mspire 0.2.4 → 0.3.0

data/lib/spec_id/sequest.rb

@@ -1,1675 +1,5 @@
+require 'spec_id/sequest/params'
 
-require 'sample_enzyme'
-require 'spec/mzxml/parser'
-require 'hash_by'
-require 'set_from_hash'
-require 'spec_id/bioworks'
-require 'instance_var_set_from_hash'
-require 'spec/msrun'
-require 'spec_id/srf'
-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
-
-##########################################
-# NEED TO ADD MODIFICATIONS and generally verify pepxml creation!!! :
-# HERE's an excerpt from an example file from tpp 2.9.2 that I'm going to follow:
-=begin
-<search_summary base_name="/regis/data3/search/akeller/LCQ/COMET/LIGHT/haloICAT2_41" search_engine="COMET" precursor_mass_type="average" fragment_mass_type="average">
-<sequence_search_constraint sequence="C"/>
-<aminoacid_modification aminoacid="C" massdiff="8.049" mass="553.765" variable="Y" binary="N"/>
-<aminoacid_modification aminoacid="C" massdiff="442.5772" mass="545.7160" variable="N"/>
-<aminoacid_modification aminoacid="M" massdiff="16.0000" mass="147.1926" variable="Y" binary="N" symbol="1"/>
-<parameter name="peptide_mass_tol" value="3.0000"/>
-<parameter name="peptide_mass_tol_units" value="DA"/>
-<parameter name="num_output_lines" value="10"/>
-<parameter name="remove_precursor_peak" value="0"/>
-<parameter name="num_dup_headers" value="1"/>
-<parameter name="email_address" value=""/>
-<parameter name="ion_series" value="010000010"/>
-<parameter name="max_num_var_mod_residues" value="3"/>
-<parameter name="md5_check_sum" value="2547286a77a35abe2af3f2e9825ab814"/>
-</search_summary>
-=end
-
-# and a guy with modifications:
-=begin
-<search_result spectrum="haloICAT2_41.1110.1110.2" start_scan="1110" end_scan="1110" precursor_neutral_mass="2000.6641" assumed_charge="2" index="28">
-<search_hit hit_rank="1" peptide="GCMPSKEVLSAGAHR" peptide_prev_aa="R" peptide_next_aa="Y" protein="Chr_ORF0132" num_tot_proteins="1" num_matched_ions="19" tot_num_ions="30" calc_neutral_pep_mass="2001.3685" massdiff="-0.704" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
-<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>
-<search_score name="dotproduct" value="359"/>
-<search_score name="delta" value="0.296"/>
-<search_score name="deltastar" value="0"/>
-<search_score name="zscore" value="5.290"/>
-<search_score name="expect" value="0.000E+00"/>
-<peptideprophet_result probability="0.9994" all_ntt_prob="(0.3713,0.4360,0.9994)">
-<search_score_summary>
-<parameter name="fval" value="3.4002"/>
-<parameter name="ntt" value="2"/>
-<parameter name="nmc" value="1"/>
-<parameter name="massd" value="-0.704"/>
-</search_score_summary>
-</peptideprophet_result>
-=end
-
-# sequest.params option:
-# diff_search_options = 15.994910 M 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y
-# permanent mods are at the bottom: ...
-# add_A_Alanine = 0.0000                   ; added to A
-# add_S_Serine = 0.0000                    ; added to S
-# add_P_Proline = 0.0000                   ; added to P
-# add_V_Valine = 0.0000                    ; added to V
-# add_T_Threonine = 0.0000                 ; added to T
-# ...
