mspire 0.6.22 → 0.6.24
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- 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
@@ -16,6 +16,8 @@ Jeweler::Tasks.new do |gem|
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|
16
16
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gem.add_dependency "bsearch", ">= 1.5.0"
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17
17
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gem.add_dependency "andand", ">= 1.3.1"
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18
18
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gem.add_dependency "obo", ">= 0.1.0"
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19
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+
gem.add_dependency "builder", ">= 3.0.0"
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20
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+
gem.add_dependency "trollop", ">= 1.16.2"
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19
21
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gem.add_development_dependency "rspec", "~> 2.6"
|
20
22
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gem.add_development_dependency "jeweler", "~> 1.5.2"
|
21
23
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gem.add_development_dependency "rcov", ">= 0"
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
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
@@ -0,0 +1,93 @@
|
|
1
|
+
require 'yaml'
|
2
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+
|
3
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+
module MS
|
4
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+
class Isotope
|
5
|
+
MEMBERS = [:atomic_number, :element, :mass_number, :atomic_mass, :relative_abundance, :average_mass, :mono]
|
6
|
+
MEMBERS.each {|key| attr_accessor key }
|
7
|
+
|
8
|
+
INFO_FILE = 'nist_isotope_info.yml'
|
9
|
+
INFO_FILE_FULL_PATH = File.expand_path(File.dirname(__FILE__) + "/isotope/#{INFO_FILE}")
|
10
|
+
|
11
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+
|
12
|
+
def initialize(*args)
|
13
|
+
MEMBERS.zip(args) {|k,val| self.send("#{k}=", val) }
|
14
|
+
end
|
15
|
+
|
16
|
+
# Creates an isotope from a nist entry. Sets mono to false, which is not
|
17
|
+
# always correct (but needs to be corrected with additional info)
|
18
|
+
def self.from_nist_line(*args)
|
19
|
+
# atomic_number and mass_number are ints
|
20
|
+
[0,2].each {|i| args[i] = args[i].to_i }
|
21
|
+
# element is a downcase sym
|
22
|
+
args[1] = args[1].downcase.to_sym
|
23
|
+
# atomic_mass, relative_abundance, and average_mass as floats
|
24
|
+
[3, 4, 5].each {|i| args[i] = args[i][/([\w.]*)/].to_f }
|
25
|
+
# by default call every isotope the non-monoisotopic peak
|
26
|
+
# (will correct it as a group)
|
27
|
+
args << false
|
28
|
+
self.new(*args)
|
29
|
+
end
|
30
|
+
|
31
|
+
if File.exist?(INFO_FILE_FULL_PATH)
|
32
|
+
|
33
|
+
ISOTOPES = YAML.load_file(INFO_FILE_FULL_PATH).map {|ar| MS::Isotope.new *ar }
|
34
|
+
BY_ELEMENT = ISOTOPES.group_by(&:element)
|
35
|
+
|
36
|
+
else
|
37
|
+
unless __FILE__ == $0
|
38
|
+
warn "no file #{INFO_FILE_FULL_PATH} to read isotope information from"
|
39
|
+
warn "directly running the file: #{__FILE__}"
|
40
|
+
warn "will generate the file from NIST data"
|
41
|
+
end
|
42
|
+
end
|
43
|
+
|
44
|
+
class Updater
|
45
|
+
NIST_ISOTOPE_SITE = 'http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2&isotype=some'
|
46
|
+
class << self
|
47
|
+
|
48
|
+
def write_nist_info(filename)
|
49
|
+
isotopes = isotopes_from_nist_site
|
50
|
+
File.write(filename, isotopes.map {|isotope| MEMBERS.map {|key| isotope.send(key) }}.to_yaml)
|
51
|
+
end
|
52
|
+
|
53
|
+
def isotopes_from_nist_site(deuterium_is_kind_of_hydrogen=true)
|
54
|
+
require 'mechanize'
|
55
|
+
body = Mechanize.new.get(NIST_ISOTOPE_SITE).body.split("\n")
|
56
|
+
body.delete_if {|l| l[/^(<|\/)/]}
|
57
|
+
body.shift(22)
|
58
|
+
isotopes = body.each_slice(8).map do |lines|
|
59
|
+
arr = (1..4).to_a.map {|i| match lines[i] }
|
60
|
+
rel, avg = match(lines[5]), match(lines[6])
|
61
|
+
next if rel.nil?
