mspire 0.6.12 → 0.6.18
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- data/VERSION +1 -1
- data/lib/ms/mzml.rb +2 -0
- data/lib/ms/mzml/data_array.rb +31 -11
- data/lib/ms/mzml/data_array_container_like.rb +9 -1
- data/lib/ms/mzml/scan_list.rb +1 -1
- data/obo/ims.obo +1 -1
- metadata +15 -15
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
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-
0.6.
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1
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+
0.6.18
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data/lib/ms/mzml.rb
CHANGED
@@ -9,6 +9,8 @@ require 'ms/mzml/file_description'
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|
9
9
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require 'ms/mzml/software'
|
10
10
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require 'ms/mzml/scan_list'
|
11
11
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require 'ms/mzml/scan'
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12
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+
require 'ms/mzml/scan_settings'
|
13
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+
require 'ms/mzml/processing_method'
|
12
14
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require 'ms/mzml/run'
|
13
15
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require 'ms/mzml/spectrum_list'
|
14
16
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require 'ms/mzml/chromatogram_list'
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data/lib/ms/mzml/data_array.rb
CHANGED
@@ -1,9 +1,11 @@
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|
1
1
|
require 'base64'
|
2
2
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require 'zlib'
|
3
|
+
require 'ms/cv/paramable'
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3
4
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|
4
5
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module MS
|
5
6
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class Mzml
|
6
7
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class DataArray < Array
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8
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+
include MS::CV::Paramable
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7
9
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|
8
10
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DEFAULT_DTYPE = :float64
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9
11
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DEFAULT_COMPRESSION = true
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@@ -18,13 +20,14 @@ module MS
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18
20
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# the type of data array (:mz or :intensity)
|
19
21
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attr_accessor :type
|
20
22
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|
21
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-
# requires a type, :mz or :
|
22
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-
|
23
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+
# requires a type, :mz, :intensity, :mz_external, or :intensity_external
|
24
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+
# (external types used in imzml)
|
25
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+
def initialize(_type, opts={params: []})
|
23
26
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@type = _type
|
24
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-
|
27
|
+
@external = !!(@type.to_s =~ /external$/)
|
25
28
|
end
|
26
29
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|
27
|
-
def self.
|
30
|
+
def self.to_binary(array_ish, dtype=DEFAULT_DTYPE, compression=DEFAULT_COMPRESSION)
|
28
31
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pack_code =
|
29
32
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case dtype
|
30
33
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when :float64 ; 'E*'
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@@ -40,12 +43,22 @@ module MS
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|
40
43
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end
|
41
44
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|
42
45
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def to_xml(builder, dtype=DEFAULT_DTYPE, compression=DEFAULT_COMPRESSION)
|
43
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-
|
44
|
-
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
46
|
+
encoded_length =
|
47
|
+
if @external
|
48
|
+
0
|
49
|
+
else
|
50
|
+
base64 = self.class.to_binary(self, dtype, compression)
|
51
|
+
base64.bytesize
|
52
|
+
end
|
53
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+
|
54
|
+
builder.binaryDataArray(encodedLength: encoded_length) do |bda_n|
|
55
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+
@params.each {|param| param.to_xml(bda_n) } if @params
|
56
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+
unless @external
|
57
|
+
MS::CV::Param[ DTYPE_TO_ACC[dtype] ].to_xml(bda_n)
|
58
|
+
MS::CV::Param[ compression ? 'MS:1000574' : 'MS:1000576' ].to_xml(bda_n)
|
59
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+
MS::CV::Param[ (@type == :mz) ? 'MS:1000514' : 'MS:1000515' ].to_xml(bda_n) # must be m/z or intensity
|
60
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+
bda_n.binary(base64)
|
61
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+
end
|
49
62
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end
|
50
63
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end
|
51
64
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@@ -53,7 +66,14 @@ module MS
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53
66
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def self.list_xml(arrays, builder)
|
54
67
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builder.binaryDataArrayList(count: arrays.size) do |bdal_n|
|
55
68
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arrays.zip([:mz, :intensity]) do |data_ar, typ|
|
56
|
-
ar =
|
69
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+
ar =
|
70
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+
if data_ar.is_a?(MS::Mzml::DataArray)
|
71
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+
data_ar
|
72
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+
else
|
73
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+
real_data_array = MS::Mzml::DataArray.new(typ)
|
74
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+
real_data_array.replace(data_ar)
|
75
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+
real_data_array
|
76
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+
end
|
57
77
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ar.type = typ unless ar.type
|
58
78
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ar.to_xml(bdal_n)
|
59
79
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end
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@@ -32,7 +32,15 @@ module MS
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32
32
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end
|
33
33
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|
34
34
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def default_array_length
|
35
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-
|
35
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+
if @data_arrays
|
36
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+
if @data_arrays.first
|
37
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+
@data_arrays.first.size
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38
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+
else
|
39
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+
0
|
40
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+
end
|
41
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+
else
|
42
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+
0
|
43
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+
end
|
36
44
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end
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37
45
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|
38
46
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# see SpectrumList for generating the entire list
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data/lib/ms/mzml/scan_list.rb
CHANGED
data/obo/ims.obo
CHANGED
@@ -299,7 +299,7 @@ relationship: is_a IMS:1000001 ! Ibd Offest Handle
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299
299
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relationship: has_units UO:0000189 ! Count
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300
300
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301
301
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[Term]
|
302
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-
id: IMS:
|
302
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+
id: IMS:1000104
|
303
303
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name: external encoded length
|
304
304
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def: "Describes the length of the written data." [COMPUTIS:IMS]
|
305
305
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xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: mspire
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.6.
