msf 0.1.0

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.
Files changed (80) hide show
  1. data/.document +5 -0
  2. data/.rspec +1 -0
  3. data/Gemfile +24 -0
  4. data/Gemfile.lock +67 -0
  5. data/LICENSE.txt +20 -0
  6. data/README.md +45 -0
  7. data/Rakefile +43 -0
  8. data/VERSION +1 -0
  9. data/bin/ibspectra +43 -0
  10. data/erd/config.png +0 -0
  11. data/erd/empty.png +0 -0
  12. data/erd/erd.png +0 -0
  13. data/erd/msf.xcdatamodeld/.xccurrentversion +8 -0
  14. data/erd/msf.xcdatamodeld/msf.xcdatamodel/contents +330 -0
  15. data/erd/schema.txt +666 -0
  16. data/lib/msf.rb +2 -0
  17. data/lib/msf/models.rb +4 -0
  18. data/lib/msf/models/amino_acid.rb +50 -0
  19. data/lib/msf/models/amino_acid_modification.rb +55 -0
  20. data/lib/msf/models/amino_acid_modification_neutral_loss.rb +31 -0
  21. data/lib/msf/models/amino_acid_modifications_amino_acid_nls.rb +23 -0
  22. data/lib/msf/models/amino_acid_modifications_amino_acids.rb +27 -0
  23. data/lib/msf/models/annotation_data_version.rb +20 -0
  24. data/lib/msf/models/annotation_dataset.rb +29 -0
  25. data/lib/msf/models/annotation_group.rb +38 -0
  26. data/lib/msf/models/annotation_type.rb +23 -0
  27. data/lib/msf/models/chromatogram.rb +26 -0
  28. data/lib/msf/models/custom_data_field.rb +56 -0
  29. data/lib/msf/models/custom_data_peptide.rb +25 -0
  30. data/lib/msf/models/custom_data_processing_node.rb +25 -0
  31. data/lib/msf/models/custom_data_protein.rb +25 -0
  32. data/lib/msf/models/custom_data_spectrum.rb +25 -0
  33. data/lib/msf/models/enzyme.rb +32 -0
  34. data/lib/msf/models/fasta_file.rb +50 -0
  35. data/lib/msf/models/file_info.rb +41 -0
  36. data/lib/msf/models/mass_peak.rb +36 -0
  37. data/lib/msf/models/peptide.rb +118 -0
  38. data/lib/msf/models/peptide_score.rb +34 -0
  39. data/lib/msf/models/peptide_score_decoy.rb +34 -0
  40. data/lib/msf/models/peptide_terminal_modification.rb +29 -0
  41. data/lib/msf/models/peptides_amino_acid_modifications.rb +32 -0
  42. data/lib/msf/models/peptides_proteins.rb +27 -0
  43. data/lib/msf/models/processing_node.rb +65 -0
  44. data/lib/msf/models/processing_node_score.rb +45 -0
  45. data/lib/msf/models/protein.rb +38 -0
  46. data/lib/msf/models/protein_annotation.rb +35 -0
  47. data/lib/msf/models/protein_identification_group.rb +19 -0
  48. data/lib/msf/models/protein_score.rb +34 -0
  49. data/lib/msf/models/reporter_ion_quan_result.rb +31 -0
  50. data/lib/msf/models/reporter_ion_quan_result_search_spectrum.rb +29 -0
  51. data/lib/msf/models/scan_event.rb +37 -0
  52. data/lib/msf/models/schema_info.rb +29 -0
  53. data/lib/msf/models/spectrum.rb +34 -0
  54. data/lib/msf/models/spectrum_header.rb +63 -0
  55. data/lib/msf/models/spectrum_score.rb +24 -0
  56. data/lib/msf/models/taxonomy_name.rb +26 -0
  57. data/lib/msf/models/workflow_info.rb +46 -0
  58. data/lib/msf/models/workflow_message.rb +31 -0
  59. data/lib/msf/msf.rb +32 -0
  60. data/lib/msf/sql/enzyme_cleavage_specificity.rb +16 -0
  61. data/lib/msf/sql/false_discovery_rate.rb +24 -0
  62. data/lib/msf/sql/fasta_file_protein_annotation.rb +17 -0
  63. data/lib/msf/sql/mass_peak_relation.rb +17 -0
  64. data/lib/msf/sql/peptide_amino_acid_modification_decoy.rb +23 -0
  65. data/lib/msf/sql/peptide_decoy.rb +32 -0
  66. data/lib/msf/sql/peptide_terminal_modification_decoy.rb +20 -0
  67. data/lib/msf/sql/precursor_ion_quan_result.rb +29 -0
  68. data/lib/msf/sql/precursor_ion_quan_result_event_spectrum.rb +17 -0
  69. data/lib/msf/sql/precursor_ion_quan_result_search_spectrum.rb +20 -0
  70. data/lib/msf/sql/processing_node_filter_parameter.rb +29 -0
