Class: Ms::Msrun::Index

Inherits:
Array
  • Object
show all
Includes:
Enumerable
Defined in:
lib/ms/msrun/index.rb

Overview

an index by scan number of the doublets where each doublet = [start_byte, length] for the scan. Index objects are enumerable and yield doublets. Index#scan_nums gives an array of the scan numbers. Index#first and Index#last return the first and the last scan, regardless of the scan numbers.

index.scan_nums  # -> [1,2,3,4]
index.each do |starting_byte, length|
  IO.read(myfile.mzXML, length, starting_byte) # -> xml for each scan
end
index[0]         # -> nil
index.first      # -> [<start_byte>, <length>] # for scan number 1

Constant Summary collapse

MZXML_INDEX_TAG = 
'indexOffset'
MZML_INDEX_TAG = 
'indexListOffset'

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from Array

#sum

Constructor Details

#initialize(filename_or_io) ⇒ Index

takes an mzxml filename or io object and returns an array of offsets and lengths for the scans note that the offset



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# File 'lib/ms/msrun/index.rb', line 35

def initialize(filename_or_io)
  (ft, version) = Ms::Msrun.filetype_and_version(filename_or_io)
  tag = case ft
        when :mzml ; MZML_INDEX_TAG
        when :mzxml ; MZXML_INDEX_TAG
        end
  fn = 
    if filename_or_io.is_a? String
      filename_or_io  # a filename
    else # a File object
      filename_or_io.path
    end
  size = File.size(fn)
  io =
    if filename_or_io.is_a? String
      File.open(filename_or_io)
    else
      filename_or_io
    end
  (offset, length) = index_offset(io, size, tag)
  io.pos = offset
  xml = io.read(length)
  io.close if filename_or_io.is_a?(String)
  self.replace( index_to_array(xml, offset, ft) )
  self
end

Instance Attribute Details

#scan_nums ⇒ Object (readonly)

returns an array of the scan numbers



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# File 'lib/ms/msrun/index.rb', line 30

def scan_nums
  @scan_nums
end

Instance Method Details

#each(&block) ⇒ Object 



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# File 'lib/ms/msrun/index.rb', line 62

def each(&block)
  scan_nums.each do |scan_num|
    block.call( self[scan_num] )
  end
end

#first ⇒ Object 



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# File 'lib/ms/msrun/index.rb', line 68

def first
  self[scan_nums.first]
end

#header_length ⇒ Object

returns the length from the start to the first scan



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# File 'lib/ms/msrun/index.rb', line 25

def header_length
  self.each {|pair| return (pair.first) }
end

#index_offset(io, size, tag = MZML_INDEX_TAG, bytes_backwards = 150) ⇒ Object

returns [index_offset, length_of_index]



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# File 'lib/ms/msrun/index.rb', line 77

def index_offset(io, size, tag=MZML_INDEX_TAG, bytes_backwards=150) # :nodoc:
  tag_re = /<#{tag}>([\-\d]+)<\/#{tag}>/
    io.pos = size-1
  io.pos = io.pos - bytes_backwards
  index_offset = nil
  index_end = nil
  io.each do |line|
    if line =~ tag_re
      index_offset = $1.to_i
      index_end = io.pos - line.size
      break
    end
  end
  if index_offset
    [index_offset, index_end - index_offset]
  else
    [nil,nil]
  end
end

#index_to_array(xml_string, last_offset, type = :mzml) ⇒ Object

last_offset is used to calculate the length of the last scan object (or whatever)



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# File 'lib/ms/msrun/index.rb', line 99

def index_to_array(xml_string, last_offset, type=:mzml) # :nodoc:
  indices = []
  @scan_nums = []
  case type
  when :mzxml
    xml_string.each_line("\n") do |line|
      if line =~ /id="(\d+)".*>(\d+)</
        @scan_nums << $1.to_i
        indices << $2.to_i
      end
    end
    #doc = Nokogiri::XML.parse(xml_string, *Ms::Msrun::Nokogiri::PARSER_ARGS)
    #root_el = doc.root
    #raise RuntimeError, "expecting scan index!" unless root_el['name'] == 'scan'
    #root_el.children.each do |el|
    #  indices << el.text.to_i
    #  @scan_nums << el['id'].to_i
    #end
  when :mzml
    xml_string.each_line("\n") do |line|
      if line =~ /<offset idRef=".*scan=(\d+)".*>(\d+)</
        @scan_nums << $1.to_i
        indices << $2.to_i
      end
    end
  end
  indices << last_offset

  new_indices = []
  0.upto(indices.size-2) do |i|
    val = indices[i]
    next unless val
    new_indices[@scan_nums[i]] = [indices[i], indices[i+1] - indices[i]]
  end
  new_indices
end

#last ⇒ Object 



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# File 'lib/ms/msrun/index.rb', line 72

def last
  self[scan_nums.last]
end