|
62
|
+
rel.size > 0 ? Isotope.from_nist_line(*arr, rel, avg) : nil
|
63
|
+
end.compact!
|
64
|
+
|
65
|
+
# deuterium should be grouped with hydrogen, not as its own element!
|
66
|
+
isotopes.find {|iso| iso.element == :d }.element = :h if deuterium_is_kind_of_hydrogen
|
67
|
+
|
68
|
+
# update the mono boolean if this is the highest abundance peak
|
69
|
+
isotopes.group_by(&:element).values.each do |set|
|
70
|
+
set.max_by(&:relative_abundance).mono = true
|
71
|
+
end
|
72
|
+
isotopes
|
73
|
+
end
|
74
|
+
|
75
|
+
private
|
76
|
+
|
77
|
+
def match(string)
|
78
|
+
unless string.nil?
|
79
|
+
if string.empty?
|
80
|
+
nil
|
81
|
+
else
|
82
|
+
string[/= (.*)/,1]
|
83
|
+
end
|
84
|
+
end
|
85
|
+
end
|
86
|
+
end
|
87
|
+
end
|
88
|
+
end
|
89
|
+
end
|
90
|
+
|
91
|
+
if __FILE__ == $0
|
92
|
+
MS::Isotope::Updater.write_nist_info(MS::Isotope::INFO_FILE_FULL_PATH)
|
93
|
+
end
|
data/lib/ms/isotope/aa.rb
CHANGED
@@ -0,0 +1,2017 @@
|
|
1
|
+
---
|
2
|
+
- - 1
|
3
|
+
- :h
|
4
|
+
- 1
|
5
|
+
- 1.00782503207
|
6
|
+
- 0.999885
|
7
|
+
- 1.00794
|
8
|
+
- true
|
9
|
+
- - 1
|
10
|
+
- :h
|
11
|
+
- 2
|
12
|
+
- 2.0141017778
|
13
|
+
- 0.000115
|
14
|
+
- 1.00794
|
15
|
+
- false
|
16
|
+
- - 2
|
17
|
+
- :he
|
18
|
+
- 3
|
19
|
+
- 3.0160293191
|
20
|
+
- 1.34e-06
|
21
|
+
- 4.002602
|
22
|
+
- false
|
23
|
+
- - 2
|
24
|
+
- :he
|
25
|
+
- 4
|
26
|
+
- 4.00260325415
|
27
|
+
- 0.99999866
|
28
|
+
- 4.002602
|
29
|
+
- true
|
30
|
+
- - 3
|
31
|
+
- :li
|
32
|
+
- 6
|
33
|
+
- 6.015122795
|
34
|
+
- 0.0759
|
35
|
+
- 6.941
|
36
|
+
- false
|
37
|
+
- - 3
|
38
|
+
- :li
|
39
|
+
- 7
|
40
|
+
- 7.01600455
|
41
|
+
- 0.9241
|
42
|
+
- 6.941
|
43
|
+
- true
|
44
|
+
- - 4
|
45
|
+
- :be
|
46
|
+
- 9
|
47
|
+
- 9.0121822
|
48
|
+
- 1.0
|
49
|
+
- 9.012182
|
50
|
+
- true
|
51
|
+
- - 5
|
52
|
+
- :b
|
53
|
+
- 10
|
54
|
+
- 10.012937
|
55
|
+
- 0.199
|
56
|
+
- 10.811
|
57
|
+
- false
|
58
|
+
- - 5
|
59
|
+
- :b
|
60
|
+
- 11
|
61
|
+
- 11.0093054
|
62
|
+
- 0.801
|
63
|
+
- 10.811
|
64
|
+
- true
|
65
|
+
- - 6
|
66
|
+
- :c
|
67
|
+
- 12
|
68
|
+
- 12.0
|
69
|
+
- 0.9893
|
70
|
+
- 12.0107
|
71
|
+
- true
|
72
|
+
- - 6
|
73
|
+
- :c
|
74
|
+
- 13
|
75
|
+
- 13.0033548378
|
76
|
+
- 0.0107
|
77
|
+
- 12.0107
|
78
|
+
- false
|
79
|
+
- - 7
|
80
|
+
- :n
|
81
|
+
- 14
|
82
|
+
- 14.0030740048
|
83
|
+
- 0.99636
|
84
|
+
- 14.0067
|
85
|
+
- true
|
86
|
+
- - 7
|
87
|
+
- :n
|
88
|
+
- 15
|
89
|
+
- 15.0001088982
|
90
|
+
- 0.00364
|
91
|
+
- 14.0067
|
92
|
+
- false
|
93
|
+
- - 8
|
94
|
+
- :o
|
95
|
+
- 16
|
96
|
+
- 15.99491461956
|
97
|
+
- 0.99757
|
98
|
+
- 15.9994
|
99
|
+
- true
|
100
|
+
- - 8
|
101
|
+
- :o
|
102
|
+
- 17
|
103
|
+
- 16.9991317
|
104
|
+
- 0.00038
|
105
|
+
- 15.9994
|
106
|
+
- false
|
107
|
+
- - 8
|
108
|
+
- :o
|
109
|
+
- 18
|
110
|
+
- 17.999161
|
111
|
+
- 0.00205
|
112
|
+
- 15.9994
|
113
|
+
- false
|
114
|
+
- - 9
|
115
|
+
- :f
|
116
|
+
- 19
|
117
|
+
- 18.99840322
|
118
|
+
- 1.0
|
119
|
+
- 18.9984032
|
120
|
+
- true
|
121
|
+
- - 10
|
122
|
+
- :ne
|
123
|
+
- 20
|
124
|
+
- 19.9924401754
|
125
|
+
- 0.9048
|
126
|
+
- 20.1797
|
127
|
+
- true
|
128
|
+
- - 10
|
129
|
+
- :ne
|
130
|
+
- 21
|
131
|
+
- 20.99384668
|
132
|
+
- 0.0027
|
133
|
+
- 20.1797
|
134
|
+
- false
|
135
|
+
- - 10
|
136
|
+
- :ne
|
137
|
+
- 22
|
138
|
+
- 21.991385114
|
139
|
+
- 0.0925
|
140
|
+
- 20.1797
|
141
|
+
- false
|
142
|
+
- - 11
|
143
|
+
- :na
|
144
|
+
- 23
|
145
|
+
- 22.9897692809
|
146
|
+
- 1.0
|
147
|
+
- 22.98976928
|
148
|
+
- true
|
149
|
+
- - 12
|
150
|
+
- :mg
|
151
|
+
- 24
|
152
|
+
- 23.9850417
|
153
|
+
- 0.7899
|
154
|
+
- 24.305
|
155
|
+
- true
|
156
|
+
- - 12
|
157
|
+
- :mg
|
158
|
+
- 25
|
159
|
+
- 24.98583692
|
160
|
+
- 0.1
|
161
|
+
- 24.305
|
162
|
+
- false
|
163
|
+
- - 12
|
164
|
+
- :mg
|
165
|
+
- 26
|
166
|
+
- 25.982592929
|
167
|
+
- 0.1101
|
168
|
+
- 24.305
|
169
|
+
- false
|
170
|
+
- - 13
|
171
|
+
- :al
|
172
|
+
- 27
|
173
|
+
- 26.98153863
|
174
|
+
- 1.0
|
175
|
+
- 26.9815386
|
176
|
+
- true
|
177
|
+
- - 14
|
178
|
+
- :si
|
179
|
+
- 28
|
180
|
+
- 27.9769265325
|
181
|
+
- 0.92223
|
182
|
+
- 28.0855
|
183
|
+
- true
|
184
|
+
- - 14
|
185
|
+
- :si
|
186
|
+
- 29
|
187
|
+
- 28.9764947
|
188
|
+
- 0.04685
|
189
|
+
- 28.0855
|
190
|
+
- false
|
191
|
+
- - 14
|
192
|
+
- :si
|
193
|
+
- 30
|
194
|
+
- 29.97377017
|
195
|
+
- 0.03092
|
196
|
+
- 28.0855
|
197
|
+
- false
|
198
|
+
- - 15
|
199
|
+
- :p
|
200
|
+
- 31
|
201
|
+
- 30.97376163
|
202
|
+
- 1.0
|
203
|
+
- 30.973762
|
204
|
+
- true
|
205
|
+
- - 16
|
206
|
+
- :s
|
207
|
+
- 32
|
208
|
+
- 31.972071
|
209
|
+
- 0.9499
|
210
|
+
- 32.065
|
211
|
+
- true
|
212
|
+
- - 16
|
213
|
+
- :s
|
214
|
+
- 33
|
215
|
+
- 32.97145876
|
216
|
+
- 0.0075
|
217
|
+
- 32.065
|
218
|
+
- false
|
219
|
+
- - 16
|
220
|
+
- :s
|
221
|
+
- 34
|
222
|
+
- 33.9678669
|
223
|
+
- 0.0425
|
224
|
+
- 32.065
|
225
|
+
- false
|
226
|
+
- - 16
|
227
|
+
- :s
|
228
|
+
- 36
|
229
|
+
- 35.96708076
|
230
|
+
- 0.0001
|
231
|
+
- 32.065
|
232
|
+
- false
|
233
|
+
- - 17
|
234
|
+
- :cl
|
235
|
+
- 35
|
236
|
+
- 34.96885268
|
237
|
+
- 0.7576
|
238
|
+