  71. data/lib/msf/sql/processing_node_interface.rb +19 -0
  72. data/lib/msf/sql/processing_node_parameter.rb +46 -0
  73. data/lib/msf/sql/processing_node_spectrum.rb +16 -0
  74. data/lib/msf/sql/quan_result.rb +40 -0
  75. data/lib/msf/sql/result_filter_set.rb +12 -0
  76. data/lib/msf/sql/taxonomy_node.rb +26 -0
  77. data/msf.gemspec +143 -0
  78. data/spec/msf_spec.rb +7 -0
  79. data/spec/spec_helper.rb +14 -0
  80. metadata +275 -0
@@ -0,0 +1,46 @@
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+ module ThermoMSF
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+ module Model
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+ class ProcessingNodeParameter < Sequel::Model(:ProcessingNodeParameters)
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+ set_primary_key [:ProcessingNodeNumber, :ParameterName]
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+ # ruby style accessors
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+ def processing_node_number
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+ self.ProcessingNodeNumber
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+ end
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+ def parameter_name
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+ self.ParameterName
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+ end
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+ def friendly_name
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+ self.FriendlyName
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+ end
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+ def processing_node_id
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+ self.ProcessingNodeID
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+ end
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+ def intended_purpose
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+ self.IntendedPurpose
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+ end
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+ def purpose_details
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+ self.PurposeDetails
23
+ end
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+ def hidden
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+ self.Hidden
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+ end
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+ def advanced
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+ self.Advanced
29
+ end
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+ def category
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+ self.Category
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+ end
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+ def position
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+ self.Position
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+ end
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+ def parameter_value
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+ self.ParameterValue
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+ end
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+ def value_display_string
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+ self.ValueDisplayString
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+ end
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+ # associations
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+ many_to_one processing_node, :key => :ProcessingNodeID
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+ end
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+ end
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+ end
@@ -0,0 +1,16 @@
1
