ms-sequest 0.0.11 → 0.0.12

metadata

@@ -1,10 +1,10 @@
 --- !ruby/object:Gem::Specification 
 name: ms-sequest
 version: !ruby/object:Gem::Version 
-  version: 0.0.11
+  version: 0.0.12
 platform: ruby
 authors: 
-- John Prince
+- John T. Prince
 autorequire: 
 bindir: bin
 cert_chain: []
@@ -52,6 +52,26 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: 0.2.3
     version: 
+- !ruby/object:Gem::Dependency 
+  name: ms-testdata
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.18.0
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: spec/more
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
 description: reads .SRF, .SQT and supports conversions
 email: jtprince@gmail.com
 executables: 
@@ -60,32 +80,55 @@ executables:
 extensions: []
 
 extra_rdoc_files: 
-- README
-- MIT-LICENSE
-- History
+- LICENSE
+- README.rdoc
 files: 
+- .autotest
+- .gitignore
+- .gitmodules
+- History
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/srf_to_search.rb
+- bin/srf_to_sqt.rb
+- lib/ms/sequest.rb
+- lib/ms/sequest/bioworks.rb
 - lib/ms/sequest/params.rb
+- lib/ms/sequest/pepxml.rb
+- lib/ms/sequest/sqt.rb
+- lib/ms/sequest/srf.rb
 - lib/ms/sequest/srf/search.rb
 - lib/ms/sequest/srf/search/tap.rb
 - lib/ms/sequest/srf/sqt.rb
-- lib/ms/sequest/srf.rb
-- lib/ms/sequest/sqt.rb
-- lib/ms/sequest.rb
-- README
-- MIT-LICENSE
-- History
+- script/fasta_ipi_to_ncbi-ish.rb
+- spec/ms/sequest/bioworks_spec.rb
+- spec/ms/sequest/params_spec.rb
+- spec/ms/sequest/pepxml_spec.rb
+- spec/ms/sequest/sqt_spec.rb
+- spec/ms/sequest/sqt_spec_helper.rb
+- spec/ms/sequest/srf/search_spec.rb
+- spec/ms/sequest/srf/search_spec_helper.rb
+- spec/ms/sequest/srf/sqt_spec.rb
+- spec/ms/sequest/srf_spec.rb
+- spec/ms/sequest/srf_spec_helper.rb
+- spec/spec_helper.rb
+- spec/testfiles/7MIX_STD_110802_1.sequest_params_fragment.srf
+- spec/testfiles/bioworks31.params
+- spec/testfiles/bioworks32.params
+- spec/testfiles/bioworks33.params
+- spec/testfiles/corrupted_900.srf
+- spec/testfiles/small.sqt
+- spec/testfiles/small2.sqt
+- tap.yml
 has_rdoc: true
-homepage: http://mspire.rubyforge.org/projects/ms-sequest/
+homepage: http://jtprince.github.com/ms-sequest
 licenses: []
 
 post_install_message: 
 rdoc_options: 
-- --main
-- README
-- -S
-- -N
-- --title
-- Ms-Sequest
+- --charset=UTF-8
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
@@ -102,10 +145,20 @@ required_rubygems_version: !ruby/object:Gem::Requirement
   version: 
 requirements: []
 
-rubyforge_project: 
+rubyforge_project: mspire
 rubygems_version: 1.3.5
 signing_key: 
 specification_version: 3
 summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc
-test_files: []
-
+test_files: 
+- spec/ms/sequest/srf/search_spec.rb
+- spec/ms/sequest/srf/sqt_spec.rb
+- spec/ms/sequest/srf/search_spec_helper.rb
+- spec/ms/sequest/sqt_spec.rb
+- spec/ms/sequest/params_spec.rb
+- spec/ms/sequest/bioworks_spec.rb
+- spec/ms/sequest/srf_spec.rb
+- spec/ms/sequest/srf_spec_helper.rb
+- spec/ms/sequest/sqt_spec_helper.rb
+- spec/ms/sequest/pepxml_spec.rb
+- spec/spec_helper.rb

data/README

@@ -1,23 +0,0 @@
-= {Ms-Sequest}[http://mspire.rubyforge.org/projects/ms-sequest]
-
-An {Mspire}[http://mspire.rubyforge.org] library supporting SEQUEST, Bioworks, SQT and associated formats.
-
-== Description
-
-* Lighthouse[http://bahuvrihi.lighthouseapp.com/projects/16692-mspire/tickets]
-* Github[http://github.com/jtprince/ms-sequest/tree/master]
-* {Google Group}[http://groups.google.com/group/mspire-forum]
-
-== Installation
-
-Ms-Sequest is available as a gem on RubyForge[http://rubyforge.org/projects/mspire].  Use:
-
-  % gem install ms-sequest
-
-== Info 
-
-Copyright (c) 2006 University of Texas at Austin
-Copyright (c) Regents of the University of Colorado and Howard Hughes Medical Institute.
-Developer:: {John Prince}, {Edward Marcotte Lab}[http://polaris.icmb.utexas.edu/home.html], {Natalie Ahn Lab}[http://www.colorado.edu/chem/people/ahnn.html], {Howard Hughes Medical Institute}[http://www.hhmi.org/], {BYU Dept. of Chemistry and Biochemistry}[http://www.chem.byu.edu/]
-Support:: 
-Licence:: {MIT-Style}[link:files/MIT-LICENSE.html]