mspire 0.6.22 → 0.6.24
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/Rakefile +2 -0
- data/VERSION +1 -1
- data/lib/ms/isotope.rb +93 -0
- data/lib/ms/isotope/aa.rb +2 -1
- data/lib/ms/isotope/nist_isotope_info.yml +2017 -0
- data/lib/ms/mzml.rb +0 -18
- data/lib/ms/mzml/data_array.rb +79 -11
- data/lib/ms/mzml/spectrum.rb +2 -3
- data/mspire.gemspec +14 -3
- data/script/mzml_read_binary.rb +34 -0
- data/spec/ms/isotope_spec.rb +31 -0
- data/spec/ms/mzml/data_array_spec.rb +38 -0
- data/spec/ms/mzml_spec.rb +5 -62
- data/spec/testfiles/ms/mzml/{mspire_simulated.noidx.check.mzML → mspire_simulated.MSn.check.mzML} +14 -4
- metadata +44 -17
data/Rakefile
CHANGED
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@@ -16,6 +16,8 @@ Jeweler::Tasks.new do |gem|
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gem.add_dependency "bsearch", ">= 1.5.0"
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gem.add_dependency "andand", ">= 1.3.1"
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gem.add_dependency "obo", ">= 0.1.0"
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gem.add_dependency "builder", ">= 3.0.0"
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gem.add_dependency "trollop", ">= 1.16.2"
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gem.add_development_dependency "rspec", "~> 2.6"
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gem.add_development_dependency "jeweler", "~> 1.5.2"
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gem.add_development_dependency "rcov", ">= 0"
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data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
0.6.
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1
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0.6.24
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data/lib/ms/isotope.rb
ADDED
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@@ -0,0 +1,93 @@
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require 'yaml'
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module MS
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class Isotope
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MEMBERS = [:atomic_number, :element, :mass_number, :atomic_mass, :relative_abundance, :average_mass, :mono]
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MEMBERS.each {|key| attr_accessor key }
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INFO_FILE = 'nist_isotope_info.yml'
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INFO_FILE_FULL_PATH = File.expand_path(File.dirname(__FILE__) + "/isotope/#{INFO_FILE}")
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def initialize(*args)
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MEMBERS.zip(args) {|k,val| self.send("#{k}=", val) }
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end
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# Creates an isotope from a nist entry. Sets mono to false, which is not
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# always correct (but needs to be corrected with additional info)
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def self.from_nist_line(*args)
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# atomic_number and mass_number are ints
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[0,2].each {|i| args[i] = args[i].to_i }
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# element is a downcase sym
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args[1] = args[1].downcase.to_sym
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# atomic_mass, relative_abundance, and average_mass as floats
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[3, 4, 5].each {|i| args[i] = args[i][/([\w.]*)/].to_f }
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# by default call every isotope the non-monoisotopic peak
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# (will correct it as a group)
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args << false
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self.new(*args)
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end
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if File.exist?(INFO_FILE_FULL_PATH)
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ISOTOPES = YAML.load_file(INFO_FILE_FULL_PATH).map {|ar| MS::Isotope.new *ar }
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BY_ELEMENT = ISOTOPES.group_by(&:element)
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else
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unless __FILE__ == $0
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warn "no file #{INFO_FILE_FULL_PATH} to read isotope information from"
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warn "directly running the file: #{__FILE__}"
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warn "will generate the file from NIST data"
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end
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end
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class Updater
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NIST_ISOTOPE_SITE = 'http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2&isotype=some'
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class << self
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def write_nist_info(filename)
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isotopes = isotopes_from_nist_site
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File.write(filename, isotopes.map {|isotope| MEMBERS.map {|key| isotope.send(key) }}.to_yaml)
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end
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def isotopes_from_nist_site(deuterium_is_kind_of_hydrogen=true)
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require 'mechanize'
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body = Mechanize.new.get(NIST_ISOTOPE_SITE).body.split("\n")
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body.delete_if {|l| l[/^(<|\/)/]}
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body.shift(22)
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isotopes = body.each_slice(8).map do |lines|
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arr = (1..4).to_a.map {|i| match lines[i] }
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rel, avg = match(lines[5]), match(lines[6])
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next if rel.nil?
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rel.size > 0 ? Isotope.from_nist_line(*arr, rel, avg) : nil
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end.compact!
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# deuterium should be grouped with hydrogen, not as its own element!
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isotopes.find {|iso| iso.element == :d }.element = :h if deuterium_is_kind_of_hydrogen
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# update the mono boolean if this is the highest abundance peak
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isotopes.group_by(&:element).values.each do |set|
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set.max_by(&:relative_abundance).mono = true
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end
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isotopes
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end
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private
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def match(string)
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unless string.nil?