-
-
-
-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(':')}"
-      when 0 ; Time.new.to_s
-      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 0
-      element_xml(:msms_pipeline_analysis, [:date, :summary_xml]) do
-        @msms_run_summary.to_pepxml
-      end
-    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 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
-    when 0
-      #      element_xml(:msms_run_summary, [:base_name, :search_engine, :database, :raw_data_type, :raw_data, :out_data_type, :out_data, :sample_enzyme]) do
-      #        element_xml(:search_summary, [:base_name, :search_engine, :precursor_mass_type, :fragment_mass_type]) do
-      #          [
-      #            @params.short_element_xml(:enzymatic_search_constraint, [:enzyme, :max_num_internal_cleavages, :min_number_termini]),
-      #            @params.short_element_xml(:sequence_search_constraint, [:sequence]),
-      #            @params.short_element_xml(:sequence_search_constraint, [:sequence]),
-      #            @params.pepxml_parameters(:peptide_mass_tol, :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)
-      #          ].join("\n")
-      #        end  + "\n" +
-      #          @spectrum_queries.collect {|result| result.to_pepxml }.join("\n")
-      #      end
-    end
-  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 0
-    '<?xml-stylesheet type="text/xsl" href="/isb/std_xsl/pepXML_std.xsl"?>' + "\n"
-    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 0 ; xml_version + doctype + style_sheet
-    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.to_s
-        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
-    :sample_enzyme => 'trypsin',
-    :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 SampleEnzyme object if necessary
-    unless opts[:sample_enzyme].is_a? SampleEnzyme
-      opts[:sample_enzyme] = SampleEnzyme.new(opts[:sample_enzyme])
-    end
-
-    ## 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 = Spec::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.exe 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
-
-      # Sort the hits
-      hits = out_files[i].hits
-      arr = hits.sort_by{|v| v.xcorr }
-
-      # Get proper deltacn and deltacnstar
-      # Prophet deltacn is not the same as the native Sequest deltacn
-      # It is the deltacn of the second best hit!
-      top_hit = arr.pop
-      second_hit = arr.last
-      if second_hit 
-        top_hit[1] = second_hit[1]
-        deltacnstar = '0'
-      else 
-        top_hit[1] = '1.0'
-        deltacnstar = '1'
-      end
-
-
-
-      ## mass calculations:
-      precursor_neutral_mass = dta_file.mh - h_plus
-      calc_neutral_pep_mass = top_hit[0] - h_plus
-      massdiff = precursor_neutral_mass - calc_neutral_pep_mass
-      if massdiff >= 0 ; massdiff = "+" + massdiff.to_s
-      else ; massdiff = massdiff.to_s end
-
-      (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,
-        :pepxml_version => ppxml_version,
-        :index => files_with_hits_index,
-      }
-
-      spectrum_query = Sequest::PepXML::SpectrumQuery.new(sq_hash)
-
-      sequence = top_hit[8]
-
-      #  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)
-      #  ind_keys = {:mh => 0, :deltacn => 1, :sp => 2, :xcorr => 3, :id => 4, :rsp => 5, :ions_matched => 6, :ions_total => 7, :peptide => 8, :reference => 9 }
-
-      sh_hash = {
-        :hit_rank => "1",
-        :peptide => pepseq,
-        :peptide_prev_aa => prevaa,
-        :peptide_next_aa => nextaa,
-        :protein => top_hit[9].first.reference.split(" ").first, 
-        :num_tot_proteins => top_hit[9].size,
-        :num_matched_ions => top_hit[6],
-        :tot_num_ions => top_hit[7],
-        :calc_neutral_pep_mass => calc_neutral_pep_mass,
-        :massdiff => massdiff, 
-        :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[1],
-        :deltacnstar => deltacnstar,
-        :spscore => top_hit[2],
-        :sprank => top_hit[5],
-        :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, sample_enzyme, 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, :sample_enzyme, :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 = [0,18]
-
-    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
-    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
-
-    ## 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:
-    bioworks.peps.hash_by(:base_name).map do |base_name, pep_arr|
-
-      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 => SampleEnzyme.new(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 
-      when 0
-        ## @TODO: NEED TO REVAMP THIS:
-        #        Sequest::PepXML.new(pepxml_version).set_from_hash({
-        #          :params => params,
-        #          :search_results => spectrum_queries_arr,
-        #          :base_name => self.make_base_name( File.expand_path(out_path), base_name),
-        #          :search_engine => params.search_engine,
-        #          :database => params.database,
-        #          :raw_data_type => "mzXML",
-        #          :raw_data => ".mzXML",
-        #          :out_data_type => "out",
-        #          :out_data => ".tgz",
-        #          :sample_enzyme => params.enzyme,
-        #        })
-      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
-        prec_mz_arr = Spec::MSRun.precursor_mz_by_scan(File.join(ms_data, base_name))
-      when /3.3/
-        calc_prec_by = :deltamass
-      else
-        abort "invalid BioworksBrowser version: #{x}"
-      end
-
-      if opts[:copy_mzxml]
-        to_copy = Spec::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.to_i, 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)
-        massdiff = precursor_neutral_mass - calc_neutral_pep_mass
-        if massdiff >= 0 ; massdiff = "+" + massdiff.to_s
-        else ; massdiff = massdiff.to_s end #already has a -
-        # 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.to_s,
-          :assumed_charge => top_pep.charge,
-          :pepxml_version => pepxml_version,
-        }) 
-
-
-        search_result = Sequest::PepXML::SearchResult.new 
-
-        ## 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.to_s,
-          :massdiff => massdiff, 
-          :num_tol_term => Sequest::PepXML::SearchHit.calc_num_tol_term(params, top_pep.sequence).to_s,
-          :num_missed_cleavages => Sequest::PepXML::SearchHit.calc_num_missed_cleavages(params, top_pep.sequence).to_s,
-          :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]),
-        })
-        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
-  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
-      return path + File.basename(filename)
-    else
-      return 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^\.]+$/, '')
-  end
-
-
-end # PepXML
-
-##
-# In the future, this guy should accept any version of bioworks params file
-# and spit out any param queried.
