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Contents
require 'mspire/mzml/parser'
require 'mspire/mzml/spectrum'
require 'mspire/mzml/chromatogram'
module Mspire
class Mzml
# an index that retrieves its objects on the fly by index from the IO object.
class IOIndex
include Enumerable
attr_reader :io
attr_reader :byte_index
# hash of relevant hashes and objects for linking
attr_accessor :link
# byte_index will typically be an Mspire::Mzml::Index object.
#
# link will have the following keys:
#
# :ref_hash
# :data_processing_hash
# :(<sample>|<chromatogram>)_default_data_processing
#
# may have:
#
# :source_file_hash
#
def initialize(io, byte_index, link)
@io, @byte_index, @link = io, byte_index, link
@object_class = Mspire::Mzml.const_get(@byte_index.name.to_s.capitalize)
@closetag_regexp = %r{</#{name}>}
end
def name
@byte_index.name
end
def each(&block)
return to_enum(__method__) unless block
(0...byte_index.size).each do |int|
block.call(self[int])
end
end
def [](index)
@object_class.from_xml(fetch_xml_node(index), @link)
end
def length
@byte_index.length
end
alias_method :size, :length
# gets the data string through to last element
def get_xml_string(start_byte)
@io.seek(start_byte)
data = ""
@io.each_line do |line|
data << line
break if @closetag_regexp.match(line)
end
data
end
def xml_node_from_start_byte(start_byte)
xml = get_xml_string(start_byte)
Nokogiri::XML.parse(xml, nil, @encoding, Parser::NOBLANKS).root
end
def fetch_xml_node(index)
xml_node_from_start_byte(byte_index[index])
end
end
end
end
Version data entries
14 entries across 14 versions & 1 rubygems