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if string.empty?
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nil
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else
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string[/= (.*)/,1]
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end
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end
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end
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end
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end
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end
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end
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if __FILE__ == $0
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MS::Isotope::Updater.write_nist_info(MS::Isotope::INFO_FILE_FULL_PATH)
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end
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data/lib/ms/isotope/aa.rb
CHANGED
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@@ -0,0 +1,2017 @@
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---
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- - 1
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- :h
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- 1
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- 1.00782503207
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- 0.999885
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- 1.00794
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- true
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- - 1
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- :h
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- 2
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- 2.0141017778
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- 0.000115
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- 1.00794
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- false
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- - 2
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- :he
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- 3
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- 3.0160293191
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- 1.34e-06
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- 4.002602
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- false
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- - 2
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- :he
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- 4
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- 4.00260325415
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- 0.99999866
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- 4.002602
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- true
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- - 3
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- :li
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- 6
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- 6.015122795
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- 0.0759
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- 6.941
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- false
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- - 3
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- :li
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- 7
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- 7.01600455
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- 0.9241
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- 6.941
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- true
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- - 4
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- :be
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- 9
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- 9.0121822
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- 1.0
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- 9.012182
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- true
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- - 5
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- :b
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- 10
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- 10.012937
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- 0.199
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- 10.811
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- false
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- - 5
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- :b
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- 11
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- 11.0093054
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- 0.801
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- 10.811
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- true
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- - 6
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- :c
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- 12
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- 12.0
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- 0.9893
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- 12.0107
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- true
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- - 6
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- :c
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- 13
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- 13.0033548378
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- 0.0107
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- 12.0107
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- false
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- - 7
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- :n
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- 14
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- 14.0030740048
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- 0.99636
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- 14.0067
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- true
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- - 7
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- :n
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- 15
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- 15.0001088982
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- 0.00364
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- 14.0067
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- false
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- - 8
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- :o
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- 16
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- 15.99491461956
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- 0.99757
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- 15.9994
