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'

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 SpecID::Sequest; end
class SpecID::Sequest::PepXML; end

class SpecID::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 SpecID::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 SpecID::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: #{SpecID::Sequest::PepXML.pepxml_version}"
    end
  end

end

class SpecID::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 SpecID::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 SpecID::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(:sequence).each do |seq, pep_arr|
      prots = pep_arr.collect { |pep| pep.prot }
      prots.uniq!
      _size = prots.size 
      pep_arr.each do |pep|
        pep._num_prots = _size.to_s
        pep._first_prot = prots.first
      end
    end
  end


  Default_Options = {
    :out_path => nil,
    :backup_db_path => '/project/marcotte/marcotte/ms/database',
    # 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',
    :ms_ionization => 'ESI',
    :ms_mass_analyzer => 'Ion Trap',
    :ms_detector => 'UNKNOWN',
    :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??
  }

  # 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
  def self.new_from_srf(srf_file, opts={})
    opts = Default_Options.merge(opts)

    ## set the outpath
    out_path = opts.delete(:out_path)
    unless out_path
      out_path = File.dirname(srf_file)
    end

    ## read the srf file
    srf = SRF.new(srf_file)

    params = srf.params

    ## check to see if we need backup_db
    backup_db_path = opts.delete(:backup_db_path)
    unless File.exist? params.database
      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 => SpecID::Sequest::PepXML::SearchDatabase.new(params),
      :base_name => full_base_name_no_ext,
      :out_data_type => out_data_type,
      :out_data => out_data
    }
    opts[:search_summary] = SpecID::Sequest::PepXML::SearchSummary.new( params, 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
    pepxml_obj = SpecID::Sequest::PepXML.new(ppxml_version, params) 
    ## name some common variables we'll need
    h_plus = pepxml_obj.h_plus
    avg_parent = pepxml_obj.avg_parent

    #######################################################################
    # 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,
      }

      #  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::Sequest::PepXML::SearchHit.prepare_sequence(top_hit[8])
      #  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].split(" ").first, 
        :num_tot_proteins => top_hit[10],
        :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 => SpecID::Sequest::PepXML::SearchHit.calc_num_tol_term(params, top_hit[8]),
        :num_missed_cleavages => SpecID::Sequest::PepXML::SearchHit.calc_num_missed_cleavages(params, top_hit[8]),
        :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],
      }

      spectrum_queries_arr[files_with_hits_index] = SpecID::Sequest::PepXML::SpectrumQuery.new(sq_hash) do
        search_result = SpecID::Sequest::PepXML::SearchResult.new do
          [ SpecID::Sequest::PepXML::SearchHit.new(sh_hash) ] # there can be multiple hits
        end # SearchResult
        [search_result] # can be multiple
      end
    end
    spectrum_queries_arr.compact!

    #######################################################################
    # ADD the pipeline analysis
    #######################################################################

    pipeline = SpecID::Sequest::PepXML::MSMSPipelineAnalysis.new({:date=>nil,:summary_xml=> bn_noext +'.xml'}) do
      SpecID::Sequest::PepXML::MSMSRunSummary.new(opts) { spectrum_queries_arr }
    end
    pepxml_obj.msms_pipeline_analysis = pipeline
    pepxml_obj.base_name = pipeline.msms_run_summary.base_name
    pepxml_obj
  end

  # Takes bioworks 3.2/3.3 xml output (with no filters)
  # Returns a list of PepXML objects
  # msdata = path to mzXML files (or .timeIndex files) (or @TODO: path to sqt file(s))
  # 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(params, bioworks, msdata, out_path, pepxml_version=18, sample_enzyme='trypsin', ms_manufacturer='ThermoFinnigan', ms_model='LCQ Deca XP Plus', ms_ionization='ESI', ms_mass_analyzer='Ion Trap', ms_detector='UNKNOWN', raw_data_type="raw", raw_data=".mzXML", out_data_type="out", out_data=".tgz")
    supported_versions = [0,18]

    unless supported_versions.include?(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 == SpecID::Sequest::Params  # OK!
    elsif params.class == String ; params = SpecID::Sequest::Params.new(params)
    else                         ; abort "Don't recognize #{params} as object or string!"
    end
    # Bioworks:
    if bioworks.class == SpecID::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 != SpecID::Bioworks::Pep ; puts "trying to pass as pep: "; p pep; abort "NOT a pep!" end }


    ## Start
    split_bio_objs = []

    ## Create a hash by pep object containing num_tot_proteins
    ## This is only valid if all hits are present (no previous thresholding)
    self._prot_num_and_first_prot_by_pep(bioworks.peps)
    ## (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"