+ module ThermoMSF
2
+ module Model
3
+ class ProcessingNodeSpectrum < Sequel::Model(:ProcessingNodesSpectra)
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+ set_primary_key [:SendingProcessingNodeNumber, :SpectrumID]
5
+ # ruby style accessors
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+ def sending_processing_node_number
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+ self.SendingProcessingNodeNumber
8
+ end
9
+ def spectrum_id
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+ self.SpectrumID
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+ end
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+ # associations
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+ many_to_one spectrum, :key => :SpectrumID
14
+ end
15
+ end
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+ end
@@ -0,0 +1,40 @@
1
+ module ThermoMSF
2
+ module Model
3
+ class QuanResult < Sequel::Model(:QuanResults)
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+ set_primary_key [:QuanResultID, :SpectrumID]
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+ # ruby style accessors
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+ def quan_result_id
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+ self.QuanResultID
8
+ end
9
+ def spectrum_id
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+ self.SpectrumID
11
+ end
12
+ def height
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+ self.Height
14
+ end
15
+ def area
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+ self.Area
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+ end
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+ def start_time
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+ self.StartTime
20
+ end
21
+ def end_time
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+ self.EndTime
23
+ end
24
+ def start_peak_time
25
+ self.StartPeakTime
26
+ end
27
+ def start_peak_intensity
28
+ self.StartPeakIntensity
29
+ end
30
+ def end_peak_time
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+ self.EndPeakTime
32
+ end
33
+ def end_peak_intensity
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+ self.EndPeakIntensity
35
+ end
36
+ # associations
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+ many_to_one spectrum, :key => :SpectrumID
38
+ end
39
+ end
40
+ end
@@ -0,0 +1,12 @@
1
+ module ThermoMSF
2
+ module Model
3
+ class ResultFilterSet < Sequel::Model(:ResultFilterSet)
4
+ set_primary_key :
5
+ # ruby style accessors
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+ def result_filter_set
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+ self.ResultFilterSet
8
+ end
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+ # associations
10
+ end
11
+ end
12
+ end
@@ -0,0 +1,26 @@
1
+ module ThermoMSF
2
+ module Model
3
+ class TaxonomyNode < Sequel::Model(:TaxonomyNodes)
4
+ set_primary_key :TaxonomyID
5
+ # ruby style accessors
6
+ def taxonomy_id
7
+ self.TaxonomyID
8
+ end
9
+ def parent_taxonomy_id
10
+ self.ParentTaxonomyID
11
+ end
12
+ def taxonomy_rank
13
+ self.TaxonomyRank
14
+ end
15
+ def left_node_index
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+ self.LeftNodeIndex
17
+ end
18
+ def right_node_index
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+ self.RightNodeIndex
20
+ end
21
+ # associations
22
+ many_to_one taxonomy, :key => :TaxonomyID
23
+ many_to_one parent_taxonomy, :key => :ParentTaxonomyID
24
+ end
25
+ end
26
+ end
@@ -0,0 +1,143 @@
1
+ # Generated by jeweler
2
+ # DO NOT EDIT THIS FILE DIRECTLY
3
+ # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
4
+ # -*- encoding: utf-8 -*-
5
+
6