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- true
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100
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- - 8
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- :o
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102
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- 17
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103
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- 16.9991317
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104
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- 0.00038
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- 15.9994
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- false
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- - 8
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- :o
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- 18
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- 17.999161
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- 0.00205
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- 15.9994
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- false
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- - 9
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- :f
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- 19
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- 18.99840322
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- 1.0
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- 18.9984032
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- true
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- - 10
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- :ne
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- 20
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- 19.9924401754
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- 0.9048
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- 20.1797
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- true
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- - 10
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- :ne
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- 21
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- 20.99384668
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- 0.0027
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- 20.1797
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- false
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- - 10
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- :ne
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- 22
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- 21.991385114
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- 0.0925
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- 20.1797
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141
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- false
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142
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- - 11
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143
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- :na
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- 23
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- 22.9897692809
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- 1.0
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- 22.98976928
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- true
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- - 12
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- :mg
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- 24
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- 23.9850417
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153
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- 0.7899
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- 24.305
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- true
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- - 12
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- :mg
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- 25
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- 24.98583692
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- 0.1
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- 24.305
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- false
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163
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- - 12
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- :mg
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- 26
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- 25.982592929
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- 0.1101
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- 24.305
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- false
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- - 13
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- :al
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- 27
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- 26.98153863
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- 1.0
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- 26.9815386
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- true
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- - 14
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- :si
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- 28
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- 27.9769265325
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- 0.92223
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- 28.0855
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- true
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- - 14
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- :si
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- 29
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- 28.9764947
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- 0.04685
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- 28.0855
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- false
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- - 14
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- :si
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- 30
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- 29.97377017
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- 0.03092
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- 28.0855
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- false
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- - 15
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- :p
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- 31
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- 30.97376163
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- 1.0
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- 30.973762
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- true
