mspire 0.6.26 → 0.7.2

data/spec/{ms → mspire}/user_param_spec.rb

@@ -1,22 +1,22 @@
 require 'spec_helper'
 
-require 'ms/user_param'
-require 'ms/cv/param'
+require 'mspire/user_param'
+require 'mspire/cv/param'
 
-describe MS::UserParam do
+describe Mspire::UserParam do
 
   describe 'initializing with various args' do
 
     it 'can be initialized with the name' do
       arg = 'special_user_param'
-      param = MS::UserParam.new arg
+      param = Mspire::UserParam.new arg
       param.name.should == arg
       param.unit.should be_nil
     end
 
     it' can be initialized with an included UO accession' do
       arg = 'special_user_param'
-      param = MS::UserParam.new arg, 'UO:0000108'
+      param = Mspire::UserParam.new arg, 'UO:0000108'
       param.name.should == arg
       param.unit.should_not be_nil
       param.unit.accession.should == 'UO:0000108'
@@ -24,7 +24,7 @@ describe MS::UserParam do
 
     it' can be initialized with an included CV::Param (unit)' do
       arg = 'special_user_param'
-      param = MS::UserParam.new arg, MS::CV::Param['UO:0000108']
+      param = Mspire::UserParam.new arg, Mspire::CV::Param['UO:0000108']
       param.name.should == arg
       param.unit.should_not be_nil
       param.unit.accession.should == 'UO:0000108'
@@ -32,14 +32,14 @@ describe MS::UserParam do
 
     it 'can be initialized with a name and value (and type)' do
       args = %w(some_user_param 88 xsd:float)
-      param = MS::UserParam.new *args
+      param = Mspire::UserParam.new *args
       param.name.should == args[0]
       param.value.should == args[1]
       param.type.should == args[2]
       param.unit.should be_nil
 