+ Gem::Specification.new do |s|
7
+ s.name = "msf"
8
+ s.version = "0.1.0"
9
+
10
+ s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
11
+ s.authors = ["William Van Etten"]
12
+ s.date = "2012-11-07"
13
+ s.description = "An MSF file is sqlite3 dtabase. ActiveRecord is a great ORM for accessing the data. Much taken from Angel Pizarro's thermo_msf."
14
+ s.email = "bill@bioteam.net"
15
+ s.executables = ["ibspectra"]
16
+ s.extra_rdoc_files = [
17
+ "LICENSE.txt",
18
+ "README.md"
19
+ ]
20
+ s.files = [
21
+ ".document",
22
+ ".rspec",
23
+ "Gemfile",
24
+ "Gemfile.lock",
25
+ "LICENSE.txt",
26
+ "README.md",
27
+ "Rakefile",
28
+ "VERSION",
29
+ "bin/ibspectra",
30
+ "erd/config.png",
31
+ "erd/empty.png",
32
+ "erd/erd.png",
33
+ "erd/msf.xcdatamodeld/.xccurrentversion",
34
+ "erd/msf.xcdatamodeld/msf.xcdatamodel/contents",
35
+ "erd/schema.txt",
36
+ "lib/msf.rb",
37
+ "lib/msf/models.rb",
38
+ "lib/msf/models/amino_acid.rb",
39
+ "lib/msf/models/amino_acid_modification.rb",
40
+ "lib/msf/models/amino_acid_modification_neutral_loss.rb",
41
+ "lib/msf/models/amino_acid_modifications_amino_acid_nls.rb",
42
+ "lib/msf/models/amino_acid_modifications_amino_acids.rb",
43
+ "lib/msf/models/annotation_data_version.rb",
44
+ "lib/msf/models/annotation_dataset.rb",
45
+ "lib/msf/models/annotation_group.rb",
46
+ "lib/msf/models/annotation_type.rb",
47
+ "lib/msf/models/chromatogram.rb",
48
+ "lib/msf/models/custom_data_field.rb",
49
+ "lib/msf/models/custom_data_peptide.rb",
50
+ "lib/msf/models/custom_data_processing_node.rb",
51
+ "lib/msf/models/custom_data_protein.rb",
52
+ "lib/msf/models/custom_data_spectrum.rb",
53
+ "lib/msf/models/enzyme.rb",
54
+ "lib/msf/models/fasta_file.rb",
55
+ "lib/msf/models/file_info.rb",
56
+ "lib/msf/models/mass_peak.rb",
57
+ "lib/msf/models/peptide.rb",
58
+ "lib/msf/models/peptide_score.rb",
59
+ "lib/msf/models/peptide_score_decoy.rb",
60
+ "lib/msf/models/peptide_terminal_modification.rb",
61
+ "lib/msf/models/peptides_amino_acid_modifications.rb",
62
+ "lib/msf/models/peptides_proteins.rb",
63
+ "lib/msf/models/processing_node.rb",
64
+ "lib/msf/models/processing_node_score.rb",
65
+ "lib/msf/models/protein.rb",
66
+ "lib/msf/models/protein_annotation.rb",
67
+ "lib/msf/models/protein_identification_group.rb",
68
+ "lib/msf/models/protein_score.rb",
69
+ "lib/msf/models/reporter_ion_quan_result.rb",
70
+ "lib/msf/models/reporter_ion_quan_result_search_spectrum.rb",
71
+ "lib/msf/models/scan_event.rb",
72
+ "lib/msf/models/schema_info.rb",
73
+ "lib/msf/models/spectrum.rb",
74
+ "lib/msf/models/spectrum_header.rb",
75
+ "lib/msf/models/spectrum_score.rb",
76
+ "lib/msf/models/taxonomy_name.rb",
77
+ "lib/msf/models/workflow_info.rb",
78
+ "lib/msf/models/workflow_message.rb",
79
+ "lib/msf/msf.rb",
80
+ "lib/msf/sql/enzyme_cleavage_specificity.rb",
81
+ "lib/msf/sql/false_discovery_rate.rb",
82
+ "lib/msf/sql/fasta_file_protein_annotation.rb",
83
+ "lib/msf/sql/mass_peak_relation.rb",
84
+ "lib/msf/sql/peptide_amino_acid_modification_decoy.rb",
85
+ "lib/msf/sql/peptide_decoy.rb",
86
+ "lib/msf/sql/peptide_terminal_modification_decoy.rb",
87
+ "lib/msf/sql/precursor_ion_quan_result.rb",
88
+ "lib/msf/sql/precursor_ion_quan_result_event_spectrum.rb",
89
+ "lib/msf/sql/precursor_ion_quan_result_search_spectrum.rb",
90
+ "lib/msf/sql/processing_node_filter_parameter.rb",
91
+ "lib/msf/sql/processing_node_interface.rb",
92
+ "lib/msf/sql/processing_node_parameter.rb",
93
+ "lib/msf/sql/processing_node_spectrum.rb",
94
+ "lib/msf/sql/quan_result.rb",
95
+ "lib/msf/sql/result_filter_set.rb",
96
+ "lib/msf/sql/taxonomy_node.rb",
97
+ "msf.gemspec",
98
+ "spec/msf_spec.rb",
