Class: Parser

Inherits:
Object
  • Object
show all
Defined in:
lib/spectral_summing.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(file) ⇒ Parser

Returns a new instance of Parser.



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# File 'lib/spectral_summing.rb', line 5

def initialize(file)
	@file = file
end

Instance Attribute Details

#spectra ⇒ Object

Returns the value of attribute spectra.



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# File 'lib/spectral_summing.rb', line 4

def spectra
  @spectra
end

Instance Method Details

#parse(file = nil) ⇒ Object 



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# File 'lib/spectral_summing.rb', line 8

def parse(file = nil)
	file ||= @file
	require 'ms/msrun'
	@spectra = []
	Ms::Msrun.open(file) do |ms|
		ms.each(:ms_level => 2) do |scan|
			@spectra << Spectrum.new(scan, scan.num, scan.time, (scan.start_mz..scan.end_mz), scan.precursor.mz, scan.precursor.charge_states, scan.spectrum.intensities, scan.spectrum.mzs)
		end
	end
end

#parse_by_scan_num(scan_nums, file = nil) ⇒ Object 



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# File 'lib/spectral_summing.rb', line 18

def parse_by_scan_num(scan_nums, file = nil)
	file ||= @file
	require 'ms/msrun'
	@spectra = []
	Ms::Msrun.open(file) do |ms|
		ms.each(:ms_level => 2) do |scan|
			if scan_nums.include?(scan.num)
				@spectra << Spectrum.new(scan, scan.num, scan.time, (scan.start_mz..scan.end_mz), scan.precursor.mz, scan.precursor.charge_states, scan.spectrum.intensities, scan.spectrum.mzs)
			end
		end
	end
end