       args = %w(some_user_param 88 xsd:float UO:0000108)
-      param = MS::UserParam.new *args
+      param = Mspire::UserParam.new *args
       param.name.should == args[0]
       param.value.should == args[1]
       param.type.should == args[2]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.6.26
+  version: 0.7.2
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-15 00:00:00.000000000 Z
+date: 2012-03-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &19248100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,15 +22,10 @@ dependencies:
         version: '1.5'
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '1.5'
+  version_requirements: *19248100
 - !ruby/object:Gem::Dependency
   name: bsearch
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &19245800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -38,15 +33,10 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.5.0
+  version_requirements: *19245800
 - !ruby/object:Gem::Dependency
   name: andand
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &19243220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,15 +44,10 @@ dependencies:
         version: 1.3.1
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.3.1
+  version_requirements: *19243220
 - !ruby/object:Gem::Dependency
   name: obo
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &19629860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -70,15 +55,10 @@ dependencies:
         version: 0.1.0
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 0.1.0
+  version_requirements: *19629860
 - !ruby/object:Gem::Dependency
   name: builder
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &19626740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -86,15 +66,10 @@ dependencies:
         version: 3.0.0
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 3.0.0
+  version_requirements: *19626740
 - !ruby/object:Gem::Dependency
   name: trollop
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &19624700 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -102,15 +77,10 @@ dependencies:
         version: 1.16.2
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.16.2
+  version_requirements: *19624700
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &19713620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -118,15 +88,10 @@ dependencies:
         version: '2.6'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '2.6'
+  version_requirements: *19713620
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &19712460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -134,15 +99,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.5.2
+  version_requirements: *19712460
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &19709160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -150,12 +110,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
+  version_requirements: *19709160
 description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
   merging of ms-* gems
 email: jtprince@gmail.com
@@ -176,84 +131,83 @@ files:
 - lib/cv/referenceable_param_group_ref.rb
 - lib/io/bookmark.rb
 - lib/merge.rb
-- lib/ms.rb
-- lib/ms/cv.rb
-- lib/ms/cv/param.rb
-- lib/ms/cv/paramable.rb
-- lib/ms/digester.rb
-- lib/ms/error_rate/decoy.rb
-- lib/ms/error_rate/qvalue.rb
-- lib/ms/fasta.rb
-- lib/ms/ident.rb
-- lib/ms/ident/peptide.rb
-- lib/ms/ident/peptide/db.rb
-- lib/ms/ident/peptide_hit.rb
-- lib/ms/ident/peptide_hit/qvalue.rb
-- lib/ms/ident/pepxml.rb
-- lib/ms/ident/pepxml/modifications.rb
-- lib/ms/ident/pepxml/msms_pipeline_analysis.rb
-- lib/ms/ident/pepxml/msms_run_summary.rb
-- lib/ms/ident/pepxml/parameters.rb
-- lib/ms/ident/pepxml/sample_enzyme.rb
-- lib/ms/ident/pepxml/search_database.rb
-- lib/ms/ident/pepxml/search_hit.rb
-- lib/ms/ident/pepxml/search_hit/modification_info.rb
-- lib/ms/ident/pepxml/search_result.rb
-- lib/ms/ident/pepxml/search_summary.rb
-- lib/ms/ident/pepxml/spectrum_query.rb
-- lib/ms/ident/protein.rb
-- lib/ms/ident/protein_group.rb
-- lib/ms/ident/search.rb
-- lib/ms/isotope.rb
-- lib/ms/isotope/aa.rb
-- lib/ms/isotope/distribution.rb
-- lib/ms/isotope/nist_isotope_info.yml
-- lib/ms/mascot.rb
-- lib/ms/mass.rb
-- lib/ms/mass/aa.rb
-- lib/ms/molecular_formula.rb
-- lib/ms/mzml.rb
-- lib/ms/mzml/activation.rb
-- lib/ms/mzml/chromatogram.rb
-- lib/ms/mzml/chromatogram_list.rb
-- lib/ms/mzml/component.rb
-- lib/ms/mzml/contact.rb
