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
metadata
CHANGED
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@@ -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: 0.6.24
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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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@@ -10,11 +10,11 @@ authors:
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10
10
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autorequire:
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11
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bindir: bin
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12
12
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cert_chain: []
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13
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-
date: 2012-
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13
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+
date: 2012-03-13 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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+
requirement: &13307340 !ruby/object:Gem::Requirement
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none: false
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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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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
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25
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-
version_requirements: *
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25
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+
version_requirements: *13307340
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26
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- !ruby/object:Gem::Dependency
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27
27
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name: bsearch
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28
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-
requirement: &
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28
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+
requirement: &13323080 !ruby/object:Gem::Requirement
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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
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34
34
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type: :runtime
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35
35
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prerelease: false
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36
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-
version_requirements: *
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36
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+
version_requirements: *13323080
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37
37
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- !ruby/object:Gem::Dependency
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38
38
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name: andand
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39
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-
requirement: &
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39
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+
requirement: &13322420 !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
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45
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type: :runtime
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46
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prerelease: false
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47
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-
version_requirements: *
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47
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+
version_requirements: *13322420
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48
48
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- !ruby/object:Gem::Dependency
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49
49
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name: obo
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|
50
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-
requirement: &
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50
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+
requirement: &13321500 !ruby/object:Gem::Requirement
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51
51
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none: false
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52
52
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requirements:
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53
53
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- - ! '>='
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@@ -55,10 +55,32 @@ dependencies:
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version: 0.1.0
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type: :runtime
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57
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prerelease: false
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58
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-
version_requirements: *
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58
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+
version_requirements: *13321500
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59
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+
- !ruby/object:Gem::Dependency
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|
60
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+
name: builder
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|
61
|
+
requirement: &13320060 !ruby/object:Gem::Requirement
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|
62
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+
none: false
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|
63
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+
requirements:
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|
64
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+
- - ! '>='
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|
65
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+
- !ruby/object:Gem::Version
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|
66
|
+
version: 3.0.0
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|
67
|
+
type: :runtime
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|
68
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+
prerelease: false
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|
69
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+
version_requirements: *13320060
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|
70
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+
- !ruby/object:Gem::Dependency
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|
71
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+
name: trollop
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|
72
|
+
requirement: &13319460 !ruby/object:Gem::Requirement
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|
73
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+
none: false
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|
74
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+
requirements:
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|
75
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+
- - ! '>='
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76
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+
- !ruby/object:Gem::Version
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|
77
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+
version: 1.16.2
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78
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+
type: :runtime
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|
79
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+
prerelease: false
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|
80
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+
version_requirements: *13319460
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59
81
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- !ruby/object:Gem::Dependency
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60
82
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name: rspec
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61
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-
requirement: &
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83
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+
requirement: &13318520 !ruby/object:Gem::Requirement
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none: false
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63
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requirements:
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64
86
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- - ~>
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@@ -66,10 +88,10 @@ dependencies:
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66
88
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version: '2.6'
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67
89
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type: :development
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68
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prerelease: false
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69
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-
version_requirements: *
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91
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+
version_requirements: *13318520
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70
92
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- !ruby/object:Gem::Dependency
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71
93
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name: jeweler
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72
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-
requirement: &
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|
94
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+
requirement: &13317560 !ruby/object:Gem::Requirement
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73
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none: false
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74
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requirements:
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75
97
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- - ~>
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@@ -77,10 +99,10 @@ dependencies:
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77
99
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version: 1.5.2
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78
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type: :development
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79
101
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prerelease: false
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|
80
|
-
version_requirements: *
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|
102
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+
version_requirements: *13317560
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|
81
103
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- !ruby/object:Gem::Dependency
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|
82
104
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name: rcov
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|
83
|
-
requirement: &
|
|
105
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+
requirement: &13316940 !ruby/object:Gem::Requirement
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|
84
106
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none: false
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85
107
|
requirements:
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|
86
108
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- - ! '>='
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@@ -88,7 +110,7 @@ dependencies:
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88
110
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version: '0'
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|
89
111
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type: :development
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|
90
112
|
prerelease: false
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|
91
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-
version_requirements: *
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|
113
|
+
version_requirements: *13316940
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|
92
114
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description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
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93
115
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merging of ms-* gems
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94
116
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email: jtprince@gmail.com
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@@ -137,7 +159,9 @@ files:
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|
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137
159
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- lib/ms/ident/protein.rb
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|
138
160
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- lib/ms/ident/protein_group.rb
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|
139
161
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- lib/ms/ident/search.rb
|
|
162
|
+
- lib/ms/isotope.rb
|
|
140
163
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- lib/ms/isotope/aa.rb
|
|
164
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+
- lib/ms/isotope/nist_isotope_info.yml
|
|
141
165
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- lib/ms/mascot.rb
|
|
142
166
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- lib/ms/mass.rb
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143
167
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- lib/ms/mass/aa.rb
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@@ -193,6 +217,7 @@ files:
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193
217
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- obo/ims.obo
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194
218
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- obo/ms.obo
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|
195
219
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- obo/unit.obo
|
|
220
|
+
- script/mzml_read_binary.rb
|
|
196
221
|
- spec/bin_spec.rb
|
|
197
222
|
- spec/ms/cv/param_spec.rb
|
|
198
223
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- spec/ms/digester_spec.rb
|
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@@ -204,8 +229,10 @@ files:
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204
229
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- spec/ms/ident/pepxml_spec.rb
|
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205
230
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- spec/ms/ident/protein_group_spec.rb
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206
231
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- spec/ms/isotope/aa_spec.rb
|
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232
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+
- spec/ms/isotope_spec.rb
|
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207
233
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- spec/ms/mass_spec.rb
|
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208
234
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- spec/ms/mzml/cv_spec.rb
|
|
235
|
+
- spec/ms/mzml/data_array_spec.rb
|
|
209
236
|
- spec/ms/mzml/file_content_spec.rb
|
|
210
237
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- spec/ms/mzml/file_description_spec.rb
|
|
211
238
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- spec/ms/mzml/index_list_spec.rb
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@@ -223,7 +250,7 @@ files:
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223
250
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- spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta
|
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224
251
|
- spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
|
|
225
252
|
- spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML
|
|
226
|
-
- spec/testfiles/ms/mzml/mspire_simulated.
|
|
253
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+
- spec/testfiles/ms/mzml/mspire_simulated.MSn.check.mzML
|
|
227
254
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- spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML
|
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228
255
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- spec/testfiles/ms/quant/kill_extra_tabs.rb
|
|
229
256
|
- spec/testfiles/ms/quant/max_quant_output.provenance.txt
|