mod, :nucleotide_reading_frame, :num_output_lines, :remove_precursor_peak, :ion_cutoff_percentage, :match_peak_count, :match_peak_allowed_error, :match_peak_tolerance, :protein_mass_filter, :sequence_header_filter)
-  end
-end
-
-class Sequest::PepXML::Modifications
-  include SpecIDXML
-
-  # sequest params object
-  attr_accessor :params
-  # array holding AAModifications 
-  attr_accessor :aa_mods
-  # array holding TerminalModifications
-  attr_accessor :term_mods
-  # a hash of all differential modifications present by aa_one_letter_symbol
-  # and special_symbol. This is NOT the mass difference but the total mass {
-  # 'M*' => 155.5, 'S@' => 190.3 }.  NOTE: Since the termini are dependent on
-  # the amino acid sequence, they are give the *differential* mass.  The
-  # termini are given the special symbol as in sequest e.g. '[' => 12.22, #
-  # cterminus    ']' => 14.55 # nterminus
-  attr_accessor :masses_by_diff_mod_hash
-  # a hash, key is [AA_one_letter_symbol.to_sym, difference.to_f]
-  # values are the special_symbols
-  attr_accessor :mod_symbols_hash
-
-  # The modification symbols string looks like this:
-  # (M* +15.90000) (M# +29.00000) (S@ +80.00000) (C^ +12.00000) (ct[ +12.33000) (nt] +14.20000)
-  # ct is cterminal peptide (differential)
-  # nt is nterminal peptide (differential)
-  # the C is just cysteine
-  # will set_modifications and masses_by_diff_mod hash
-  def initialize(params=nil, modification_symbols_string='')
-    @params = params
-    if @params
-      set_modifications(params, modification_symbols_string)
-    end
-  end
-
-  # set the masses_by_diff_mod and mod_symbols_hash from 
-  def set_hashes(modification_symbols_string)
-
-    @mod_symbols_hash = {}
-    @masses_by_diff_mod = {}
-    if (modification_symbols_string == nil || modification_symbols_string == '')
-      return nil
-    end
-    table = @params.mass_table
-    modification_symbols_string.split(/\)\s+\(/).each do |mod|
-      if mod =~ /\(?(\w+)(.) (.[\d\.]+)\)?/
-        if $1 == 'ct' || $1 == 'nt' 
-          mass_diff = $3.to_f
-          @masses_by_diff_mod[$2] = mass_diff
-          @mod_symbols_hash[[$1.to_sym, mass_diff]] = $2.dup
-          # changed from below to match tests, is this right?
-          # @mod_symbols_hash[[$1, mass_diff]] = $2.dup
-        else
-          symbol_string = $2.dup 
-          mass_diff = $3.to_f
-          $1.split('').each do |aa|
-            aa_as_sym = aa.to_sym
-            @masses_by_diff_mod[aa+symbol_string] = mass_diff + table[aa_as_sym]
-            @mod_symbols_hash[[aa_as_sym, mass_diff]] = symbol_string
-          end
-        end
-      end
-    end
-  end
-
-  # given a bare peptide (no end pieces) returns a ModificationInfo object
-  # e.g. given "]PEPT*IDE", NOT 'K.PEPTIDE.R'
-  # if there are no modifications, returns nil
-  def modification_info(peptide)
-    if @masses_by_diff_mod.size == 0
-      return nil
-    end
-    hash = {}
-    hash[:modified_peptide] = peptide.dup
-    hsh = @masses_by_diff_mod  
-    table = @params.mass_table
-    h = table[:h]  # this? or h_plus ??
