mspire 0.6.19 → 0.6.20

data/VERSION

@@ -1 +1 @@
-0.6.19
+0.6.20

data/lib/ms/fasta.rb

@@ -45,6 +45,7 @@ module MS
 
     # yields each Bio::FastaFormat object in turn
     def self.foreach(file, &block)
+      block or return enum_for(__method__, file)
       Bio::FlatFile.open(Bio::FastaFormat, file) do |fasta|
         fasta.each(&block)
       end

data/lib/ms/mzml/spectrum.rb

@@ -73,7 +73,12 @@ module MS
           params[cvparam[:accession]] = cvparam[:value]
         end
         spec.ms_level = params['MS:1000511'].to_i
+        # we assume centroid if they don't tell us profile
+        spec.centroided = !params.key?("MS:1000128") # profile spectrum 
+        # centroid -> "MS:1000127"
+
         # TODO: need to slot in all the other info in reasonable ways
+        # TODO: need to make sure we deal with referencable params
 
         data_arrays = xml.xpath('./binaryDataArrayList/binaryDataArray').map do |binary_data_array_n|
           accessions = binary_data_array_n.xpath('./cvParam').map {|node| node['accession'] }

data/lib/ms/spectrum.rb

@@ -52,7 +52,7 @@ module MS
       def merge(spectra, opts={})
         opt = DEFAULT_MERGE.merge(opts)
         (spectrum, returned_data) =  
-          if spectra.first.centroided?
+          unless spectra.first.centroided? == false
             # find the min and max across all spectra
             first_mzs = spectra.first.mzs
             min = first_mzs.first ; max = first_mzs.last

data/spec/ms/mzml_spec.rb

@@ -40,8 +40,10 @@ describe MS::Mzml do
 
       it 'goes through spectrum with #each or #each_spectrum' do
         mz_sizes = [20168, 315, 634]
+        centroided = [false, true, true]
         @mzml.each do |spec|
           spec.mzs.size.should == mz_sizes.shift
+          spec.centroided?.should == centroided.shift
         end
       end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.6.19
+  version: 0.6.20
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2012-02-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &10271800 !ruby/object:Gem::Requirement
+  requirement: &23959880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: '1.5'
   type: :runtime
   prerelease: false
-  version_requirements: *10271800
+  version_requirements: *23959880
 - !ruby/object:Gem::Dependency
   name: bsearch
-  requirement: &10656900 !ruby/object:Gem::Requirement
+  requirement: &23959360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *10656900
+  version_requirements: *23959360
 - !ruby/object:Gem::Dependency
   name: andand
-  requirement: &10739280 !ruby/object:Gem::Requirement
+  requirement: &23958860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: 1.3.1
   type: :runtime
   prerelease: false
-  version_requirements: *10739280
+  version_requirements: *23958860
 - !ruby/object:Gem::Dependency
   name: obo
-  requirement: &10814460 !ruby/object:Gem::Requirement
+  requirement: &23958340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *10814460
+  version_requirements: *23958340
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &10811160 !ruby/object:Gem::Requirement
+  requirement: &23974240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: '2.6'
   type: :development
   prerelease: false
-  version_requirements: *10811160
+  version_requirements: *23974240
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &10888880 !ruby/object:Gem::Requirement
+  requirement: &23973760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *10888880
+  version_requirements: *23973760
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &10902860 !ruby/object:Gem::Requirement
+  requirement: &23973280 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *10902860
+  version_requirements: *23973280
 description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
   merging of ms-* gems
 email: jtprince@gmail.com