99
+ "spec/spec_helper.rb"
100
+ ]
101
+ s.homepage = "http://github.com/vanetten/msf"
102
+ s.licenses = ["MIT"]
103
+ s.require_paths = ["lib"]
104
+ s.rubygems_version = "1.8.24"
105
+ s.summary = "ActiveRecord access to MSF file (sqlite3 database)."
106
+
107
+ if s.respond_to? :specification_version then
108
+ s.specification_version = 3
109
+
110
+ if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
111
+ s.add_runtime_dependency(%q<bundler>, ["~> 1.2.1"])
112
+ s.add_runtime_dependency(%q<activerecord>, ["~> 3.2.0"])
113
+ s.add_runtime_dependency(%q<sqlite3>, ["~> 1.3.0"])
114
+ s.add_development_dependency(%q<rspec>, ["~> 2.8.0"])
115
+ s.add_development_dependency(%q<simplecov>, ["~> 0.7.1"])
116
+ s.add_development_dependency(%q<jeweler>, ["~> 1.8.4"])
117
+ s.add_development_dependency(%q<debugger>, [">= 1.2.0"])
118
+ s.add_development_dependency(%q<yard>, ["~> 0.7"])
119
+ s.add_development_dependency(%q<redcarpet>, ["~> 2.2.2"])
120
+ else
121
+ s.add_dependency(%q<bundler>, ["~> 1.2.1"])
122
+ s.add_dependency(%q<activerecord>, ["~> 3.2.0"])
123
+ s.add_dependency(%q<sqlite3>, ["~> 1.3.0"])
124
+ s.add_dependency(%q<rspec>, ["~> 2.8.0"])
125
+ s.add_dependency(%q<simplecov>, ["~> 0.7.1"])
126
+ s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
127
+ s.add_dependency(%q<debugger>, [">= 1.2.0"])
128
+ s.add_dependency(%q<yard>, ["~> 0.7"])
129
+ s.add_dependency(%q<redcarpet>, ["~> 2.2.2"])
130
+ end
131
+ else
132
+ s.add_dependency(%q<bundler>, ["~> 1.2.1"])
133
+ s.add_dependency(%q<activerecord>, ["~> 3.2.0"])
134
+ s.add_dependency(%q<sqlite3>, ["~> 1.3.0"])
135
+ s.add_dependency(%q<rspec>, ["~> 2.8.0"])
136
+ s.add_dependency(%q<simplecov>, ["~> 0.7.1"])
137
+ s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
138
+ s.add_dependency(%q<debugger>, [">= 1.2.0"])
139
+ s.add_dependency(%q<yard>, ["~> 0.7"])
140
+ s.add_dependency(%q<redcarpet>, ["~> 2.2.2"])
141
+ end
142
+ end
143
+
@@ -0,0 +1,7 @@
1
+ require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
2
+
3
+ describe MSF do
4
+ it "fails" do
5
+ fail "hey buddy, you should probably rename this file and start specing for real"
6
+ end
7
+ end
@@ -0,0 +1,14 @@
1
+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
2
+ $LOAD_PATH.unshift(File.dirname(__FILE__))
3
+ require 'simplecov'
4
+ SimpleCov.start
5
+ require 'rspec'
6
+ require 'msf'
7
+
8
+ # Requires supporting files with custom matchers and macros, etc,
9
+ # in ./support/ and its subdirectories.
10
+ Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
11
+
12
+ RSpec.configure do |config|
13
+
14
+ end
metadata ADDED
@@ -0,0 +1,275 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: msf
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.1.0
5
+ prerelease:
6
+ platform: ruby
7
+ authors:
8
+ - William Van Etten
9
+ autorequire:
10
+ bindir: bin
11
+ cert_chain: []
12
+ date: 2012-11-07 00:00:00.000000000 Z
13
+ dependencies:
14
+ - !ruby/object:Gem::Dependency
15
+ name: bundler
16
+ requirement: !ruby/object:Gem::Requirement
17
+ none: false
18
+ requirements:
19
+ - - ~>
20
+ - !ruby/object:Gem::Version
21
+ version: 1.2.1
22
+ type: :runtime
23
+ prerelease: false
24
+ version_requirements: !ruby/object:Gem::Requirement
25
+ none: false
26
+ requirements:
27
+ - - ~>
28
+ - !ruby/object:Gem::Version
29
+ version: 1.2.1
30
+ - !ruby/object:Gem::Dependency
31
+ name: activerecord
32
+ requirement: !ruby/object:Gem::Requirement
33
+ none: false
34
+ requirements:
35
+ - - ~>
36
+ - !ruby/object:Gem::Version
37
+ version: 3.2.0
38
+ type: :runtime
39
+ prerelease: false
40
+ version_requirements: !ruby/object:Gem::Requirement
