mspire 0.6.9 → 0.6.11

data/VERSION

@@ -1 +1 @@
-0.6.9
+0.6.11

data/lib/ms/cv/param.rb

@@ -13,7 +13,8 @@ module MS
       #     acc_num, value[, unit_acc_num]
       #
       # Where acc_num and unit_acc_num are strings containing valid accession
-      # numbers (e.g., 'MS:1000514' or 'UO:0000108')
+      # numbers (e.g., 'MS:1000514' or 'UO:0000108').  Note that sometimes units are
+      # from obo's other than UO.
       def self.[](*args)
         #puts "param args #{args.inspect}"
         unit = 
@@ -21,7 +22,7 @@ module MS
           when 1
             nil
           when 2
-            MS::CV::Param[args.pop] if args.last.to_s[0,3] == 'UO:'
+            MS::CV::Param[args.pop] if args.last.is_a?(String) && args.last =~ /^[A-Za-z]+:/
           when 3
             MS::CV::Param[args.pop]
           end

data/lib/ms/mzml/source_file.rb

@@ -22,9 +22,12 @@ module MS
         self.new DEFAULT_SOURCEFILE_ID, *uri_basename_and_path(path)
       end
 
+      # takes a filename (with a relative or expanded path) and returns the
+      # uri basename and path suitable for mzml files
       def self.uri_basename_and_path(file)
-        pathname = Pathname.new(path)
-        dir = pathname.expand_path.dirname
+        pathname = Pathname.new(file)
+        dir = pathname.expand_path.dirname.to_s
+        p dir
         dir = '/'+dir unless (dir[0] == '/')
         [pathname.basename, 'file://'+ dir]
       end

data/lib/ms/mzml/spectrum.rb

@@ -69,8 +69,10 @@ module MS
       # This would generate a spectrum of ms_level=2 :
       #
       #     MS::Mzml::Spectrum.new(0, "scan=1", 'MS:1000511')
-      def initialize(*args, &block)
-        super(*args)
+      #
+      def initialize(id, opts={params: []}, &block)
+        @id = id
+        describe! *opts[:params]
         block.call(self) if block
       end
 

data/lib/ms/mzml/spectrum_list.rb

@@ -12,9 +12,10 @@ module MS
         super(spectra)
       end
 
-      # This method takes an MS::Spectrum object and transforms it into an
-      # MS::Mzml::Spectrum object and puts it in the internal list
-      def add_ms_spectrum(spectrum, id)
+      # This method takes an object responding to :data, creates a new
+      # MS::Mzml::Spectrum object with that data and puts it in the internal
+      # list
+      def add_ms_spectrum!(spectrum, id)
         mzml_spec = MS::Mzml::Spectrum.new(id)
         mzml_spec.data = spectrum.data
         self << mzml_spec
@@ -22,7 +23,7 @@ module MS
 
       # takes an array of spectra and performs add_spectrum on each
       # returns self
-      def add_spectra(spectra, ids=[])
+      def add_ms_spectra!(spectra, ids=[])
         spectra.zip(ids).each_with_index {|(spec,id),i| add_spectrum(spec, "spectrum=#{i+1}") }
         self
       end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.6.9
+  version: 0.6.11
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-02-21 00:00:00.000000000 Z
+date: 2012-02-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &15540200 !ruby/object:Gem::Requirement
+  requirement: &12116300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: '1.5'
   type: :runtime
   prerelease: false
-  version_requirements: *15540200
+  version_requirements: *12116300
 - !ruby/object:Gem::Dependency
   name: bsearch
-  requirement: &15538300 !ruby/object:Gem::Requirement
+  requirement: &12499740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *15538300
+  version_requirements: *12499740
 - !ruby/object:Gem::Dependency
   name: andand
-  requirement: &15535660 !ruby/object:Gem::Requirement
+  requirement: &12584220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: 1.3.1
   type: :runtime
   prerelease: false
-  version_requirements: *15535660
+  version_requirements: *12584220
 - !ruby/object:Gem::Dependency
   name: obo
-  requirement: &15553840 !ruby/object:Gem::Requirement
+  requirement: &12659560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *15553840
+  version_requirements: *12659560
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &15552520 !ruby/object:Gem::Requirement
+  requirement: &12656320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: '2.6'
   type: :development
   prerelease: false
-  version_requirements: *15552520
+  version_requirements: *12656320
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &15551260 !ruby/object:Gem::Requirement
+  requirement: &12733980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *15551260
+  version_requirements: *12733980
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &15550400 !ruby/object:Gem::Requirement
+  requirement: &12747720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *15550400
+  version_requirements: *12747720
 description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
   merging of ms-* gems
 email: jtprince@gmail.com