mspire 0.2.4 → 0.3.0

data/lib/spec_id/sequest/pepxml.rb

@@ -0,0 +1,1513 @@
+
+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']
+
+    sample_enzyme_n = node.find_first("child::sample_enzyme")
+    @sample_enzyme = SampleEnzyme.from_pepxml_node(sample_enzyme_n)
+
+    search_summary_n = sample_enzyme_n.find_first("following-sibling::search_summary")
+    spectrum_queries = search_summary_n.find("following-sibling::spectrum_query")
+    @spectrum_queries = spectrum_queries.map do |sq_n|
+      Sequest::PepXML::SpectrumQuery.from_pepxml_node(sq_n, self) 
+    end
+
+    ## NOTE: this is currently just the xml node!!!! TODO: wrap everything up
+    #into a better search summary object (to eventually depracate the params object)
+    @search_summary = node  ## in future call SearchSummary.from_pepxml_node
+    @peps = [] 
+    @spectrum_queries.each do |sq|
+      sq.search_results.each do |sr|
+        @peps.push( *(sr.search_hits) )
+      end
+    end
+    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:
+    opts[:sample_enzyme] = params.sample_enzyme
+
+    ## 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
+    srf.dta_files.each_with_index do |dta_file,i|
+      next if out_files[i].num_hits == 0
+      files_with_hits_index += 1
+
+      # We don't need to sort the hits by xcorr since it comes pre-sorted in
+      # srf files!
+      #arr = hits.sort_by{|v| v.xcorr }
+
+      # Get proper deltacn and deltacnstar
+      # under new srf, deltacn is already corrected for what prophet wants,
+      # deltacn_orig 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!
+
+      hits = out_files[i].hits
+      top_hit = hits[0]
+      second_hit = hits[1]
+      deltacnstar =
+        if second_hit ; '0'
+        else ; '1'
+        end
+       
+      ## mass calculations:
+      precursor_neutral_mass = dta_file.mh - h_plus
+      calc_neutral_pep_mass = top_hit[0] - h_plus
+
+      (start_scan, end_scan, charge) = srf_index[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)
+
+      sequence = top_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 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
+
+      sh_hash = {
+        :hit_rank => 1,
+        :peptide => pepseq,
+        :peptide_prev_aa => prevaa,
+        :peptide_next_aa => nextaa,
+        :protein => top_hit[10].first.reference.split(" ").first, 
+        :num_tot_proteins => top_hit[10].size,
+        :num_matched_ions => top_hit[7],
+        :tot_num_ions => top_hit[8],
+        :calc_neutral_pep_mass => calc_neutral_pep_mass,
+        :massdiff => precursor_neutral_mass - calc_neutral_pep_mass, 
+        :num_tol_term => Sequest::PepXML::SearchHit.calc_num_tol_term(params, sequence),
+        :num_missed_cleavages => Sequest::PepXML::SearchHit.calc_num_missed_cleavages(params, sequence),
+        :is_rejected => 0,
+        # These are search score attributes:
+        :xcorr => top_hit[3],
+        :deltacn => top_hit[19],
+        :deltacnstar => deltacnstar,
+        :spscore => top_hit[2],
+        :sprank => top_hit[6],
+        :modification_info => modifications_obj.modification_info(SpecID::Pep.split_sequence(sequence)[1]),
+      }
+      search_hit = Sequest::PepXML::SearchHit.new(sh_hash) # there can be multiple hits
+
+      search_result = Sequest::PepXML::SearchResult.new
+      search_result.search_hits = [search_hit]
+      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
+  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
+
+    #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 => 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).collect 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 => Sequest::PepXML::SearchHit.calc_num_tol_term(params, top_pep.sequence),
+          :num_missed_cleavages => Sequest::PepXML::SearchHit.calc_num_missed_cleavages(params, top_pep.sequence),
+          :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)
+    file.gsub!("\\", '/')
+    File.basename(file).sub(/\.[\w^\.]+$/, '')
+  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
+    if block_given? ; @search_hits = yield
+    else ; @search_hits = [] end
+  end
+
+  def to_pepxml
+    element_xml_no_atts(:search_result) do
+      @search_hits.map {|sh| sh.to_pepxml }.join
+    end
+  end
+
+  def self.from_pepxml_node(node, spec_query)
+    self.new.from_pepxml_node(node, spec_query)
+  end
+
+  def from_pepxml_node(node, spec_query, msmsrun_obj)
+    sh_klass = msmsrun_obj.search_hit_class
+    @search_hits = node.children.map do |sh_n|
+      sh_klass.from_pepxml_node(sh_n, spec_query)
+    end
+    self
+  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 +
+        short_element_xml(:enzymatic_search_constraint, [:enzyme, :max_num_internal_cleavages, :min_number_termini]) +
+        @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, msmsrun_obj)
+    self.new.from_pepxml_node(node, msmsrun_obj)
+  end
+
+  def from_pepxml_node(node, msmsrun_obj)
+    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[6] = node.children.map do |v|   
+      sh = Sequest::PepXML::SearchResult.new
+      sh.from_pepxml_node(v, self, msmsrun_obj)
+    end
+    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\.\-]/
+
+
+  # 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(@@arr_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
+
+  # requires Params object and full sequence (with heads and tails)
+  def self.calc_num_missed_cleavages(params, sequence)
+    num_missed = 0
+    offset, split_after, except_before = params.enzyme_specificity
+    first, middle, last = SpecID::Pep.split_sequence(sequence)
+    to_regexp = "[#{split_after}]"
+    if except_before.size > 0
+      to_regexp << "[^#{except_before}]"
+    end
+    regexp = /#{to_regexp}/
+    arr = middle.scan(regexp)
+    num = arr.size
+    if middle[-1,1] =~ regexp
+      # if the regexp is a single letter (exceptions) and the last letter
+      # matches, then it will count when it is not a missed cleavage
+      # we can correct for this and get the right answer
+      num -= 1
+    else
+      num
+    end
+  end
+
+  # requires Params object and full sequence (with heads and tails)
+  def self.calc_num_tol_term(params, sequence)
+    num_tol = 0
+    offset, split_after, except_before = params.enzyme_specificity
+    first, middle, last = SpecID::Pep.split_sequence(sequence)
+    last_of_middle = middle[-1,1]
+    first_of_middle = middle[0,1]
+    if ( split_after.include?(first) && !except_before.include?(first_of_middle) ) || first == '-'
+      num_tol += 1
+    end
+    if split_after.include?(last_of_middle) && !except_before.include?(last) || last == '-'
+      num_tol += 1
+    end
+    num_tol
+  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 self.from_pepxml_node(node, spec_query)
+    self.new.from_pepxml_node(node, spec_query)
+  end
+
+  def from_pepxml_node(node, spec_query)
+    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
+    if modinfo_node = node.find_first("child::modification_info")
+      self[18] = Sequest::PepXML::SearchHit::ModificationInfo.from_pepxml_node(modinfo_node)
+    end
+    node.find("child::search_score").each do |ss_n|
+      case ss_n['name']
+      when 'deltacnstar'
+        self[13] = ss_n['value'].to_i
+      when 'xcorr'
+        self[14] = ss_n['value'].to_f
+      when 'deltacn'
+        self[15] = ss_n['value'].to_f
+      when 'spscore'
+        self[16] = ss_n['value'].to_f
+      when 'sprank'
+        self[17] = ss_n['value'].to_i
+      end
+    end
+    self[19] = spec_query
+    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))