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- - 16
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- :s
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- 32
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- 31.972071
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- 0.9499
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- 32.065
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- true
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- - 16
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- :s
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- 33
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- 32.97145876
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- 0.0075
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- 32.065
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- false
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- - 16
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- :s
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- 34
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- 33.9678669
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- 0.0425
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- 32.065
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- false
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- - 16
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- :s
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- 35.96708076
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- 0.0001
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- 32.065
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- false
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- - 17
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- :cl
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- 35
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- 34.96885268
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- :os
|
|
1782
|
+
- 186
|
|
1783
|
+
- 185.9538382
|
|
1784
|
+
- 0.0159
|
|
1785
|
+
- 190.23
|
|
1786
|
+
- false
|
|
1787
|
+
- - 76
|
|
1788
|
+
- :os
|
|
1789
|
+
- 187
|
|
1790
|
+
- 186.9557505
|
|
1791
|
+
- 0.0196
|
|
1792
|
+
- 190.23
|
|
1793
|
+
- false
|
|
1794
|
+
- - 76
|
|
1795
|
+
- :os
|
|
1796
|
+
- 188
|
|
1797
|
+
- 187.9558382
|
|
1798
|
+
- 0.1324
|
|
1799
|
+
- 190.23
|
|
1800
|
+
- false
|
|
1801
|
+
- - 76
|
|
1802
|
+
- :os
|
|
1803
|
+
- 189
|
|
1804
|
+
- 188.9581475
|
|
1805
|
+
- 0.1615
|
|
1806
|
+
- 190.23
|
|
1807
|
+
- false
|
|
1808
|
+
- - 76
|
|
1809
|
+
- :os
|
|
1810
|
+
- 190
|
|
1811
|
+
- 189.958447
|
|
1812
|
+
- 0.2626
|
|
1813
|
+
- 190.23
|
|
1814
|
+
- false
|
|
1815
|
+
- - 76
|
|
1816
|
+
- :os
|
|
1817
|
+
- 192
|
|
1818
|
+
- 191.9614807
|
|
1819
|
+
- 0.4078
|
|
1820
|
+
- 190.23
|
|
1821
|
+
- true
|
|
1822
|
+
- - 77
|
|
1823
|
+
- :ir
|
|
1824
|
+
- 191
|
|
1825
|
+
- 190.960594
|
|
1826
|
+
- 0.373
|
|
1827
|
+
- 192.217
|
|
1828
|
+
- false
|
|
1829
|
+
- - 77
|
|
1830
|
+
- :ir
|
|
1831
|
+
- 193
|
|
1832
|
+
- 192.9629264
|
|
1833
|
+
- 0.627
|
|
1834
|
+
- 192.217
|
|
1835
|
+
- true
|
|
1836
|
+
- - 78
|
|
1837
|
+
- :pt
|
|
1838
|
+
- 190
|
|
1839
|
+
- 189.959932
|
|
1840
|
+
- 0.00014
|
|
1841
|
+
- 195.084
|
|
1842
|
+
- false
|
|
1843
|
+
- - 78
|
|
1844
|
+
- :pt
|
|
1845
|
+
- 192
|
|
1846
|
+
- 191.961038
|
|
1847
|
+
- 0.00782
|
|
1848
|
+
- 195.084
|
|
1849
|
+
- false
|
|
1850
|
+
- - 78
|
|
1851
|
+
- :pt
|
|
1852
|
+
- 194
|
|
1853
|
+
- 193.9626803
|
|
1854
|
+
- 0.32967
|
|
1855
|
+
- 195.084
|
|
1856
|
+
- false
|
|
1857
|
+
- - 78
|
|
1858
|
+
- :pt
|
|
1859
|
+
- 195
|
|
1860
|
+
- 194.9647911
|
|
1861
|
+
- 0.33832
|
|
1862
|
+
- 195.084
|
|
1863
|
+
- true
|
|
1864
|
+
- - 78
|
|
1865
|
+
- :pt
|
|
1866
|
+
- 196
|
|
1867
|
+
- 195.9649515
|
|
1868
|
+
- 0.25242
|
|
1869
|
+
- 195.084
|
|
1870
|
+
- false
|
|
1871
|
+
- - 78
|
|
1872
|
+
- :pt
|
|
1873
|
+
- 198
|
|
1874
|
+
- 197.967893
|
|
1875
|
+
- 0.07163
|
|
1876
|
+
- 195.084
|
|
1877
|
+
- false
|
|
1878
|
+
- - 79
|
|
1879
|
+
- :au
|
|
1880
|
+
- 197
|
|
1881
|
+
- 196.9665687
|
|
1882
|
+
- 1.0
|
|
1883
|
+
- 196.966569
|
|
1884
|
+
- true
|
|
1885
|
+
- - 80
|
|
1886
|
+
- :hg
|
|
1887
|
+
- 196
|
|
1888
|
+
- 195.965833
|
|
1889
|
+
- 0.0015
|
|
1890
|
+
- 200.59
|
|
1891
|
+
- false
|
|
1892
|
+
- - 80
|
|
1893
|
+
- :hg
|
|
1894
|
+
- 198
|
|
1895
|
+
- 197.966769
|
|
1896
|
+
- 0.0997
|
|
1897
|
+
- 200.59
|
|
1898
|
+
- false
|
|
1899
|
+
- - 80
|
|
1900
|
+
- :hg
|
|
1901
|
+
- 199
|
|
1902
|
+
- 198.9682799
|
|
1903
|
+
- 0.1687
|
|
1904
|
+
- 200.59
|
|
1905
|
+
- false
|
|
1906
|
+
- - 80
|
|
1907
|
+
- :hg
|
|
1908
|
+
- 200
|
|
1909
|
+
- 199.968326
|
|
1910
|
+
- 0.231
|
|
1911
|
+
- 200.59
|
|
1912
|
+
- false
|
|
1913
|
+
- - 80
|
|
1914
|
+
- :hg
|
|
1915
|
+
- 201
|
|
1916
|
+
- 200.9703023
|
|
1917
|
+
- 0.1318
|
|
1918
|
+
- 200.59
|
|
1919
|
+
- false
|
|
1920
|
+
- - 80
|
|
1921
|
+
- :hg
|
|
1922
|
+
- 202
|
|
1923
|
+
- 201.970643
|
|
1924
|
+
- 0.2986
|
|
1925
|
+
- 200.59
|
|
1926
|
+
- true
|
|
1927
|
+
- - 80
|
|
1928
|
+
- :hg
|
|
1929
|
+
- 204
|
|
1930
|
+
- 203.9734939
|
|
1931
|
+
- 0.0687
|
|
1932
|
+
- 200.59
|
|
1933
|
+
- false
|
|
1934
|
+
- - 81
|
|
1935
|
+
- :tl
|
|
1936
|
+
- 203
|
|
1937
|
+
- 202.9723442
|
|
1938
|
+
- 0.2952
|
|
1939
|
+
- 204.3833
|
|
1940
|
+
- false
|
|
1941
|
+
- - 81
|
|
1942
|
+
- :tl
|
|
1943
|
+
- 205
|
|
1944
|
+
- 204.9744275
|
|
1945
|
+
- 0.7048
|
|
1946
|
+
- 204.3833
|
|
1947
|
+
- true
|
|
1948
|
+
- - 82
|
|
1949
|
+
- :pb
|
|
1950
|
+
- 204
|
|
1951
|
+
- 203.9730436
|
|
1952
|
+
- 0.014
|
|
1953
|
+
- 207.2
|
|
1954
|
+
- false
|
|
1955
|
+
- - 82
|
|
1956
|
+
- :pb
|
|
1957
|
+
- 206
|
|
1958
|
+
- 205.9744653
|
|
1959
|
+
- 0.241
|
|
1960
|
+
- 207.2
|
|
1961
|
+
- false
|
|
1962
|
+
- - 82
|
|
1963
|
+
- :pb
|
|
1964
|
+
- 207
|
|
1965
|
+
- 206.9758969
|
|
1966
|
+
- 0.221
|
|
1967
|
+
- 207.2
|
|
1968
|
+
- false
|
|
1969
|
+
- - 82
|
|
1970
|
+
- :pb
|
|
1971
|
+
- 208
|
|
1972
|
+
- 207.9766521
|
|
1973
|
+
- 0.524
|
|
1974
|
+
- 207.2
|
|
1975
|
+
- true
|
|
1976
|
+
- - 83
|
|
1977
|
+
- :bi
|
|
1978
|
+
- 209
|
|
1979
|
+
- 208.9803987
|
|
1980
|
+
- 1.0
|
|
1981
|
+
- 208.9804
|
|
1982
|
+
- true
|
|
1983
|
+
- - 90
|
|
1984
|
+
- :th
|
|
1985
|
+
- 232
|
|
1986
|
+
- 232.0380553
|
|
1987
|
+
- 1.0
|
|
1988
|
+
- 232.03806
|
|
1989
|
+
- true
|
|
1990
|
+
- - 91
|
|
1991
|
+
- :pa
|
|
1992
|
+
- 231
|
|
1993
|
+
- 231.035884
|
|
1994
|
+
- 1.0
|
|
1995
|
+
- 231.03588
|
|
1996
|
+
- true
|
|
1997
|
+
- - 92
|
|
1998
|
+
- :u
|
|
1999
|
+
- 234
|
|
2000
|
+
- 234.0409521
|
|
2001
|
+
- 5.4e-05
|
|
2002
|
+
- 238.02891
|
|
2003
|
+
- false
|
|
2004
|
+
- - 92
|
|
2005
|
+
- :u
|
|
2006
|
+
- 235
|
|
2007
|
+
- 235.0439299
|
|
2008
|
+
- 0.007204
|
|
2009
|
+
- 238.02891
|
|
2010
|
+
- false
|
|
2011
|
+
- - 92
|
|
2012
|
+
- :u
|
|
2013
|
+
- 238
|
|
2014
|
+
- 238.0507882
|
|
2015
|
+
- 0.992742
|
|
2016
|
+
- 238.02891
|
|
2017
|
+
- true
|