-- lib/ms/mzml/cv.rb
-- lib/ms/mzml/data_array.rb
-- lib/ms/mzml/data_array_container_like.rb
-- lib/ms/mzml/data_processing.rb
-- lib/ms/mzml/file_content.rb
-- lib/ms/mzml/file_description.rb
-- lib/ms/mzml/index_list.rb
-- lib/ms/mzml/instrument_configuration.rb
-- lib/ms/mzml/isolation_window.rb
-- lib/ms/mzml/list.rb
-- lib/ms/mzml/plms1.rb
-- lib/ms/mzml/precursor.rb
-- lib/ms/mzml/processing_method.rb
-- lib/ms/mzml/product.rb
-- lib/ms/mzml/referenceable_param_group.rb
-- lib/ms/mzml/run.rb
-- lib/ms/mzml/sample.rb
-- lib/ms/mzml/scan.rb
-- lib/ms/mzml/scan_list.rb
-- lib/ms/mzml/scan_settings.rb
-- lib/ms/mzml/selected_ion.rb
-- lib/ms/mzml/software.rb
-- lib/ms/mzml/source_file.rb
-- lib/ms/mzml/spectrum.rb
-- lib/ms/mzml/spectrum_list.rb
-- lib/ms/obo.rb
-- lib/ms/peak.rb
-- lib/ms/peak/point.rb
-- lib/ms/plms1.rb
-- lib/ms/quant/qspec.rb
-- lib/ms/quant/qspec/protein_group_comparison.rb
-- lib/ms/spectrum.rb
-- lib/ms/spectrum/centroid.rb
-- lib/ms/spectrum_like.rb
-- lib/ms/user_param.rb
 - lib/mspire.rb
+- lib/mspire/cv.rb
+- lib/mspire/cv/param.rb
+- lib/mspire/cv/paramable.rb
+- lib/mspire/digester.rb
+- lib/mspire/error_rate/decoy.rb
+- lib/mspire/error_rate/qvalue.rb
+- lib/mspire/fasta.rb
+- lib/mspire/ident.rb
+- lib/mspire/ident/peptide.rb
+- lib/mspire/ident/peptide/db.rb
+- lib/mspire/ident/peptide_hit.rb
+- lib/mspire/ident/peptide_hit/qvalue.rb
+- lib/mspire/ident/pepxml.rb
+- lib/mspire/ident/pepxml/modifications.rb
+- lib/mspire/ident/pepxml/msms_pipeline_analysis.rb
+- lib/mspire/ident/pepxml/msms_run_summary.rb
+- lib/mspire/ident/pepxml/parameters.rb
+- lib/mspire/ident/pepxml/sample_enzyme.rb
+- lib/mspire/ident/pepxml/search_database.rb
+- lib/mspire/ident/pepxml/search_hit.rb
+- lib/mspire/ident/pepxml/search_hit/modification_info.rb
+- lib/mspire/ident/pepxml/search_result.rb
+- lib/mspire/ident/pepxml/search_summary.rb
+- lib/mspire/ident/pepxml/spectrum_query.rb
+- lib/mspire/ident/protein.rb
+- lib/mspire/ident/protein_group.rb
+- lib/mspire/ident/search.rb
+- lib/mspire/isotope.rb
+- lib/mspire/isotope/aa.rb
+- lib/mspire/isotope/distribution.rb
+- lib/mspire/isotope/nist_isotope_info.yml
+- lib/mspire/mascot.rb
+- lib/mspire/mass.rb
+- lib/mspire/mass/aa.rb
+- lib/mspire/molecular_formula.rb
+- lib/mspire/mzml.rb
+- lib/mspire/mzml/activation.rb
+- lib/mspire/mzml/chromatogram.rb
+- lib/mspire/mzml/chromatogram_list.rb
+- lib/mspire/mzml/component.rb
+- lib/mspire/mzml/contact.rb
+- lib/mspire/mzml/cv.rb
+- lib/mspire/mzml/data_array.rb
+- lib/mspire/mzml/data_array_container_like.rb
+- lib/mspire/mzml/data_processing.rb
+- lib/mspire/mzml/file_content.rb
+- lib/mspire/mzml/file_description.rb
+- lib/mspire/mzml/index_list.rb
+- lib/mspire/mzml/instrument_configuration.rb
+- lib/mspire/mzml/isolation_window.rb
+- lib/mspire/mzml/list.rb
+- lib/mspire/mzml/plms1.rb
+- lib/mspire/mzml/precursor.rb
+- lib/mspire/mzml/processing_method.rb
+- lib/mspire/mzml/product.rb
+- lib/mspire/mzml/referenceable_param_group.rb
+- lib/mspire/mzml/run.rb
+- lib/mspire/mzml/sample.rb
+- lib/mspire/mzml/scan.rb
+- lib/mspire/mzml/scan_list.rb
+- lib/mspire/mzml/scan_settings.rb
+- lib/mspire/mzml/selected_ion.rb
+- lib/mspire/mzml/software.rb
+- lib/mspire/mzml/source_file.rb
+- lib/mspire/mzml/spectrum.rb
+- lib/mspire/mzml/spectrum_list.rb
+- lib/mspire/obo.rb
+- lib/mspire/peak.rb
+- lib/mspire/peak/point.rb
+- lib/mspire/plms1.rb
+- lib/mspire/quant/qspec.rb
+- lib/mspire/quant/qspec/protein_group_comparison.rb
+- lib/mspire/spectrum.rb
+- lib/mspire/spectrum/centroid.rb
+- lib/mspire/spectrum_like.rb
+- lib/mspire/user_param.rb
 - lib/obo/ims.rb
 - lib/obo/ms.rb
 - lib/obo/ontology.rb
@@ -266,60 +220,60 @@ files:
 - obo/unit.obo
 - script/mzml_read_binary.rb
 - spec/bin_spec.rb
-- spec/ms/cv/param_spec.rb
-- spec/ms/digester_spec.rb
-- spec/ms/error_rate/qvalue_spec.rb
-- spec/ms/fasta_spec.rb
-- spec/ms/ident/peptide/db_spec.rb
-- spec/ms/ident/pepxml/sample_enzyme_spec.rb
-- spec/ms/ident/pepxml/search_hit/modification_info_spec.rb
-- spec/ms/ident/pepxml_spec.rb
-- spec/ms/ident/protein_group_spec.rb
-- spec/ms/isotope/aa_spec.rb
-- spec/ms/isotope/distribution_spec.rb
-- spec/ms/isotope_spec.rb
-- spec/ms/mass_spec.rb
-- spec/ms/molecular_formula_spec.rb
-- spec/ms/mzml/cv_spec.rb
-- spec/ms/mzml/data_array_spec.rb
-- spec/ms/mzml/file_content_spec.rb
-- spec/ms/mzml/file_description_spec.rb
