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Versions: 14
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Contents
require 'mspire/plms1'
module Mspire
class Mzml
# will use scan numbers if use_scan_nums is true, otherwise it will use index
# numbers in place of scan nums
def to_plms1(use_scan_nums=true)
spectrum_index_list = self.index_list[:spectrum]
scan_nums =
if use_scan_nums
spectrum_index_list.create_scan_to_index.keys
else
(0...spectrum_index_list.size).to_a
end
retention_times = self.enum_for(:each_spectrum_node).map do |xml_node|
rt_xml_node=xml_node.xpath("scanList/scan/cvParam[@accession='MS:1000016']")[0]
raise 'no retention time xml node' unless rt_xml_node
retention_time = rt_xml_node['value'].to_f
case rt_xml_node['unitName']
when 'minute'
retention_time * 60
when 'second'
retention_time
else
raise 'retention time must be in minutes or seconds (or add some code to handle)'
end
end
# plms1 only requires that the obect respond to :each, giving a spectrum
# object, so an Mzml object will work.
Mspire::Plms1.new(scan_nums, retention_times, self)
end
end
end
Version data entries
14 entries across 14 versions & 1 rubygems