-    oh = table[:o] + h
-    ## only the termini can match a single char
-    if hsh.key? peptide[0,1]
-      # AA + H + differential_mod
-      hash[:mod_nterm_mass] = table[peptide[1,1].to_sym] + h + hsh[peptide[0,1]]
-      peptide = peptide[1...(peptide.size)]
-    end
-    if hsh.key? peptide[(peptide.size-1),1]
-      # AA + OH + differential_mod
-      hash[:mod_cterm_mass] = table[peptide[(peptide.size-2),1].to_sym] + oh + hsh[peptide[-1,1]]
-      peptide.slice!( 0..-2 )
-      peptide = peptide[0...(peptide.size-1)]
-    end
-    mod_array = []
-    (0...peptide.size).each do |i|
-      if hsh.key? peptide[i,2]
-        mod_array << Sequest::PepXML::SearchHit::ModificationInfo::ModAminoacidMass.new([ i+1 , hsh[peptide[i,2]] ])
-      end
-    end
-    if mod_array.size > 0
-      hash[:mod_aminoacid_masses] = mod_array
-    end
-    if hash.size > 1  # if there is more than just the modified peptide there
-      Sequest::PepXML::SearchHit::ModificationInfo.new(hash)
-      #Sequest::PepXML::SearchHit::ModificationInfo.new(hash.values_at(:modified_peptide, :mod_aminoacid_masses, :mod_nterm_mass, :mod_cterm_mass)
-    else
-      nil
-    end
-  end
-
-  # returns an array of static mod objects and static terminal mod objects
-  def create_static_mods(params)
-
-    ####################################
-    ## static mods
-    ####################################
-
-    static_mods = [] # [[one_letter_amino_acid.to_sym, add_amount.to_f], ...]
-    static_terminal_mods = [] # e.g. [add_Cterm_peptide, amount.to_f]
-
-    params.mods.each do |k,v|
-      v_to_f = v.to_f
-      if v_to_f != 0.0
-        if k =~ /add_(\w)_/
-          static_mods << [$1.to_sym, v_to_f]
-        else
-          static_terminal_mods << [k, v_to_f]
-        end
-      end
-    end
-    aa_hash = params.mass_table
-
-    ## Create the static_mods objects
-    static_mods.map! do |mod|
-      hash = {
-        :aminoacid => mod[0].to_s,
-        :massdiff => mod[1],
-        :mass => aa_hash[mod[0]] + mod[1],
-        :variable => 'N',
-        :binary => 'Y',
-      } 
-      Sequest::PepXML::AAModification.new(hash)
-    end
-
-    ## Create the static_terminal_mods objects
-    static_terminal_mods.map! do |mod|
-      terminus = if mod[0] =~ /Cterm/ ; 'c'
-                 else                 ; 'n' # only two possible termini
-                 end
-      protein_terminus = case mod[0] 
-                         when /Nterm_protein/ ; 'n'
-                         when /Cterm_protein/ ; 'c'
-                         else nil
-                         end
-
-      # create the hash                            
-      hash = {
-        :terminus => terminus,
-        :massdiff => mod[1],
-        :variable => 'N',
-        :description => mod[0],
-      }
-      hash[:protein_terminus] = protein_terminus if protein_terminus
-      Sequest::PepXML::TerminalModification.new(hash)
-    end
-    [static_mods, static_terminal_mods]
-  end
-
-  # 1. sets aa_mods and term_mods from a sequest params object
-  # 2. sets @params
-  # 3. sets @masses_by_diff_mod
-  def set_modifications(params, modification_symbols_string)
-    @params = params
-
-    set_hashes(modification_symbols_string)
-    (static_mods, static_terminal_mods) = create_static_mods(params)
-
-    aa_hash = params.mass_table
-    #################################
-    # Variable Mods:
-    #################################
-    arr = params.diff_search_options.rstrip.split(/\s+/)
-    # [aa.to_sym, diff.to_f]
-    variable_mods = []
-    (0...arr.size).step(2) do |i|
-      if arr[i].to_f != 0.0
-        variable_mods << [arr[i+1], arr[i].to_f]
