require 'xml_style_parser'
require 'ms/spectrum'
require 'ms/scan'


class MS::Parser::MzXML::DOM
  include XMLStyleParser
  include MS::Parser::MzXML

  #@@scan_atts = %w(num msLevel retentionTime startMz endMz precursors spectrum)

  def initialize(parse_type=:msrun, version='1.0')
    @method = parse_type
    @version = version
  end

  def new_scan_from_hash(node)
    scan = MS::Scan.new  # array class creates one with 9 positions
    scan[0] = node['num'].to_i
    scan[1] = node['msLevel'].to_i
    scan[2] = node['retentionTime'][2...-1].to_f
    if x = node['startMz']
      scan[3] = x.to_f
      scan[4] = node['endMz'].to_f
    end
    scan
  end

  # takes a scan node and creates a scan object
  # the parent scan is the one directly above it in mslevel
  # if the 
  def create_scan(scan_n, scans_by_num, get_spectra=true)
    if @version < '3.0'
      scan = new_scan_from_hash(scan_n)
      precs = []
      scan_n.each do |node|
        case node.name
        when 'precursorMz'
          # should be able to do this!!!
          #scan[5] = scan_n.find('child::precursorMz').map do |prec_n|
          prec = MS::Precursor.new
          prec[1] = node['precursorIntensity'].to_f
          prec[0] = node.content.to_f
          if x = node['precursorScanNum']
            prec[2] = scans_by_num[x.to_i]
          end
          precs << prec
        when 'peaks'
          next unless get_spectra
          # SHOULD be able to do this!!
          #peaks_n = scan_n.find_first('child::peaks')
          scan[6] = MS::Spectrum.from_base64_peaks(node.content, node['precision'].to_i)
        end
      end
      scan[5] = precs
      scan
    else  # for version > 3.0 
      abort 'not supporting version 3.0 just yet'
      # note that mzXML version 3.0 *can* have more than one peak...
      # I'm not sure how to deal with that since I have one spectrum/scan
    end
  end


  # returns an array of msrun objects
  def msruns(file)
    raise NotImplementedError
  end

  # returns a string with double </scan></scan> tags into single and missing
  # </scan> tags after peaks added in
  # we do this in windows style since these are generated off a windows
  # machine only
  def fix_bad_scan_tags(file)
    IO.read(file).gsub(/<\/scan>\s+<\/scan>/m, '</scan>').gsub(/<\/peaks>\s+<scan/m, "</peaks>\r\n  </scan>\r\n  <scan")
  end

  # right now cannot parse multiple runs out of an mzXML version 2 file since
  # this is built around a single run per file
  # OPTIONS:
  #   :msrun => MSRun    # use this object instead of creating one
  #   :spectra => *true|false   # if false don't get spectra
  def msrun(file, opts={})
    unless opts.key?(:spectra)
      opts[:spectra] = true
    end

    msrun_obj = 
      if x = opts[:msrun]
        msrun_obj = x
      else
        MS::MSRun.new
      end

    root = 
      if @version == '2.0'
        string = fix_bad_scan_tags(file)
        get_root_node_from_string(string)
      else
        get_root_node_from_file(file)
      end

    # right now we are only finding the first msRun (probably a rare case of
    # multiple runs in an mzXML file...)
    msrun_n = 
      if @version >= '2.0' 
        kids = root.children.select {|v| v.name == 'msRun' }
        raise(NotImplementedError, "one msrun per doc right now" ) if kids.size > 1
        kids.first
      else
        root
      end
    if msrun_n.name != 'msRun'
      raise RuntimeError, "extra node slipped in somehow"
    end

    ## HEADER
    scan_count = msrun_n['scanCount'].to_i
    msrun_obj.scan_count = scan_count
    scans_by_num = Array.new(scan_count + 1)
    
    ## SPECTRUM
    parent = nil
    scans = Array.new( scan_count )
    scn_index = 0

    # we should be able to do this, but it's not working!!!
    #scan_n = msrun_n.find_first('scan')
    #while (scn_index < scan_count)
    get_spectra = opts[:spectra]

    msrun_n.each do |scan_n|
      next unless scan_n.name == 'scan'
      scan = create_scan(scan_n, scans_by_num, get_spectra)
      scans[scn_index] = scan
      #sc = scan_n.next
      scans_by_num[scan[0]] = scan 
      scn_index += 1
    end


    ## update the scan's parents
    MS::MSRun.add_parent_scan(scans)

    # note that startTime and endTime are optional AND in >2.2 are dateTime
    # instead of duration types!, so we will just use scan times...
    # Also, note that startTime and endTime are BROKEN on readw -> mzXML 2.0
    # export.  They give the start and end time in seconds, but they are
    # really minutes.  All the more reason to use the first and last scans!
    msrun_obj.start_time = scans.first.time
    msrun_obj.end_time = scans.last.time

    msrun_obj.scans = scans
  end

end