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4
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+
version: 0.6.18
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5
5
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prerelease:
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6
6
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platform: ruby
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7
7
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authors:
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@@ -14,7 +14,7 @@ date: 2012-02-23 00:00:00.000000000 Z
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14
14
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dependencies:
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15
15
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- !ruby/object:Gem::Dependency
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16
16
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name: nokogiri
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17
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-
requirement: &
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17
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+
requirement: &19554840 !ruby/object:Gem::Requirement
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18
18
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none: false
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19
19
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requirements:
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20
20
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- - ~>
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@@ -22,10 +22,10 @@ dependencies:
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22
22
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version: '1.5'
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23
23
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type: :runtime
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24
24
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prerelease: false
|
25
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-
version_requirements: *
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25
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+
version_requirements: *19554840
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26
26
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- !ruby/object:Gem::Dependency
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27
27
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name: bsearch
|
28
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-
requirement: &
|
28
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+
requirement: &19553820 !ruby/object:Gem::Requirement
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29
29
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none: false
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30
30
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requirements:
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31
31
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- - ! '>='
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@@ -33,10 +33,10 @@ dependencies:
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33
33
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version: 1.5.0
|
34
34
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type: :runtime
|
35
35
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prerelease: false
|
36
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-
version_requirements: *
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36
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+
version_requirements: *19553820
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37
37
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- !ruby/object:Gem::Dependency
|
38
38
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name: andand
|
39
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-
requirement: &
|
39
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+
requirement: &19552180 !ruby/object:Gem::Requirement
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40
40
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none: false
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41
41
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requirements:
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42
42
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- - ! '>='
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@@ -44,10 +44,10 @@ dependencies:
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44
44
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version: 1.3.1
|
45
45
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type: :runtime
|
46
46
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prerelease: false
|
47
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-
version_requirements: *
|
47
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+
version_requirements: *19552180
|
48
48
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- !ruby/object:Gem::Dependency
|
49
49
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name: obo
|
50
|
-
requirement: &
|
50
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+
requirement: &19550640 !ruby/object:Gem::Requirement
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51
51
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none: false
|
52
52
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requirements:
|
53
53
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- - ! '>='
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@@ -55,10 +55,10 @@ dependencies:
|
|
55
55
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version: 0.1.0
|
56
56
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type: :runtime
|
57
57
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prerelease: false
|
58
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-
version_requirements: *
|
58
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+
version_requirements: *19550640
|
59
59
|
- !ruby/object:Gem::Dependency
|
60
60
|
name: rspec
|
61
|
-
requirement: &
|
61
|
+
requirement: &19565640 !ruby/object:Gem::Requirement
|
62
62
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none: false
|
63
63
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requirements:
|
64
64
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- - ~>
|
@@ -66,10 +66,10 @@ dependencies:
|
|
66
66
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version: '2.6'
|
67
67
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type: :development
|
68
68
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prerelease: false
|
69
|
-
version_requirements: *
|
69
|
+
version_requirements: *19565640
|
70
70
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- !ruby/object:Gem::Dependency
|
71
71
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name: jeweler
|
72
|
-
requirement: &
|
72
|
+
requirement: &19564260 !ruby/object:Gem::Requirement
|
73
73
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none: false
|
74
74
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requirements:
|
75
75
|
- - ~>
|
@@ -77,10 +77,10 @@ dependencies:
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77
77
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version: 1.5.2
|
78
78
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type: :development
|
79
79
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prerelease: false
|
80
|
-
version_requirements: *
|
80
|
+
version_requirements: *19564260
|
81
81
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- !ruby/object:Gem::Dependency
|
82
82
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name: rcov
|
83
|
-
requirement: &
|
83
|
+
requirement: &19563540 !ruby/object:Gem::Requirement
|
84
84
|
none: false
|
85
85
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requirements:
|
86
86
|
- - ! '>='
|
@@ -88,7 +88,7 @@ dependencies:
|
|
88
88
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version: '0'
|
89
89
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type: :development
|
90
90
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prerelease: false
|
91
|
-
version_requirements: *
|
91
|
+
version_requirements: *19563540
|
92
92
|
description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
|
93
93
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merging of ms-* gems
|
94
94
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email: jtprince@gmail.com
|