-      end
-    end
-    mod_objects = []
-    variable_mods.each do |mod|
-      mod[0].split('').each do |aa|
-        hash = {
-          
-          :aminoacid => aa,
-          :massdiff => mod[1],
-          :mass => aa_hash[aa.to_sym] + mod[1],
-          :variable => 'Y',
-          :binary => 'N',
-          :symbol => @mod_symbols_hash[[aa.to_sym, mod[1]]],
-        }
-        mod_objects << Sequest::PepXML::AAModification.new(hash)
-      end
-    end
-    variable_mods = mod_objects
-    #################################
-    # TERMINAL Variable Mods:
-    #################################
-    # These are always peptide, not protein termini (for sequest)
-    (nterm_diff, cterm_diff) = params.term_diff_search_options.rstrip.split(/\s+/).map{|v| v.to_f }
-
-    to_add = []
-    if nterm_diff != 0.0
-      to_add << ['n',nterm_diff.to_plus_minus_string, @mod_symbols_hash[:nt, nterm_diff]]
-    end
-    if cterm_diff != 0.0
-      to_add << ['c', cterm_diff.to_plus_minus_string, @mod_symbols_hash[:ct, cterm_diff]]
-    end
-
-    variable_terminal_mods = to_add.map do |term, mssdiff, symb|
-      hash = {
-        :terminus => term,
-        :massdiff => mssdiff,
-        :variable => 'Y',
-        :symbol => symb,
-      }
-      Sequest::PepXML::TerminalModification.new(hash)
-    end
-
-    #########################
-    # COLLECT THEM
-    #########################
-    @aa_mods = static_mods + variable_mods
-    @term_mods = static_terminal_mods + variable_terminal_mods
-  end
-
-  ## Generates the pepxml for static and differential amino acid mods based on
-  ## sequest object
-  def to_pepxml
-    st = ''
-    if @aa_mods
-      st << @aa_mods.map {|v| v.to_pepxml }.join
-    end
-    if @term_mods
-      st << @term_mods.map {|v| v.to_pepxml }.join
-    end
-    st
-  end
-
-end
-
-# Modified aminoacid, static or variable
-# unless otherwise stated, all attributes can be anything
-class Sequest::PepXML::AAModification
-  include SpecIDXML
-
-  # The amino acid (one letter code)
-  attr_accessor :aminoacid
-  # Must be a string!!!!
-  # Mass difference with respect to unmodified aminoacid, must begin with
-  # either + (nonnegative) or - [e.g. +1.05446 or -2.3342]
-  # consider Numeric#to_plus_minus_string at top
-  attr_accessor :massdiff
-  # Mass of modified aminoacid
-  attr_accessor :mass
-  # Y if both modified and unmodified aminoacid could be present in the
-  # dataset, N if only modified aminoacid can be present
-  attr_accessor :variable
-  # whether modification can reside only at protein terminus (specified 'n',
-  # 'c', or 'nc')
-  attr_accessor :peptide_terminus
-  # MSial symbol used by search engine to designate this modification
-  attr_accessor :symbol
-  # Y if each peptide must have only modified or unmodified aminoacid, N if a
-  # peptide may contain both modified and unmodified aminoacid
-  attr_accessor :binary
-
-  def initialize(hash=nil)
-    instance_var_set_from_hash(hash) if hash # can use unless there are weird methods
-  end
-
-  def to_pepxml
-    # note massdiff
-    short_element_xml_and_att_string("aminoacid_modification", "aminoacid=\"#{aminoacid}\" massdiff=\"#{massdiff.to_plus_minus_string}\" mass=\"#{mass}\" variable=\"#{variable}\" peptide_terminus=\"#{peptide_terminus}\" symbol=\"#{symbol}\" binary=\"#{binary}\"")
-  end
-
-end
-
-# Modified aminoacid, static or variable
-class Sequest::PepXML::TerminalModification
-  include SpecIDXML
-
-  # n for N-terminus, c for C-terminus
-  attr_accessor :terminus
-  # Mass difference with respect to unmodified terminus
-  attr_accessor :massdiff
-  # Mass of modified terminus
