Module: Ms::Data

Defined in:
lib/ms/data.rb,
lib/ms/data/simple.rb,
lib/ms/data/lazy_io.rb,
lib/ms/data/transposed.rb,
lib/ms/data/interleaved.rb,
lib/ms/data/lazy_string.rb

Overview

The Data module contains a number of classes providing a standard way to resolve various data storage formats into a ‘simple’ data array.

type               format
simple             [[mzs,...], [intensities...]]
transposed         [[mz,intensity], [mz,intensity], ...]
interleaved        [mz,intensity,mz,intensity,...]

For instance:

s = Data.new([[1,2,3], [4,5,6]], :simple)
s.resolve.data        # => [[1,2,3], [4,5,6]]

t = Data.new([[1,4],[2,5],[3,6]], :transposed)
t.resolve.data        # => [[1,2,3], [4,5,6]]

i = Data.new([1,4,2,5,3,6], :interleaved)
i.resolve.data        # => [[1,2,3], [4,5,6]]

Data is always resolved by calling to_a on the unresolved data object and then rearranging as needed (in the case of simple data, to_a is also called on each member of the unresolved data array). This lazy resolution allows the use of non-array unresolved_data objects such as Data::LazyString:

str = [[1,4,2,5,3,6].pack("g*")].pack("m")
unresolved_data = Data::LazyString.new(str)

i = Data.new(unresolved_data, :interleaved)
i.resolve.data        # => [[1,2,3], [4,5,6]]

Obviously the big advantage of lazy data resolution is that Data objects may be instantiated cheaply while expensive operations like unpacking and rearrangement may be put off or not executed at all.

Defined Under Namespace

Classes: Interleaved, LazyIO, LazyString, Simple, Transposed

Class Method Summary collapse

Class Method Details

.new(data, type = :simple) ⇒ Object

Initializes a new data array of the specified type by forwarding data to the “new_<type>” method.

simple = Ms::Data.new([[1,2,3], [4,5,6]], :simple)
simple.class           # => Ms::Data::Simple

interleaved = Ms::Data.new([1,4,2,5,3,6], :interleaved)
interleaved.class      # => Ms::Data::Interleaved



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# File 'lib/ms/data.rb', line 54

def new(data, type=:simple)
  send("new_#{type}", data)  
end

.new_interleaved(unresolved_data, n = 2) ⇒ Object

Initializes a new interleaved data array.



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# File 'lib/ms/data/interleaved.rb', line 8

def new_interleaved(unresolved_data, n=2)
  Interleaved.new(unresolved_data, n=2)
end

.new_simple(unresolved_data) ⇒ Object

Initializes a new simple data array.



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# File 'lib/ms/data/simple.rb', line 6

def new_simple(unresolved_data)
  Simple.new(unresolved_data)
end

.new_transposed(unresolved_data) ⇒ Object

Initializes a new transposed data array.



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# File 'lib/ms/data/transposed.rb', line 8

def new_transposed(unresolved_data)
  Transposed.new(unresolved_data)
end