-class Sequest::Params
-  include SpecIDXML
-
-  # current attributes supported are:
-  # bioworks 3.2:
-  @@param_re = / = ?/o
-  @@param_two_split = ';'
-
-  # opts are the general options
-  # mods are the weights added to amino acids
-  attr_accessor :opts, :mods
-
-  # all keys and values stored as strings!
-  def initialize(file=nil)
-    if file
-      parse(file)
-    end
-  end
-
-  # returns hash of params for continuous lines of non-whitespace
-  def grab_params(fh)
-    hash = {}
-    while line = fh.gets
-      if line =~ /[^\s]/
-        one,two = line.split @@param_re
-        two,comment = two.split @@param_two_split
-        hash[one] = two.rstrip
-        # it is necessary to add this break so that params files inside srf
-        # files can be read.  This will terminate the reading at the end of
-        # the file even though there are more lines
-        if line =~ /added to U/ || line =~ /digest_mass_range/## Will only work on bioworks 3.2 & 3.3 (bioworks 3.1 last line => Elastase/Tryp...)
-          break
-        end
-        if line =~ /digest_mass_range/  # there is no space in the srf params files
-          break
-        end
-      else
-        break
-      end
-    end
-    hash
-  end
-
-  # returns self
-  def parse_handle(fh)
-    sequest_line = fh.gets #[SEQUEST]
-    @opts = grab_params(fh)
-    @opts["search_engine"] = "SEQUEST"
-    @mods = grab_params(fh)
-
-    ## this gets rid of the .hdr postfix on indexed databases
-    @opts["first_database_name"] = @opts["first_database_name"].sub(/\.hdr$/, '')
-    self
-  end
-
-  ## parses file
-  ## and drops the .hdr behind indexed fasta files
-  ## returns self
-  def parse(file)
-    File.open(file) do |fh|
-      parse_handle(fh)
-    end
-    self
-  end
-
-  # returns( split_after, except_before)
-  def enzyme_specificity
-    if version == "3.2"
-      arr = enzyme_info.split(/\s+/)[3,2]
-      arr.collect! do |str|
-        if str && str.class == String ; str
-        else ; ""
-        end
-      end
-      return *arr
-    end
-  end
-
-  # Returns the version of the sequest.params file
-  # Returns String "3.2" if contains "enyzme_info"
-  # Returns String "3.1" if contains "enzyme_number"
-  def version
-    if @opts["enzyme_info"] ; return "3.2"
-    elsif @opts["enzyme_number"] ; return "3.1"
-    end
-  end
-
-  ####################################################
-  # TO PEPXML
-  ####################################################
-  # In some ways, this is merely translating to the older Bioworks
-  # sequest.params files
-
-  # I'm not sure if this is the right mapping for sequence_search_constraint?
-  def sequence
-    pseq = @opts['partial_sequence'] 
-    if !pseq || pseq == "" ; pseq = "0" end
-    pseq
-  end
-
-  # Returns xml in the form <parameter name="#{method_name}"
-  # value="#{method_value}"/> for list of symbols
-  def pepxml_parameters
-    keys_as_symbols = @opts.sort.map do |k,v| k.to_s end
-    params_xml(*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
-
-  def precursor_mass_type
-    case @opts['mass_type_parent']
-    when '0' ; "average" 
-    when '1' ; "monoisotopic"
-    else ; abort "error in mass_type_parent in sequest!"