-  attr_accessor :mass
-  # Y if both modified and unmodified terminus could be present in the
-  # dataset, N if only modified terminus can be present
-  attr_accessor :variable
-  # MSial symbol used by search engine to designate this modification
-  attr_accessor :symbol
-  # whether modification can reside only at protein terminus (specified n or
-  # c)
-  attr_accessor :protein_terminus
-  attr_accessor :description
-
-  def initialize(hash=nil)
-    instance_var_set_from_hash(hash) if hash # can use unless there are weird methods
-  end
-
-  def to_pepxml
-    #short_element_xml_from_instance_vars("terminal_modification")
-    short_element_xml_and_att_string("terminal_modification", "terminus=\"#{terminus}\" massdiff=\"#{massdiff.to_plus_minus_string}\" mass=\"#{mass}\" variable=\"#{variable}\" symbol=\"#{symbol}\" protein_terminus=\"#{protein_terminus}\" description=\"#{description}\"")
-  end
-end
-
-
-class Sequest::PepXML::SearchDatabase
-  include SpecIDXML 
-  attr_accessor :local_path
-  attr_writer :seq_type
-  # Takes a SequestParams object
-  # Sets :local_path from the params object attr :database
-  def initialize(params=nil, args=nil)
-    @seq_type = nil
-    if params
-      @local_path = params.database
-    end
-    if args ; set_from_hash(args) end
-  end
-
-  def seq_type
-    if @seq_type ; @seq_type
-    else
-      if @local_path =~ /\.fasta/
-        'AA'
-      else
-        abort "Don't recognize type from your database local path: #{@local_path}"
-      end
-    end
-  end
-
-  def to_pepxml
-    short_element_xml_and_att_string(:search_database, "local_path=\"#{local_path}\" type=\"#{seq_type}\"")
-  end
-
-end
-
-Sequest::PepXML::SpectrumQuery = Arrayclass.new(%w(spectrum start_scan end_scan precursor_neutral_mass index assumed_charge search_results pepxml_version))
-
-class Sequest::PepXML::SpectrumQuery
-  include SpecIDXML
-
-  ############################################################
-  # FOR PEPXML:
-  ############################################################
-  def to_pepxml
-    case Sequest::PepXML.pepxml_version
-    when 18
-      element_xml("spectrum_query", [:spectrum, :start_scan, :end_scan, :precursor_neutral_mass, :assumed_charge, :index]) do
-        search_results.collect { |sr| sr.to_pepxml }.join
-      end
-    end
-  end
-
-  def self.from_pepxml_node(node)
-    self.new.from_pepxml_node(node)
-  end
-
-  def from_pepxml_node(node)
-    self[0] = node['spectrum']
-    self[1] = node['start_scan'].to_i
-    self[2] = node['end_scan'].to_i
-    self[3] = node['precursor_neutral_mass'].to_f
-    self[4] = node['index'].to_i
-    self[5] = node['assumed_charge'].to_i
-    self
-  end
-
-  # Returns the precursor_neutral based on the scans and an array indexed by
-  # scan numbers.  first and last scan and charge should be integers.
-  # This is the precursor_mz - h_plus!
-  # by=:prec_mz_arr|:deltamass
-  # if prec_mz_arr then the following arguments must be supplied:
-  # :first_scan = int, :last_scan = int, :prec_mz_arr = array with the precursor
-  # m/z for each product scan, :charge = int
-  # if deltamass then the following arguments must be supplied:
-  # m_plus_h = float, deltamass = float
-  # For both flavors, a final additional argument 'average_weights'
-  # can be used.  If true (default), average weights will be used, if false, 
-  # monoisotopic weights (currently this is simply the mass of the proton)
-  def self.calc_precursor_neutral_mass(by, *args)
-    average_weights = true
-    case by
-    when :prec_mz_arr
-      (first_scan, last_scan, prec_mz_arr, charge, average_weights) = args
