Class: Combiner

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

Constant Summary collapse

Defaults = 
{:bin_window => 0.1, :window_size => 4, :precursor_mass_tolerance_in_ppm =>	10, :tolerant => false}

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(spectra = nil, opts = {}) ⇒ Combiner

Returns a new instance of Combiner.



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# File 'lib/spectral_summing.rb', line 35

def initialize(spectra = nil, opts = {})
	@spectra = spectra
	@opts = Defaults.merge(opts)
end

Instance Attribute Details

#output_spectra ⇒ Object

Returns the value of attribute output_spectra.



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# File 'lib/spectral_summing.rb', line 34

def output_spectra
  @output_spectra
end

Instance Method Details

#calculate_daltons_from_ppm(mass, ppm) ⇒ Object 



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# File 'lib/spectral_summing.rb', line 93

def calculate_daltons_from_ppm(mass, ppm)
	diff = ppm*mass/1e6
	(mass-diff)..(mass+diff)
end

#combine(spectrum1, spectrum2) ⇒ Object 



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# File 'lib/spectral_summing.rb', line 39

def combine(spectrum1, spectrum2)
	tolerance = calculate_daltons_from_ppm(spectrum1.precursor_mass, @opts[:precursor_mass_tolerance_in_ppm] )
	if tolerance.include?(spectrum2.precursor_mass) or @opts[:tolerant]
		data_arr = summer(spectrum1.mz_values, spectrum1.intensities, spectrum2.mz_values, spectrum2.intensities)
	end
	data_arr
end

#combine_for_more_combining(spectrum1, spectrum2) ⇒ Object 



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# File 'lib/spectral_summing.rb', line 84

def combine_for_more_combining(spectrum1, spectrum2)
	arr = combine(spectrum1, spectrum2)
	joined_spectrum = Spectrum.new()
	joined_spectrum.precursor_mass = (spectrum1.precursor_mass + spectrum2.precursor_mass)/2.0
	joined_spectrum.mz_values = arr.first
	joined_spectrum.intensities = arr.last
# Spectrum = Struct.new(:spectrum, :scan_num, :scan_time, :scan_range, :precursor_mass, :charge_states, :intensities, :mz_values)
	joined_spectrum
end

#combine_to_mgf(spectrum1, spectrum2, filename) ⇒ Object

Thanks JOHN!!! Ms-Msrun 0.3.6



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# File 'lib/spectral_summing.rb', line 110

def combine_to_mgf(spectrum1, spectrum2, filename)   # Thanks JOHN!!! Ms-Msrun 0.3.6
	results = combine(spectrum1, spectrum2)
	File.open(filename, 'w') do |out|
		out.puts "BEGIN IONS"
		out.puts "TITLE=Spec1:#{spectrum1.precursor_mass}_Spec2:#{spectrum2.precursor_mass}.#{spectrum1.scan_num}_#{spectrum2.scan_num}_#{spectrum1.charge_states.first}"
		out.puts "CHARGE=#{spectrum1.charge_states.to_s}+"
		# our current mzML parser doesn't have scan.time implemented...
		results.first.each_with_index do |mz, i|
			intensity = results.last[i]
			out.puts "#{"%.5f" % mz}/t#{"%.5f" % intensity}" unless intensity == 0
		end
		out.puts "END IONS"
	end
end

#summer(x1, y1, x2, y2) ⇒ Object

What should this return?



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# File 'lib/spectral_summing.rb', line 46

def summer(x1,y1,x2,y2) # What should this return?
	endpoints = (x1+x2).each.minmax
	bin_width = @opts[:bin_window]
	num_bins = ((endpoints.last - endpoints.first)/bin_width).ceil
	data_x = [endpoints.first+bin_width/2.0]
	data_y = Array.new(num_bins, 0)
	j, k = 0,0
	one = [x1,y1]; two = [x2,y2]
	if x1.first == endpoints.first
		data_x[0] = x1.first
		data_y[0] += y1.first
		y1[0] = 0
	elsif x2.first == endpoints.first
		data_x[0] = x2.first
		data_y[0] += y2.first
		y2[0] = 0
	end
	(1..num_bins-1).each do |i|
		data_x[i] = data_x[i-1] + bin_width 
		check = data_x[i] + bin_width/2.0
		#puts "check= #{check}"
		if one.first[j]
			while one.first[j] < check 
				data_y[i] += one.last[j]
				j += 1
				break if one.first[j].nil?
			end
		end
		if two.first[k]
			while two.first[k] < check
				data_y[i] += two.last[k]
				k += 1
				break if two.first[k].nil?
			end
		end
	end
	[data_x, data_y]
end

#to_mgf(spectrum, filename) ⇒ Object 



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# File 'lib/spectral_summing.rb', line 97

def to_mgf(spectrum, filename)
	File.open(filename,'w') do |out|
		out.puts "BEGIN IONS"
		out.puts "TITLE=Spec1:#{spectrum.precursor_mass}_#{spectrum.charge_states.first}"
		out.puts "CHARGE=#{spectrum.charge_states.to_s}+"
		# our current mzML parser doesn't have scan.time implemented...
		spectrum.mz_values.each_with_index do |mz, i|
			intensity = spectrum.intensities[i]
			out.puts "#{"%.5f" % mz}/t#{"%.5f" % intensity}" unless intensity == 0
		end
		out.puts "END IONS"
	end
end