41
+ none: false
42
+ requirements:
43
+ - - ~>
44
+ - !ruby/object:Gem::Version
45
+ version: 3.2.0
46
+ - !ruby/object:Gem::Dependency
47
+ name: sqlite3
48
+ requirement: !ruby/object:Gem::Requirement
49
+ none: false
50
+ requirements:
51
+ - - ~>
52
+ - !ruby/object:Gem::Version
53
+ version: 1.3.0
54
+ type: :runtime
55
+ prerelease: false
56
+ version_requirements: !ruby/object:Gem::Requirement
57
+ none: false
58
+ requirements:
59
+ - - ~>
60
+ - !ruby/object:Gem::Version
61
+ version: 1.3.0
62
+ - !ruby/object:Gem::Dependency
63
+ name: rspec
64
+ requirement: !ruby/object:Gem::Requirement
65
+ none: false
66
+ requirements:
67
+ - - ~>
68
+ - !ruby/object:Gem::Version
69
+ version: 2.8.0
70
+ type: :development
71
+ prerelease: false
72
+ version_requirements: !ruby/object:Gem::Requirement
73
+ none: false
74
+ requirements:
75
+ - - ~>
76
+ - !ruby/object:Gem::Version
77
+ version: 2.8.0
78
+ - !ruby/object:Gem::Dependency
79
+ name: simplecov
80
+ requirement: !ruby/object:Gem::Requirement
81
+ none: false
82
+ requirements:
83
+ - - ~>
84
+ - !ruby/object:Gem::Version
85
+ version: 0.7.1
86
+ type: :development
87
+ prerelease: false
88
+ version_requirements: !ruby/object:Gem::Requirement
89
+ none: false
90
+ requirements:
91
+ - - ~>
92
+ - !ruby/object:Gem::Version
93
+ version: 0.7.1
94
+ - !ruby/object:Gem::Dependency
95
+ name: jeweler
96
+ requirement: !ruby/object:Gem::Requirement
97
+ none: false
98
+ requirements:
99
+ - - ~>
100
+ - !ruby/object:Gem::Version
101
+ version: 1.8.4
102
+ type: :development
103
+ prerelease: false
104
+ version_requirements: !ruby/object:Gem::Requirement
105
+ none: false
106
+ requirements:
107
+ - - ~>
108
+ - !ruby/object:Gem::Version
109
+ version: 1.8.4
110
+ - !ruby/object:Gem::Dependency
111
+ name: debugger
112
+ requirement: !ruby/object:Gem::Requirement
113
+ none: false
114
+ requirements:
115
+ - - ! '>='
116
+ - !ruby/object:Gem::Version
117
+ version: 1.2.0
118
+ type: :development
119
+ prerelease: false
120
+ version_requirements: !ruby/object:Gem::Requirement
121
+ none: false
122
+ requirements:
123
+ - - ! '>='
124
+ - !ruby/object:Gem::Version
125
+ version: 1.2.0
126
+ - !ruby/object:Gem::Dependency
127
+ name: yard
128
+ requirement: !ruby/object:Gem::Requirement
129
+ none: false
130
+ requirements:
131
+ - - ~>
132
+ - !ruby/object:Gem::Version
133
+ version: '0.7'
134
+ type: :development
135
+ prerelease: false
136
+ version_requirements: !ruby/object:Gem::Requirement
137
+ none: false
138
+ requirements:
139
+ - - ~>
140
+ - !ruby/object:Gem::Version
141
+ version: '0.7'
142
+ - !ruby/object:Gem::Dependency
143
+ name: redcarpet
144
+ requirement: !ruby/object:Gem::Requirement
145
+ none: false
146
+ requirements:
147
+ - - ~>
148
+ - !ruby/object:Gem::Version
149
+ version: 2.2.2
150
+ type: :development
151
+ prerelease: false
152
+ version_requirements: !ruby/object:Gem::Requirement
153
+ none: false
154
+ requirements:
155
+ - - ~>
156
+ - !ruby/object:Gem::Version
157
+ version: 2.2.2
158
+ description: An MSF file is sqlite3 dtabase. ActiveRecord is a great ORM for accessing
159
+ the data. Much taken from Angel Pizarro's thermo_msf.
160
+ email: bill@bioteam.net
161
+ executables:
162
+ - ibspectra
163
+ extensions: []
164
+ extra_rdoc_files:
165
+ - LICENSE.txt
166
+ - README.md
167
+ files:
168
+ - .document
169
+ - .rspec
170
+ - Gemfile
171
+ - Gemfile.lock
172
+ - LICENSE.txt
173
+ - README.md
174
+ - Rakefile
175
+ - VERSION
176
+ - bin/ibspectra
177
+ - erd/config.png
178
+ - erd/empty.png
179
+ - erd/erd.png
180
+ - erd/msf.xcdatamodeld/.xccurrentversion
181
+ - erd/msf.xcdatamodeld/msf.xcdatamodel/contents