    ## Create a hash of spectrum_query arrays by filename (this very big block):
    spectrum_queries_by_base_name = {}
    pepxml_objs_by_base_name = {}
    # Hash by the filenames to split into filenames:
    bioworks.peps.hash_by(:base_name).each do |base_name, 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
        inner__full_base_name_no_ext = File.join(msdata, base_name)
        prec_mz_arr = Spec::MSRun.precursor_mz_by_scan(inner__full_base_name_no_ext)
      when /3.3/
        calc_prec_by = :deltamass
      else
        abort "invalid BioworksBrowser version: #{x}"
      end

      pepxml_obj = SpecID::Sequest::PepXML.new(pepxml_version, params)
      pepxml_objs_by_base_name[base_name] = pepxml_obj

      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 = SpecID::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 = SpecID::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 = SpecID::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,
        }) do
          search_result = SpecID::Sequest::PepXML::SearchResult.new do

            ## Calculate some interdependent values;
            # NOTE: the bioworks mass is really 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::Sequest::PepXML::SearchHit.prepare_sequence(top_pep.sequence)
            (num_matched_ions, tot_num_ions) = SpecID::Sequest::PepXML::SearchHit.split_ions(top_pep.ions)
            search_hit = SpecID::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 => SpecID::Sequest::PepXML::SearchHit.calc_num_tol_term(params, top_pep.sequence).to_s,
              :num_missed_cleavages => SpecID::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,
            })
            [search_hit]   # there can be multiple search hits
          end # SearchResult
          [search_result]  # can be multiple search_results
        end # SpectrumQuery
      end # Collects the spectrum queries

      # 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}" }

      spectrum_queries_by_base_name[base_name] = spectrum_queries_ar
    end

    modifications_string = bioworks.modifications
    
    spectrum_queries_by_base_name.collect do |base_name, spectrum_queries_ar|
      case pepxml_version
      when 18
        pipeline =  SpecID::Sequest::PepXML::MSMSPipelineAnalysis.new({:date=>nil,:summary_xml=>base_name+'.xml'}) do
          full_base_name_no_ext = self.make_base_name( File.expand_path(out_path), base_name)
          SpecID::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 => SpecID::Sequest::PepXML::SearchSummary.new(params, modifications_string, {:search_database => SpecID::Sequest::PepXML::SearchDatabase.new(params), :base_name => full_base_name_no_ext, :out_data_type => out_data_type, :out_data => out_data}),
          }) { spectrum_queries_ar }
        end
        pepxml_obj = pepxml_objs_by_base_name[base_name]
        pepxml_obj.msms_pipeline_analysis = pipeline
        pepxml_obj.base_name = pipeline.msms_run_summary.base_name
        pepxml_obj 
      when 0
        ## @TODO: NEED TO REVAMP THIS:
        #        SpecID::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
    end # collects the pepxml objects

  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 SpecID::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 SpecID::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 SpecID::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 = SpecID::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 SpecID::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 =~ /\(?(\w{1,2})(.) (.[\d\.]+)\)?/
        aa_as_sym = $1.to_sym,
        @mod_symbols_hash[[aa_as_sym, $3.to_f]] = $2.dup
        if $1 == 'ct' || $1 == 'nt' 
          @masses_by_diff_mod[$2] = $3.to_f
        else
          @masses_by_diff_mod[$1+$2] = $3.to_f + table[aa_as_sym]
        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[:modified_peptide] = peptide.dup
    hash = {}
    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.slice!( 1..-1 )
    end
    if hsh.key? peptide[-1,1]
      # AA + OH + differential_mod
      hash[:mod_cterm_mass] = table[peptide[-2,1].to_sym] + oh + hsh[peptide[-1,1]]
      peptide.slice!( 0..-2 )
    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 > 0
      SpecID::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',
      } 
      SpecID::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
      SpecID::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].to_sym, arr[i].to_f]
      end
    end
    variable_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 => 'Y',
        :binary => 'N',
        :symbol => @mod_symbols_hash[mod],
      }
      SpecID::Sequest::PepXML::AAModification.new(hash)
    end
    #################################
    # 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,
      }
      SpecID::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 SpecID::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 SpecID::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 SpecID::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 SpecID::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 SpecID::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

# This object inherits from Array.  As such, it is very memory efficient
# (compared to a normal object).  However, certain operations when used on
# these objects will produce undesirable results: An array of these objects
# will be flattened (becoming a long list of attributes) when 'flatten' is
# called on them, which is not the behavior we want!  other odd behavior is
# possible.  Possible fixes are to use a delegate class or redefine the way
# this responds to flatten (so that it won't flatten).
class SpecID::Sequest::PepXML::SearchHit < Array
  include SpecIDXML

