ms-msrun 0.1.0 → 0.2.0

metadata

@@ -1,15 +1,15 @@
 --- !ruby/object:Gem::Specification 
 name: ms-msrun
 version: !ruby/object:Gem::Version 
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors: 
-- John Prince
+- John T. Prince
 autorequire: 
 bindir: bin
 cert_chain: []
 
-date: 2009-11-11 00:00:00 -07:00
+date: 2009-12-07 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -33,7 +33,7 @@ dependencies:
         version: "0"
     version: 
 - !ruby/object:Gem::Dependency 
-  name: runarray
+  name: narray
   type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
@@ -42,49 +42,95 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: "0"
     version: 
-description: A library for working with LC/MS runs. Part of mspire.  Has parsers for mzXML v1, 2, and 3, mzData and mzML.  Can convert to commonly desired search output (such as mgf)
+- !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: A library for working with LC/MS runs. Part of mspire.  Has parsers for mzXML v1, 2, and 3, mzData (currently broken) and mzML (planned).  Can convert to commonly desired search output (such as mgf).  Fast random access of scans, and fast reading of the entire file.
 email: jtprince@gmail.com
 executables: 
 - base64_to_array.rb
-- ms_to_obiwarp.rb
 - ms_to_search.rb
+- ms_to_obiwarp.rb
 extensions: []
 
 extra_rdoc_files: 
-- README
 - LICENSE
+- README.rdoc
 files: 
+- .gitignore
+- .gitmodules
+- History
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/base64_to_array.rb
+- bin/ms_to_obiwarp.rb
+- bin/ms_to_search.rb
 - lib/lmat.rb
-- lib/ms/spectrum/filter.rb
-- lib/ms/spectrum/compare.rb
-- lib/ms/scan.rb
-- lib/ms/msrun/sha1.rb
-- lib/ms/msrun/regexp/mzxml.rb
-- lib/ms/msrun/search.rb
-- lib/ms/msrun/index.rb
-- lib/ms/msrun/nokogiri/mzxml.rb
+- lib/ms/msrun.rb
 - lib/ms/msrun/axml/mzxml.rb
+- lib/ms/msrun/index.rb
 - lib/ms/msrun/mzxml.rb
 - lib/ms/msrun/nokogiri.rb
-- lib/ms/precursor.rb
+- lib/ms/msrun/nokogiri/mzxml.rb
+- lib/ms/msrun/regexp/mzxml.rb
+- lib/ms/msrun/search.rb
+- lib/ms/msrun/search_dev_notes.txt
+- lib/ms/msrun/sha1.rb
 - lib/ms/mzxml.rb
-- lib/ms/msrun.rb
+- lib/ms/precursor.rb
 - lib/ms/precursor/lazy_parent.rb
-- README
-- LICENSE
-- Rakefile
+- lib/ms/scan.rb
+- lib/ms/spectrum/compare.rb
+- lib/ms/spectrum/filter.rb
+- spec/lmat_spec.rb
+- spec/metadata/opd1/000.v1.mzXML.yml
+- spec/metadata/opd1/000.v2.1.mzXML.yml
+- spec/metadata/opd1/020.mzData.xml.yml
+- spec/metadata/opd1/020.v2.0.readw.mzXML.yml
+- spec/ms/msrun/hpricot.rb
+- spec/ms/msrun/index_spec.rb
+- spec/ms/msrun/scan_spec.rb
+- spec/ms/msrun/search_spec.rb
+- spec/ms/msrun/sha1_spec.rb
+- spec/ms/msrun/test_parsing_xml_frags/parse_test.rb
+- spec/ms/msrun/test_parsing_xml_frags/test1.xml
+- spec/ms/msrun/test_parsing_xml_frags/test2.xml
+- spec/ms/msrun/test_parsing_xml_frags/test3.xml
+- spec/ms/msrun/test_parsing_xml_frags/test4.xml
+- spec/ms/msrun/test_parsing_xml_frags/test_failures.rb
+- spec/ms/msrun_bm.rb
+- spec/ms/msrun_spec.rb
+- spec/ms/scan_spec.rb
+- spec/ms/spectrum/compare_spec.rb
+- spec/ms/spectrum/filter_spec.rb
+- spec/spec_helper.rb
+- spec/testfiles/lmat/tmp1.lmat
+- spec/testfiles/lmat/tmp1.lmata
+- spec/testfiles/lmat/tmp2.lmata
+- spec/testfiles/opd1/000.v1.mzXML
+- spec/testfiles/opd1/000.v1.mzXML.key.yml
+- spec/testfiles/opd1/000.v2.1.mzXML
+- spec/testfiles/opd1/000.v2.1.mzXML.key.yml
+- spec/testfiles/opd1/020.mzData.xml
+- spec/testfiles/opd1/020.mzData.xml.key.yml
+- spec/testfiles/opd1/020.v2.0.readw.mzXML
+- spec/testfiles/opd1/020.v2.0.readw.mzXML.key.yml
 has_rdoc: true
-homepage: http://mspire.rubyforge.org/projects/ms-msrun
+homepage: http://jtprince.github.com/ms-msrun/
 licenses: []
 
 post_install_message: 
 rdoc_options: 
-- --main
-- README
-- --title
-- ms-msrun
-- --line-numbers
-- --inline-source
+- --charset=UTF-8
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
@@ -102,17 +148,22 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: mspire
-rubygems_version: 1.3.2
+rubygems_version: 1.3.5
 signing_key: 
 specification_version: 3
-summary: A library for working with LC/MS runs
+summary: an mspire library for working with LC/MS runs (mzxml, mzData, mzML)
 test_files: 
-- spec/ms/spectrum/filter_spec.rb
-- spec/ms/spectrum/compare_spec.rb
+- spec/ms/scan_spec.rb
+- spec/ms/msrun_spec.rb
+- spec/ms/msrun_bm.rb
 - spec/ms/msrun/search_spec.rb
-- spec/ms/msrun/sha1_spec.rb
 - spec/ms/msrun/index_spec.rb
+- spec/ms/msrun/hpricot.rb
 - spec/ms/msrun/scan_spec.rb
-- spec/ms/msrun_spec.rb
-- spec/ms/scan_spec.rb
+- spec/ms/msrun/sha1_spec.rb
+- spec/ms/msrun/test_parsing_xml_frags/parse_test.rb
+- spec/ms/msrun/test_parsing_xml_frags/test_failures.rb
+- spec/ms/spectrum/compare_spec.rb
+- spec/ms/spectrum/filter_spec.rb
 - spec/lmat_spec.rb
+- spec/spec_helper.rb