-    when :deltamass
-      (m_plus_h, deltamass, average_weights) = args
-    end
-
-    if average_weights 
-      mass_h_plus = SpecID::AVG[:h_plus] 
-    else
-      mass_h_plus = SpecID::MONO[:h_plus] 
-    end
-
-    case by
-    when :prec_mz_arr
-      mz = nil
-      if first_scan != last_scan
-        sum = 0.0
-        tot_num = 0
-        (first_scan..last_scan).each do |scan|
-          val = prec_mz_arr[scan]
-          if val  # if the scan is not an mslevel 2
-            sum += val
-            tot_num += 1
-          end
-        end
-        mz = sum/tot_num
-      else
-        mz = prec_mz_arr[first_scan]
-      end
-      charge * (mz - mass_h_plus)
-    when :deltamass
-      m_plus_h - mass_h_plus + deltamass
-    else
-      abort "don't recognize 'by' in calc_precursor_neutral_mass: #{by}"
-    end
-  end
-
-end
-
-
-Sequest::PepXML::SearchHit = Arrayclass.new( %w( hit_rank peptide peptide_prev_aa peptide_next_aa protein num_tot_proteins num_matched_ions tot_num_ions calc_neutral_pep_mass massdiff num_tol_term num_missed_cleavages is_rejected deltacnstar xcorr deltacn spscore sprank modification_info spectrum_query) )
-
-# 0=hit_rank 1=peptide 2=peptide_prev_aa 3=peptide_next_aa 4=protein 5=num_tot_proteins 6=num_matched_ions 7=tot_num_ions 8=calc_neutral_pep_mass 9=massdiff 10=num_tol_term 11=num_missed_cleavages 12=is_rejected 13=deltacnstar 14=xcorr 15=deltacn 16=spscore 17=sprank 18=modification_info 19=spectrum_query
-
-class Sequest::PepXML::SearchHit
-  include SpecID::Pep
-  include SpecIDXML
-
-  Non_standard_amino_acid_char_re = /[^A-Z\.\-]/
-
-  def aaseq ; self[1] end
-  def aaseq=(arg) ; self[1] = arg end
-
-  # These are all search_score elements:
-
-  # 1 if there is no second ranked hit, 0 otherwise
-
-  tmp_verb = $VERBOSE
-  $VERBOSE = nil
-  def initialize(hash=nil)
-    super(self.class.size)
-    if hash
-      self[0,20] = [hash[:hit_rank], hash[:peptide], hash[:peptide_prev_aa], hash[:peptide_next_aa], hash[:protein], hash[:num_tot_proteins], hash[:num_matched_ions], hash[:tot_num_ions], hash[:calc_neutral_pep_mass], hash[:massdiff], hash[:num_tol_term], hash[:num_missed_cleavages], hash[:is_rejected], hash[:deltacnstar], hash[:xcorr], hash[:deltacn], hash[:spscore], hash[:sprank], hash[:modification_info], hash[:spectrum_query]]
-    end
-    self
-  end
-  $VERBOSE = tmp_verb
-
-  undef_method :inspect
-  def inspect
-    var = @@attributes.map do |m| "#{m}:#{self.send(m)}" end.join(" ")
-    "#<SearchHit #{var}>"
-  end
-
-  # Takes ions in the form XX/YY and returns [XX.to_i, YY.to_i]
-  def self.split_ions(ions)
-    ions.split("/").map {|ion| ion.to_i }
-  end
-
-  def search_score_xml(symbol)
-    "#{tabs}<search_score name=\"#{symbol}\" value=\"#{send(symbol)}\"/>"
-  end
-
-  def search_scores_xml(*symbol_list)
-    symbol_list.collect do |sy|
-      search_score_xml(sy)
-    end.join("\n") + "\n"
-  end
-
-  def to_pepxml
-    mod_pepxml = 
-      if self[18]
-        self[18].to_pepxml
-      else
-        ''
-      end
-
-    #string = element_xml_and_att_string("search_hit", [:hit_rank, :peptide, :peptide_prev_aa, :peptide_next_aa, :protein, :num_tot_proteins, :num_matched_ions, :tot_num_ions, :calc_neutral_pep_mass, :massdiff_as_string, :num_tol_term, :num_missed_cleavages, :is_rejected]) do
-    # note the to_plus_minus_string
-    #puts "MASSDIFF:"
-    #p massdiff