  Non_standard_amino_acid_char_re = /[^A-Z\.\-]/

  # num_tot_proteins = "Number of unique proteins in search database containing peptide"
  #attr_accessor 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
  #attr_accessor 13:deltacnstar
  #attr_accessor 14:xcorr, 15:deltacn, 16:spscore, 17:sprank
  ind_keys = {} ; ind_keys_w_eq = {}; @@ind = {}

  ind_keys = {: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}
  @@methods = ind_keys.keys
  def hit_rank ; self[0] end ; def hit_rank=(oth) ; self[0] = oth end
  def peptide ; self[1] end ; def peptide=(oth) ; self[1] = oth end
  def peptide_prev_aa ; self[2] end ; def peptide_prev_aa=(oth) ; self[2] = oth end
  def peptide_next_aa ; self[3] end ; def peptide_next_aa=(oth) ; self[3] = oth end
  def protein ; self[4] end ; def protein=(oth) ; self[4] = oth end
  def num_tot_proteins ; self[5] end ; def num_tot_proteins=(oth) ; self[5] = oth end
  def num_matched_ions ; self[6] end ; def num_matched_ions=(oth) ; self[6] = oth end
  def tot_num_ions ; self[7] end ; def tot_num_ions=(oth) ; self[7] = oth end
  def calc_neutral_pep_mass ; self[8] end ; def calc_neutral_pep_mass=(oth) ; self[8] = oth end
  def massdiff ; self[9] end ; def massdiff=(oth) ; self[9] = oth end
  def num_tol_term ; self[10] end ; def num_tol_term=(oth) ; self[10] = oth end
  def num_missed_cleavages ; self[11] end ; def num_missed_cleavages=(oth) ; self[11] = oth end
  def is_rejected ; self[12] end ; def is_rejected=(oth) ; self[12] = oth end
  def deltacnstar ; self[13] end ; def deltacnstar=(oth) ; self[13] = oth end
  def xcorr ; self[14] end ; def xcorr=(oth) ; self[14] = oth end
  def deltacn ; self[15] end ; def deltacn=(oth) ; self[15] = oth end
  def spscore ; self[16] end ; def spscore=(oth) ; self[16] = oth end
  def sprank ; self[17] end ; def sprank=(oth) ; self[17] = oth end

  @@arr_size = ind_keys.size
  ind_keys.each {|k,v| ind_keys_w_eq["#{k}=".to_sym] = v }
  ind_keys.merge!(ind_keys_w_eq)
  ind_keys.each {|k,v| @@ind[k] = v ; @@ind["#{k}"] = v}

  # These are all search_score elements:

  # 1 if there is no second ranked hit, 0 otherwise

  def initialize(hash=nil)
    super(@@arr_size)
    self[0,18] = [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]]
    self
    #if hash ; set_from_hash(hash) end
  end

  # remove_non_amino_acids && split_sequence
  def self.prepare_sequence(val)
    nv = remove_non_amino_acids(val)
    split_sequence(nv)
  end

  # Returns prev, peptide, next from sequence.  Parse errors return
  # nil,nil,nil
  #   R.PEPTIDE.A  # -> R, PEPTIDE, A
  #   R.PEPTIDE.-  # -> R, PEPTIDE, -
  #   PEPTIDE.A    # -> -, PEPTIDE, A
  #   A.PEPTIDE    # -> A, PEPTIDE, -
  #   PEPTIDE      # -> nil,nil,nil
  def self.split_sequence(val)
    peptide_prev_aa = ""; peptide = ""; peptide_next_aa = ""
    pieces = val.split('.') 
    case pieces.size
    when 3
      peptide_prev_aa, peptide, peptide_next_aa = *pieces
    when 2
      if pieces[0].size > 1  ## N termini
        peptide_prev_aa, peptide, peptide_next_aa = '-', pieces[0], pieces[1]
      else  ## C termini
        peptide_prev_aa, peptide, peptide_next_aa = pieces[0], pieces[1], '-'
      end
    when 1  ## this must be a parse error!
      peptide_prev_aa, peptide, peptide_next_aa = nil,nil,nil
    when 0
      peptide_prev_aa, peptide, peptide_next_aa = nil,nil,nil
    end
    return peptide_prev_aa, peptide, peptide_next_aa
  end

  # removes nonstandard chars with Non_standard_amino_acid_char_re
  # preserves A-Z and '.
  def self.remove_non_amino_acids(sequence)
    sequence.gsub(Non_standard_amino_acid_char_re, '')
  end

  def inspect
    var = @@methods.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 = self.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 = self.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
    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
      search_scores_xml(:xcorr, :deltacn, :deltacnstar, :spscore, :sprank)
    end
  end

end

# Positions and masses of modifications
class SpecID::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)
    instance_var_set_from_hash(hash)
  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