- 35.453
|
239
|
+
- true
|
240
|
+
- - 17
|
241
|
+
- :cl
|
242
|
+
- 37
|
243
|
+
- 36.96590259
|
244
|
+
- 0.2424
|
245
|
+
- 35.453
|
246
|
+
- false
|
247
|
+
- - 18
|
248
|
+
- :ar
|
249
|
+
- 36
|
250
|
+
- 35.967545106
|
251
|
+
- 0.003365
|
252
|
+
- 39.948
|
253
|
+
- false
|
254
|
+
- - 18
|
255
|
+
- :ar
|
256
|
+
- 38
|
257
|
+
- 37.9627324
|
258
|
+
- 0.000632
|
259
|
+
- 39.948
|
260
|
+
- false
|
261
|
+
- - 18
|
262
|
+
- :ar
|
263
|
+
- 40
|
264
|
+
- 39.9623831225
|
265
|
+
- 0.996003
|
266
|
+
- 39.948
|
267
|
+
- true
|
268
|
+
- - 19
|
269
|
+
- :k
|
270
|
+
- 39
|
271
|
+
- 38.96370668
|
272
|
+
- 0.932581
|
273
|
+
- 39.0983
|
274
|
+
- true
|
275
|
+
- - 19
|
276
|
+
- :k
|
277
|
+
- 40
|
278
|
+
- 39.96399848
|
279
|
+
- 0.000117
|
280
|
+
- 39.0983
|
281
|
+
- false
|
282
|
+
- - 19
|
283
|
+
- :k
|
284
|
+
- 41
|
285
|
+
- 40.96182576
|
286
|
+
- 0.067302
|
287
|
+
- 39.0983
|
288
|
+
- false
|
289
|
+
- - 20
|
290
|
+
- :ca
|
291
|
+
- 40
|
292
|
+
- 39.96259098
|
293
|
+
- 0.96941
|
294
|
+
- 40.078
|
295
|
+
- true
|
296
|
+
- - 20
|
297
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1765
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1770
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1771
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1772
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1773
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1775
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1776
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1777
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1778
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1779
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1780
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1781
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1782
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1783
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1784
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1785
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1786
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1787
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1788
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1789
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1790
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1791
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1792
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1793
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1794
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1795
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1796
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1797
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1798
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1799
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1800
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1801
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1802
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1803
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1804
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1807
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1808
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1809
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1810
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1811
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1812
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1813
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1814
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1815
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1816
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1817
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1818
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1820
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1821
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1822
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1823
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1824
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1825
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1826
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1827
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1828
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1829
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1831
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1833
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1834
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1835
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1840
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1856
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1857
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1858
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1859
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1860
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1862
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1863
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1864
