Class: Ms::Msrun::Nokogiri::Mzml

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/msrun/nokogiri/mzml.rb

Constant Summary collapse

NetworkOrder = 
false

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(msrun_object, io, version) ⇒ Mzml

Returns a new instance of Mzml.



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 15

def initialize(msrun_object, io, version)
  @msrun = msrun_object
  @io = io
  @version = version
end

Instance Attribute Details

#io ⇒ Object

Returns the value of attribute io.



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 13

def io
  @io
end

#msrun ⇒ Object

Returns the value of attribute msrun.



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 13

def msrun
  @msrun
end

#version ⇒ Object

Returns the value of attribute version.



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 13

def version
  @version
end

Instance Method Details

#lazilyGetString(binaryDataArray) ⇒ Object 



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 138

def lazilyGetString(binaryDataArray)
  unpackFormat = Ms::Data::LazyIO.unpack_code(precision(binaryDataArray), Ms::Msrun::Nokogiri::Mzml::NetworkOrder)
  compression = false
  compression = true if binaryDataArray.xpath(".//cvParam[@name=\"no compression\"]").empty?
  Ms::Data::LazyString.new(binaryDataArray.text, unpackFormat, compression)
end

#new_scan_from_node(node) ⇒ Object 



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 155

def new_scan_from_node(node)
  scan = Ms::Scan.new  # array class creates one with 9 positions
  scan[0] = $1.to_i if node['id'] =~ /scan=(\d+)/
  scan[1] = node.xpath(".//cvParam[@name=\"ms level\"]/@value").to_s.to_i
  
  if x = node['retentionTime']  #I don't see such a value in the mzML file
    scan[2] = x[2...-1].to_f
  end
  
  if x = node['startMz']  #Or this
    scan[3] = x.to_f
    scan[4] = node['endMz'].to_f
  end
  
  scan[5] = node['defaultArrayLength'].to_i
  scan[6] = node.xpath(".//cvParam[@name=\"total ion current\"]/@value").to_s.to_f
  
  if fl = node['filterLine']
    (scan[3], scan[4]) = start_end_from_filter_line(fl)
  end
  
  scan
end

#parse_header(byte_length_or_header_string) ⇒ Object

returns the msrun



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 22

def parse_header(byte_length_or_header_string)
  string = 
    if byte_length_or_header_string.is_a? Integer
      @io.rewind
      @io.read(byte_length_or_header_string)
    else
      length_or_header_string
    end
  
  doc = Nokogiri::XML.parse(string, *Ms::Msrun::Nokogiri::PARSER_ARGS)
  msrun_n = doc.root 
  
  @msrun.scan_count = msrun_n.xpath("//xmlns:spectrumList/@count").to_s.to_i
  @msrun.start_time = msrun_n.xpath("//xmlns:run/@startTimeStamp").to_s
  #@msrun.end_time = msrun_n['endTime'][2...-1].to_f  #There doesn't appear to be an endTime
  @msrun.parent_basename = msrun_n.xpath("//xmlns:sourceFile/@name").to_s
  @msrun.parent_location = msrun_n.xpath("//xmlns:sourceFile/@location").to_s
  @msrun
end

#parse_ms_level(start_byte, length) ⇒ Object

returns the ms_level as an Integer, nil if it cannot be found.



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 43

def parse_ms_level(start_byte, length)
  start_io_pos = @io.pos
  @io.pos = start_byte
  ms_level = nil
  total_length = 0
  @io.each("\n") do |line|
    if line =~ /ms level" value="(\d+)"/o
      ms_level = $1.to_i
      break
    end
    total_length += line.size
    break if total_length > length
  end
  @io.pos = start_io_pos
  
  ms_level
end

#parse_scan(start_byte, length, options = {}) ⇒ Object

assumes that the io object has been set to the beginning of the scan element. Returns an Ms::Scan object options: 

:spectrum => true | false (default is true)
:precursor => true | false (default is true)

Note that if both :spectrum and :precursor are set to false, the basic information in the scan node is parsed (such as ms_level)



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 69

def parse_scan(start_byte, length, options={})
  opts = {:spectrum => true, :precursor => true}.merge(options)
  start_io_pos = @io.pos
  @io.pos = start_byte
  
  # read in the data keeping track of peaks start and stop
  string = ""
  if opts[:spectrum]
    string = @io.read(length)
  else
    # don't bother reading all the peak information if we aren't wanting it
    # and can avoid it!  This is important for high res instruments
    # especially since the peak data is huge.
    @io.each do |line|
      if md = %r{<binary>}.match(line)
        # just add the part of the string before the <peaks> tag
        string << line.slice!(0, md.end(0) - 6)
        break
      else
        string << line
        if string.size >= length
          if string.size > length
            string.slice!(0,length)
          end
          break
        end
      end
    end
  end
  
  doc = Nokogiri::XML.parse(string, *Ms::Msrun::Nokogiri::PARSER_ARGS)
  scan_n = doc.root
  scan = new_scan_from_node(scan_n)
  prec_n = scan_n.xpath(".//precursorList")
  
  peaks_n = 
    if !prec_n.xpath(".//selectedIon").empty?
      if opts[:precursor]
        prec = Ms::Precursor.new
        prec[1] = prec_n.xpath(".//cvParam[@name=\"peak intensity\"]/@value").to_s.to_f
        prec[0] = prec_n.xpath(".//cvParam[@name=\"selected ion m/z\"]/@value").to_s.to_f
        charge = prec_n.xpath(".//cvParam[@name=\"charge state\"]/@value").to_s.to_i
        
        if charge > 0
          prec[3] = [charge]
        end
        
        scan.precursor = prec
      end
      scan_n.xpath(".//binaryDataArrayList")
    else
      scan_n.xpath(".//binaryDataArrayList")
    end
  
  if opts[:spectrum]
    # make sure packing order (Network Order is correct) and precision is correct
    mzArray = peaks_n.xpath(".//binaryDataArray[.//cvParam/@name=\"m/z array\"]")
    intensityArray = peaks_n.xpath(".//binaryDataArray[.//cvParam/@name=\"intensity array\"]")
    
    mzs = lazilyGetString(mzArray)
    intensities = lazilyGetString(intensityArray)
    spec = Ms::Spectrum.new(Ms::Data::new_simple([mzs, intensities]))  # Ms::Data
    
    scan[8] = spec
  end
  
  scan
end

#precision(peaks_n) ⇒ Object 



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 145

def precision(peaks_n)
  return 64 unless peaks_n.xpath(".//cvParam[@name=\"64-bit float\"]").empty?
  return 32 unless peaks_n.xpath(".//cvParam[@name=\"32-bit float\"]").empty?
end

#start_end_from_filter_line(line) ⇒ Object 



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# File 'lib/ms/msrun/nokogiri/mzml.rb', line 150

def start_end_from_filter_line(line)
  # "ITMS + c NSI d Full ms3 [email protected] [email protected] [160.00-1275.00]"
  /\[([^-]+)-([^-]+)\]/.match(line)[1,2].map {|v| v.to_f}
end