-    element_xml_and_att_string("search_hit", "hit_rank=\"#{hit_rank}\" peptide=\"#{peptide}\" peptide_prev_aa=\"#{peptide_prev_aa}\" peptide_next_aa=\"#{peptide_next_aa}\" protein=\"#{protein}\" num_tot_proteins=\"#{num_tot_proteins}\" num_matched_ions=\"#{num_matched_ions}\" tot_num_ions=\"#{tot_num_ions}\" calc_neutral_pep_mass=\"#{calc_neutral_pep_mass}\" massdiff=\"#{massdiff.to_plus_minus_string}\" num_tol_term=\"#{num_tol_term}\" num_missed_cleavages=\"#{num_missed_cleavages}\" is_rejected=\"#{is_rejected}\"") do
-      mod_pepxml +
-        search_scores_xml(:xcorr, :deltacn, :deltacnstar, :spscore, :sprank)
-    end
-  end
-
-  def from_pepxml_node(node)
-    self[0] = node['hit_rank'].to_i
-    self[1] = node['peptide']
-    self[2] = node['peptide_prev_aa']
-    self[3] = node['peptide_next_aa']
-    self[4] = node['protein']  ## will this be the string?? (yes, for now)
-    self[5] = node['num_tot_proteins'].to_i
-    self[6] = node['num_matched_ions'].to_i
-    self[7] = node['tot_num_ions'].to_i
-    self[8] = node['calc_neutral_pep_mass'].to_f
-    self[9] = node['massdiff'].to_f
-    self[10] = node['num_tol_term'].to_i
-    self[11] = node['num_missed_cleavages'].to_i
-    self[12] = node['is_rejected'].to_i
-    self
-  end
-
-end
-
-
-Sequest::PepXML::SearchHit::ModificationInfo = Arrayclass.new(%w(modified_peptide mod_aminoacid_masses mod_nterm_mass mod_cterm_mass))
-
-# Positions and masses of modifications
-class Sequest::PepXML::SearchHit::ModificationInfo
-  include SpecIDXML
-
-  ## Should be something like this:
-  # <modification_info mod_nterm_mass=" " mod_nterm_mass=" " modified_peptide=" ">
-  #   <mod_aminoacid_mass position=" " mass=" "/>
-  # </modification_info>
-
-  alias_method :masses, :mod_aminoacid_masses
-  alias_method :masses=, :mod_aminoacid_masses=
-
-  # Mass of modified N terminus<
-  #attr_accessor :mod_nterm_mass
-  # Mass of modified C terminus<
-  #attr_accessor :mod_cterm_mass
-  # Peptide sequence (with indicated modifications)  I'm assuming that the
-  # native sequest indicators are OK here
-  #attr_accessor :modified_peptide
-
-  # These are objects of type: ...ModAminoacidMass
-  # position ranges from 1 to peptide length
-  #attr_accessor :mod_aminoacid_masses
-
-  # Will escape any xml special chars in modified_peptide
-  def to_pepxml
-    ## Collect the modifications:
-    mod_strings = []
-    if masses and masses.size > 0
-      mod_strings = masses.map do |ar|
-        "position=\"#{ar[0]}\" mass=\"#{ar[1]}\""
-      end
-    end
-    ## Create the attribute string:
-    att_parts = []
-    if mod_nterm_mass
-      att_parts << "mod_nterm_mass=\"#{mod_nterm_mass}\""
-    end
-    if mod_cterm_mass
-      att_parts << "mod_cterm_mass=\"#{mod_cterm_mass}\""
-    end
-    if modified_peptide
-      att_parts << "modified_peptide=\"#{escape_special_chars(modified_peptide)}\""
-    end
-    element_xml_and_att_string('modification_info', att_parts.join(" ")) do
-      mod_strings.map {|st| short_element_xml_and_att_string('mod_aminoacid_mass', st) }.join
-    end
-  end
-
-  def self.from_pepxml_node(node)
-    self.new.from_pepxml_node(node)
-  end
-
-  # returns self
-  def from_pepxml_node(node)
-    self[0] = node['modified_peptide'] 
-    self[2] = node['mod_nterm_mass']
-    self[3] = node['mod_cterm_mass']
-    masses = []
-    node.children do |mass_n|
-      masses << Sequest::PepXML::SearchHit::ModificationInfo::ModAminoacidMass.new([mass_n['position'].to_i, mass_n['mass'].to_f])
-    end
-    self[1] = masses
-    self 
-  end
-
-  ## 
-
-  # <modification_info modified_peptide="GC[546]M[147]PSKEVLSAGAHR">
-  # <mod_aminoacid_mass position="2" mass="545.7160"/>
-  # <mod_aminoacid_mass position="3" mass="147.1926"/>
-  # </modification_info>
-end
-
-Sequest::PepXML::SearchHit::ModificationInfo::ModAminoacidMass = Arrayclass.new(%w(position mass))