-- spec/ms/mzml/index_list_spec.rb
-- spec/ms/mzml/plms1_spec.rb
-- spec/ms/mzml/referenceable_param_group_spec.rb
-- spec/ms/mzml_spec.rb
-- spec/ms/peak_spec.rb
-- spec/ms/plms1_spec.rb
-- spec/ms/quant/qspec_spec.rb
-- spec/ms/spectrum_spec.rb
-- spec/ms/user_param_spec.rb
+- spec/mspire/cv/param_spec.rb
+- spec/mspire/digester_spec.rb
+- spec/mspire/error_rate/qvalue_spec.rb
+- spec/mspire/fasta_spec.rb
+- spec/mspire/ident/peptide/db_spec.rb
+- spec/mspire/ident/pepxml/sample_enzyme_spec.rb
+- spec/mspire/ident/pepxml/search_hit/modification_info_spec.rb
+- spec/mspire/ident/pepxml_spec.rb
+- spec/mspire/ident/protein_group_spec.rb
+- spec/mspire/isotope/aa_spec.rb
+- spec/mspire/isotope/distribution_spec.rb
+- spec/mspire/isotope_spec.rb
+- spec/mspire/mass_spec.rb
+- spec/mspire/molecular_formula_spec.rb
+- spec/mspire/mzml/cv_spec.rb
+- spec/mspire/mzml/data_array_spec.rb
+- spec/mspire/mzml/file_content_spec.rb
+- spec/mspire/mzml/file_description_spec.rb
+- spec/mspire/mzml/index_list_spec.rb
+- spec/mspire/mzml/plms1_spec.rb
+- spec/mspire/mzml/referenceable_param_group_spec.rb
+- spec/mspire/mzml_spec.rb
+- spec/mspire/peak_spec.rb
+- spec/mspire/plms1_spec.rb
+- spec/mspire/quant/qspec_spec.rb
+- spec/mspire/spectrum_spec.rb
+- spec/mspire/user_param_spec.rb
 - spec/mspire_spec.rb
 - spec/obo_spec.rb
 - spec/spec_helper.rb
-- spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta
-- spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
-- spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML
-- spec/testfiles/ms/mzml/mspire_simulated.MSn.check.mzML
-- spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML
-- spec/testfiles/ms/quant/kill_extra_tabs.rb
-- spec/testfiles/ms/quant/max_quant_output.provenance.txt
-- spec/testfiles/ms/quant/max_quant_output.txt
-- spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv
-- spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp
-- spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv
-- spec/testfiles/ms/quant/pdcd5_final.txt
-- spec/testfiles/ms/quant/pdcd5_final.txt_qspecgp
-- spec/testfiles/ms/quant/pdcd5_lfq_qspec.CSV.csv
-- spec/testfiles/ms/quant/pdcd5_lfq_qspec.csv
-- spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.csv
-- spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv
-- spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp
-- spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv
-- spec/testfiles/ms/quant/pdcd5_lfq_qspec.txt
-- spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt
-- spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt_qspecgp
-- spec/testfiles/ms/quant/remove_rest_of_proteins.rb
-- spec/testfiles/ms/quant/unlog_transform.rb
+- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.fasta
+- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
+- spec/testfiles/mspire/mzml/j24z.idx_comp.3.mzML
+- spec/testfiles/mspire/mzml/mspire_simulated.MSn.check.mzML
+- spec/testfiles/mspire/mzml/openms.noidx_nocomp.12.mzML
+- spec/testfiles/mspire/quant/kill_extra_tabs.rb
+- spec/testfiles/mspire/quant/max_quant_output.provenance.txt
+- spec/testfiles/mspire/quant/max_quant_output.txt
+- spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv
+- spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp
+- spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv
+- spec/testfiles/mspire/quant/pdcd5_final.txt
+- spec/testfiles/mspire/quant/pdcd5_final.txt_qspecgp
+- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.CSV.csv
+- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.csv
+- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.csv
+- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv
+- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp
+- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv
+- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.txt
+- spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt
+- spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt_qspecgp
+- spec/testfiles/mspire/quant/remove_rest_of_proteins.rb
+- spec/testfiles/mspire/quant/unlog_transform.rb
 - spec/testfiles/plms1/output.key
 homepage: http://github.com/princelab/mspire
 licenses:
@@ -342,7 +296,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.18
+rubygems_version: 1.8.15
 signing_key: 
 specification_version: 3
 summary: mass spectrometry proteomics, lipidomics, and tools