-    end
-  end
-
-  def fragment_mass_type
-    fmtype = 
-      case @opts['mass_type_fragment']
-      when '0' ; "average"
-      when '1' ; "monoisotopic"
-      else ; abort "error in mass_type_fragment in sequest!"
-      end
-  end
-
-  def method_missing(name, *args)
-    string = name.to_s
-    if @opts.key?(string)    ; return @opts[string]
-    elsif @mods.key?(string) ; return @mods[string]
-    else                     ; return nil
-    end
-  end
-
-  ## We only need to define values if they are different than sequest.params
-  ## The method_missing will look them up in the hash!
-
-  # Returns a system independent basename
-  # Splits on "\" or "/"
-  def _sys_ind_basename(file)
-    return file.split(/[\\\/]/)[-1]
-  end
-
-  # changes the path of the database
-  def database_path=(newpath)
-    db = @opts["first_database_name"]
-    newpath = File.join(newpath, _sys_ind_basename(db))
-    @opts["first_database_name"] = newpath
-  end
-
-  def database
-    @opts["first_database_name"]
-  end
-
-  # returns the appropriate aminoacid mass lookup table (in spec_id.rb SpecID::MONO or
-  # SpecID::AVG based on precursor_mass_type
-  def mass_table
-    case precursor_mass_type
-    when 'average'
-      SpecID::AVG
-    when 'monoisotopic'
-      SpecID::MONO
-    end
-  end
-
-  # at least in Bioworks 3.2, the First number after the enzyme
-  # is the indication of the enzymatic end stringency (required):
-  #   1 = Fully enzymatic
-  #   2 = Either end
-  #   3 = N terminal only
-  #   4 = C terminal only
-  # So, to get min_number_termini we map like this:
-  #   1 => 2
-  #   2 => 1
-  def min_number_termini
-    termini_number = @opts["enzyme_info"].split(" ")[1]
-    if termini_number == "1"
-      return "2"
-    elsif termini_number == "2"
-      return "1"
-    else
-      puts "WARNING: Enzyme termini info might be imprecise!"
-      return "1"
-    end
-  end
-
-  def enzyme
-    #if @opts["enzyme_info"] =~ /Trypsin/ ; return "tryptic"
-    #else ; return @opts["enzyme_info"].split('(')[0] end
-    return @opts["enzyme_info"].split('(')[0]
-  end
-
-  def max_num_internal_cleavages
-    @opts["max_num_internal_cleavage_sites"]
-  end
-
-  def peptide_mass_tol
-    if @opts["peptide_mass_units"] != "0"
-      puts "WARNING: peptide_mass_tol units need to be adjusted!"
-    end
-    @opts["peptide_mass_tolerance"]
-  end
-
-  def fragment_ion_tol
-    @opts["fragment_ion_tolerance"]
-  end
-  def max_num_differential_AA_per_mod
-    @opts["max_num_differential_per_peptide"]
-  end
-
-  ## @TODO: We could add some of the parameters not currently being asked for to be more complete
-  ## @TODO: We could always add the Bioworks 3.2 specific params as params
-
-  ####################################################
-  ####################################################
-
-end
-
-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
-end
-
-class Sequest::PepXML::SearchSummary
-  include SpecIDXML
-  attr_accessor :params
-  attr_accessor :base_name
-  attr_accessor :out_data_type
-  attr_accessor :out_data
-  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(params, modifications_string='', args=nil)
-    @search_id = nil
-    @params = params
-    @modifications = Sequest::PepXML::Modifications.new(params, modifications_string)
-    if args ; set_from_hash(args) end
-  end
-
-  def method_missing(symbol, *args)
-    if @params ; @params.send(symbol, *args) end
-  end
-
-  def search_id
-    if @search_id ; @search_id
-    else ; '1' 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 +
-        @params.pepxml_parameters
-    end
-  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, modification_symbols_string='')
-    @params = params
-    set_modifications(params, modification_symbols_string)
-  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, 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 << [ i+1 , hsh[peptide[i,2]] ]
-      end
-    end
-    if mod_array.size > 0
-      hash[:mod_aminoacid_mass_array] = mod_array
-    end
-    if hash.size > 1  # if there is more than just the modified peptide there
-      Sequest::PepXML::SearchHit::ModificationInfo.new(hash)
-    else
-      nil
-    end
-  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_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].to_plus_minus_string,