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1865
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1866
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1869
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1870
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1871
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1872
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1873
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1875
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1876
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1877
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1878
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1879
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1880
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1882
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1884
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1885
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1886
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1887
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1889
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1890
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1891
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1892
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1893
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1894
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1895
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1896
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1897
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1898
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1899
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1900
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1901
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1902
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1903
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1904
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1905
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1906
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1907
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1908
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1909
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1910
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1911
|
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1912
|
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1913
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- - 80
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1914
|
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1915
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- 201
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1916
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1917
|
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|
1918
|
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|
1919
|
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1920
|
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- - 80
|
1921
|
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1922
|
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- 202
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1923
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1924
|
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1925
|
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|
1926
|
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|
1927
|
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- - 80
|
1928
|
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1929
|
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- 204
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1930
|
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1931
|
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1932
|
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1933
|
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|
1934
|
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- - 81
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1935
|
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1936
|
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- 203
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1937
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1938
|
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1939
|
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- 204.3833
|
1940
|
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|
1941
|
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- - 81
|
1942
|
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1943
|
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- 205
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1944
|
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|
1945
|
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|
1946
|
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- 204.3833
|
1947
|
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|
1948
|
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- - 82
|
1949
|
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|
1950
|
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- 204
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1951
|
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|
1952
|
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|
1953
|
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- 207.2
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1954
|
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|
1955
|
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- - 82
|
1956
|
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1957
|
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- 206
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1958
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1959
|
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1960
|
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- 207.2
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1961
|
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|
1962
|
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- - 82
|
1963
|
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- :pb
|
1964
|
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- 207
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1965
|
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|
1966
|
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|
1967
|
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|
1968
|
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|
1969
|
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- - 82
|
1970
|
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|
1971
|
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- 208
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1972
|
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|
1973
|
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1974
|
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|
1975
|
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|
1976
|
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|
1977
|
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1978
|
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- 209
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1979
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1980
|
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1981
|
+
- 208.9804
|
1982
|
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- true
|
1983
|
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- - 90
|
1984
|
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- :th
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1985
|
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- 232
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1986
|
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- 232.0380553
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1987
|
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- 1.0
|
1988
|
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- 232.03806
|
1989
|
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- true
|
1990
|
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- - 91
|
1991
|
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1992
|
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- 231
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1993
|
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- 231.035884
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1994
|
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1995
|
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- 231.03588
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1996
|
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- true
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1997
|
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- - 92
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1998
|
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1999
|
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- 234
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2000
|
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2001
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2002
|
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2003
|
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2004
|
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2005
|
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2006
|
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- 235
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2007
|
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2008
|
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2009
|
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|
2010
|
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2011
|
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|
2012
|
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|
2013
|
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- 238
|
2014
|
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|
2015
|
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|
2016
|
+
- 238.02891
|
2017
|
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