Class: Ms::Msrun::Plms1

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/msrun/plms1.rb

Overview

Prince Lab MS 1: a simple format for reading and writing MS1 level mass spec data

see Ms::Msrun::Plms1::SPECIFICATION for the file specification

Constant Summary collapse

SPECIFICATION = 
<<-HERE
  # The file format contains no newlines but is shown here broken into lines for
  # clarity.  Data should be little endian.  Comments begin with '#' but are not
  # part of the spec. Angled brackets '<>' indicate the data type and square
  # brackets '[]' the name of the data. An ellipsis '...' represents a
  # continuous array of data points.

  <uint32>[Number of scans]
  <uint32>[scan number] ...  # array of scan numbers as uint32
  <float64>[time point] ...  # array of time points as double precision floats (in seconds)
  # this is a repeating unit based on [Number of scans]:
  <uint32>[Number of data rows]  #  almost always == 2 (m/z, intensity)
  # this is a repeating unit based on [Number of data rows]
  <uint32>[Number of data points]
  <float64>[data point] ...  # array of data points as double precision floats
HERE

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(_scan_numbers = [], _times = [], _spectra = []) ⇒ Plms1

Returns a new instance of Plms1.



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# File 'lib/ms/msrun/plms1.rb', line 56

def initialize(_scan_numbers=[], _times=[], _spectra=[])
  (@scan_numbers, @times, @spectra) = [_scan_numbers, _times, _spectra]
end

Instance Attribute Details

#scan_numbers ⇒ Object

an array of scan numbers



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# File 'lib/ms/msrun/plms1.rb', line 49

def scan_numbers
  @scan_numbers
end

#spectra ⇒ Object

an array that contains parallel rows of arrays holding the actual data these are NOT bona fide spectra objects



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# File 'lib/ms/msrun/plms1.rb', line 54

def spectra
  @spectra
end

#times ⇒ Object

an array of time data



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# File 'lib/ms/msrun/plms1.rb', line 51

def times
  @times
end

Instance Method Details

#read(io_or_filename) ⇒ Object

returns self for chaining



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# File 'lib/ms/msrun/plms1.rb', line 71

def read(io_or_filename)
  io = 
    if io_or_filename.is_a?(String)
      filename = io_or_filename
      File.open(io_or_filename,'rb')
    else ; io_or_filename end

  num_scans = read_uint32(io)[0]
  @scan_numbers = read_uint32(io, num_scans)
  @times = read_float64(io, num_scans)
  @spectra = num_scans.times.map do
   read_uint32(io)[0].times.map do
      read_float64(io, read_uint32(io)[0])
    end
  end
  io.close if filename
  self
end

#read_float64(io, cnt = 1) ⇒ Object

returns an array of Floats



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# File 'lib/ms/msrun/plms1.rb', line 66

def read_float64(io, cnt=1)
  io.read(cnt*8).unpack("E*")
end

#read_uint32(io, cnt = 1) ⇒ Object

returns an array of Integers



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# File 'lib/ms/msrun/plms1.rb', line 61

def read_uint32(io, cnt=1)
  io.read(cnt*4).unpack("V*")
end

#write(filename = nil) ⇒ Object

returns the string if no filename given



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# File 'lib/ms/msrun/plms1.rb', line 101

def write(filename=nil)
  out = 
    if filename
      File.open(filename,'w')
    else
      StringIO.new
    end
  write_uint32(out, spectra.size)
  write_uint32(out, scan_numbers)
  write_float64(out, times)
  spectra.each do |spectrum|
    write_uint32(out, spectrum.size)  # number of rows
    spectrum.each do |row|
      write_uint32(out, row.size)
      write_float64(out, row)
    end
  end
  if filename
    out.close
    filename
  else
    out.string
  end
end

#write_float64(out, data) ⇒ Object 



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# File 'lib/ms/msrun/plms1.rb', line 95

def write_float64(out, data)
  to_pack = data.is_a?(Array) ? data : [data]
  out << to_pack.pack('E*')
end

#write_uint32(out, data) ⇒ Object 



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# File 'lib/ms/msrun/plms1.rb', line 90

def write_uint32(out, data)
  to_pack = data.is_a?(Array) ? data : [data]
  out << to_pack.pack('V*')
end