-        :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].to_plus_minus_string,
-        :variable => 'N',
-        :description => mod[0],
-      }
-      hash[:protein_terminus] = protein_terminus if protein_terminus
-      Sequest::PepXML::TerminalModification.new(hash)
-    end
-    #################################
-    # 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].to_plus_minus_string,
-          :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
-
+module Sequest
 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
-  # Special 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
-    short_element_xml_from_instance_vars("aminoacid_modification")
-  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
-  # Special 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")
-  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
-
-class Sequest::PepXML::SpectrumQuery
-  include SpecIDXML
-
-  # basename_noext.first_scan.last_scan.charge
-  attr_accessor :spectrum
-  attr_accessor :start_scan
-  attr_accessor :end_scan
-  attr_accessor :precursor_neutral_mass
-  attr_accessor :index
-  attr_accessor :search_results
-
-  # this is a string
-  attr_accessor :assumed_charge
-  attr_accessor :pepxml_version
-
-  # sets the search_results array 
-  # if block given, sets search_results to return value
-  def initialize(hash=nil)
-    if block_given? ; @search_results = yield
-    else ; @search_results = []
-    end
-    if hash ; set_from_hash(hash) end
-  end
-
-  ############################################################
-  # 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
-    when 0
-      #element_xml("search_result", [:spectrum, :start_scan, :end_scan, :precursor_neutral_mass, :assumed_charge, :index]) do
-      #  @search_results.collect { |search_result|
-      #    search_result.to_pepxml
-      #  }.join("\n")
-      #end
-    end
-  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.to_f
-            tot_num += 1
-          end
-        end
-        mz = sum/tot_num.to_f
-      else
-        mz = prec_mz_arr[first_scan].to_f
-      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) )
-
-# hit_rank=0 peptide=1 peptide_prev_aa=2 peptide_next_aa=3 protein=4 num_tot_proteins=5 num_matched_ions=6 tot_num_ions=7 calc_neutral_pep_mass=8 massdiff=9 num_tol_term=10 num_missed_cleavages=11 is_rejected=12 deltacnstar=13 xcorr=14 deltacn=15 spscore=16 sprank=17 modification_info=18
-
-class Sequest::PepXML::SearchHit
-  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[0,19] = [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]]
-    end
-    self
-  end
-  $VERBOSE = tmp_verb
-
-  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
-    split_after, except_before = params.enzyme_specificity
-    first, middle, last = SpecID::Pep.split_sequence(sequence)
-    arr = middle.scan(/[#{split_after}][^#{except_before}]/)
-    return arr.size
-  end
-
-  # requires Params object and full sequence (with heads and tails)
-  def self.calc_num_tol_term(params, sequence)
-    num_tol = 0
-    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
-    return num_tol
-  end
-
-  # Takes ions in the form XX/YY and returns XX, YY
-  def self.split_ions(ions)
-    return *(ions.split("/"))
-  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
-
-    element_xml("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, :num_tol_term, :num_missed_cleavages, :is_rejected]) do
-      mod_pepxml +  
-        search_scores_xml(:xcorr, :deltacn, :deltacnstar, :spscore, :sprank)
-    end
-  end
-
-end
-
-# 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>
-
-
-  # 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
-  ## A few main types:
-
-  # this should be an array of arrays: [[position, modified_mass], ...]
-  # position ranges from 1 to peptide length
-  attr_accessor :mod_aminoacid_mass_array
-
-  def initialize(hash=nil)
-    @mod_nterm_mass = nil
-    @mod_cterm_mass = nil
-    if hash
-      instance_var_set_from_hash(hash)
-    end
-  end
-
-  # Will escape any xml special chars in modified_peptide
-  def to_pepxml
-    ## Collect the modifications:
-    mod_strings = []
-    if @mod_aminoacid_mass_array
-      mod_strings = @mod_aminoacid_mass_array.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
-
-  ## 
-
-  # <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
-
-