182
+ - erd/schema.txt
183
+ - lib/msf.rb
184
+ - lib/msf/models.rb
185
+ - lib/msf/models/amino_acid.rb
186
+ - lib/msf/models/amino_acid_modification.rb
187
+ - lib/msf/models/amino_acid_modification_neutral_loss.rb
188
+ - lib/msf/models/amino_acid_modifications_amino_acid_nls.rb
189
+ - lib/msf/models/amino_acid_modifications_amino_acids.rb
190
+ - lib/msf/models/annotation_data_version.rb
191
+ - lib/msf/models/annotation_dataset.rb
192
+ - lib/msf/models/annotation_group.rb
193
+ - lib/msf/models/annotation_type.rb
194
+ - lib/msf/models/chromatogram.rb
195
+ - lib/msf/models/custom_data_field.rb
196
+ - lib/msf/models/custom_data_peptide.rb
197
+ - lib/msf/models/custom_data_processing_node.rb
198
+ - lib/msf/models/custom_data_protein.rb
199
+ - lib/msf/models/custom_data_spectrum.rb
200
+ - lib/msf/models/enzyme.rb
201
+ - lib/msf/models/fasta_file.rb
202
+ - lib/msf/models/file_info.rb
203
+ - lib/msf/models/mass_peak.rb
204
+ - lib/msf/models/peptide.rb
205
+ - lib/msf/models/peptide_score.rb
206
+ - lib/msf/models/peptide_score_decoy.rb
207
+ - lib/msf/models/peptide_terminal_modification.rb
208
+ - lib/msf/models/peptides_amino_acid_modifications.rb
209
+ - lib/msf/models/peptides_proteins.rb
210
+ - lib/msf/models/processing_node.rb
211
+ - lib/msf/models/processing_node_score.rb
212
+ - lib/msf/models/protein.rb
213
+ - lib/msf/models/protein_annotation.rb
214
+ - lib/msf/models/protein_identification_group.rb
215
+ - lib/msf/models/protein_score.rb
216
+ - lib/msf/models/reporter_ion_quan_result.rb
217
+ - lib/msf/models/reporter_ion_quan_result_search_spectrum.rb
218
+ - lib/msf/models/scan_event.rb
219
+ - lib/msf/models/schema_info.rb
220
+ - lib/msf/models/spectrum.rb
221
+ - lib/msf/models/spectrum_header.rb
222
+ - lib/msf/models/spectrum_score.rb
223
+ - lib/msf/models/taxonomy_name.rb
224
+ - lib/msf/models/workflow_info.rb
225
+ - lib/msf/models/workflow_message.rb
226
+ - lib/msf/msf.rb
227
+ - lib/msf/sql/enzyme_cleavage_specificity.rb
228
+ - lib/msf/sql/false_discovery_rate.rb
229
+ - lib/msf/sql/fasta_file_protein_annotation.rb
230
+ - lib/msf/sql/mass_peak_relation.rb
231
+ - lib/msf/sql/peptide_amino_acid_modification_decoy.rb
232
+ - lib/msf/sql/peptide_decoy.rb
233
+ - lib/msf/sql/peptide_terminal_modification_decoy.rb
234
+ - lib/msf/sql/precursor_ion_quan_result.rb
235
+ - lib/msf/sql/precursor_ion_quan_result_event_spectrum.rb
236
+ - lib/msf/sql/precursor_ion_quan_result_search_spectrum.rb
237
+ - lib/msf/sql/processing_node_filter_parameter.rb
238
+ - lib/msf/sql/processing_node_interface.rb
239
+ - lib/msf/sql/processing_node_parameter.rb
240
+ - lib/msf/sql/processing_node_spectrum.rb
241
+ - lib/msf/sql/quan_result.rb
242
+ - lib/msf/sql/result_filter_set.rb
243
+ - lib/msf/sql/taxonomy_node.rb
244
+ - msf.gemspec
245
+ - spec/msf_spec.rb
246
+ - spec/spec_helper.rb
247
+ homepage: http://github.com/vanetten/msf
248
+ licenses:
249
+ - MIT
250
+ post_install_message:
251
+ rdoc_options: []
252
+ require_paths:
253
+ - lib
254
+ required_ruby_version: !ruby/object:Gem::Requirement
255
+ none: false
256
+ requirements:
257
+ - - ! '>='
258
+ - !ruby/object:Gem::Version
259
+ version: '0'
260
+ segments:
261
+ - 0
262
+ hash: -3318715706776057630
263
+ required_rubygems_version: !ruby/object:Gem::Requirement
264
+ none: false
265
+ requirements:
266
+ - - ! '>='
267
+ - !ruby/object:Gem::Version
268
+ version: '0'
269
+ requirements: []
270
+ rubyforge_project:
271
+ rubygems_version: 1.8.24
272
+ signing_key:
273
+ specification_version: 3
274
+ summary: ActiveRecord access to MSF file (sqlite3 database).
275
+ test_files: []