Class: Ms::Spectrum

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/ms/spectrum.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(data) ⇒ Ms::Spectrum

data takes an array: [mzs, intensities]

Parameters:

  • data (Array) —

    two element array of mzs and intensities



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# File 'lib/ms/spectrum.rb', line 11

def initialize(data)
  @data = data
end

Instance Attribute Details

#data ⇒ Object (readonly)

The underlying data store.



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# File 'lib/ms/spectrum.rb', line 6

def data
  @data
end

Class Method Details

.from_peaks(ar_of_doublets) ⇒ Object 



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# File 'lib/ms/spectrum.rb', line 15

def self.from_peaks(ar_of_doublets)
  _mzs = []
  _ints = []
  ar_of_doublets.each do |mz, int|
    _mzs << mz
    _ints << int
  end
  self.new([_mzs, _ints])
end

Instance Method Details

#==(other) ⇒ Object

if the mzs and intensities are the same then the spectra are considered equal



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# File 'lib/ms/spectrum.rb', line 55

def ==(other)
  mzs == other.mzs && intensities == other.intensities
end

#[](array_index) ⇒ Object

retrieve an m/z and intensity doublet at that index



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# File 'lib/ms/spectrum.rb', line 40

def [](array_index)
  [mzs[array_index], intensities[array_index]]
end

#intensities ⇒ Object

An array of the intensities data, corresponding to mzs.



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# File 'lib/ms/spectrum.rb', line 31

def intensities
  @data[1]
end

#mzs ⇒ Object

An array of the mz data.



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# File 'lib/ms/spectrum.rb', line 26

def mzs
  @data[0]
end

#mzs_and_intensities ⇒ Object 



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# File 'lib/ms/spectrum.rb', line 35

def mzs_and_intensities
  [@data[0], @data[1]]
end

#normalize ⇒ Object

returns a new spectrum whose intensities have been normalized by the tic



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# File 'lib/ms/spectrum.rb', line 60

def normalize
  tic = self.intensities.inject(0.0) {|sum,int| sum += int }
  Ms::Spectrum.new([self.mzs, self.intensities.map {|v| v / tic }])
end

#peaks(&block) ⇒ Object Also known as: each, each_peak

yields(mz, inten) across the spectrum, or array of doublets if no block



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# File 'lib/ms/spectrum.rb', line 45

def peaks(&block)
  (m, i) = mzs_and_intensities
  m.zip(i, &block)
end