mspire 0.6.25 → 0.6.26

data/VERSION

@@ -1 +1 @@
-0.6.25
+0.6.26

data/lib/ms/molecular_formula.rb

@@ -1,13 +1,19 @@
 require 'ms/isotope'
+require 'ms/isotope/aa'
+require 'ms/mass'
 
 module MS
   class MolecularFormula < Hash
 
+    # integer desribing the charge state
+    # mass calculations will add/remove electron mass from this
+    attr_accessor :charge
     # takes a string or a hash:
     #
     #     "H22C12N1O3S2BeLi2"                    # <= order doesn't matter
     #     {h: 22, c: 12, n: 1, o: 3, s: 2}  # case and string/sym doesn't matter
-    def initialize(arg)
+    def initialize(arg, charge=0)
+      @charge = charge
       if arg.is_a?(String)
         arg.scan(/([A-Z][a-z]?)(\d*)/).each do |k,v| 
           self[k.downcase.to_sym] = (v == '' ? 1 : v.to_i)
@@ -17,5 +23,20 @@ module MS
       end
     end
 
+    def self.from_aaseq(aaseq)
+      hash = aaseq.each_char.inject({}) do |hash,aa| 
+        hash.merge(MS::Isotope::AA::ATOM_COUNTS[aa]) {|h,o,n| (o ? o : 0) +n }
+      end
+      hash[:h] += 2
+      hash[:o] += 1
+      self.new(hash)
+    end
+
+    # gives the monoisotopic mass adjusted by the current charge
+    def mass
+      mss = inject(0.0) {|sum,(el,cnt)| sum + (MS::Mass::MONO[el]*cnt) }
+      mss - (MS::Mass::ELECTRON * charge)
+    end
+
   end
 end

data/lib/ms/mzml/scan.rb

@@ -24,6 +24,10 @@ module MS
         block.call(self) if block
       end
 
+      # takes a nokogiri node
+      #def self.from_xml(xml)
+      #end
+
       def to_xml(builder)
         atts = {}
         if @from_external_source_file

data/lib/ms/mzml/spectrum.rb

@@ -64,6 +64,10 @@ module MS
       # currently being described, ordered.
       attr_accessor :products
 
+      attr_accessor :retention_time
+      # when properly implemented, this will access the first scan and the
+      # 'scan start time' cv element.
+
       # takes a Nokogiri node and sets relevant properties
       def self.from_xml(xml)
         spec = MS::Mzml::Spectrum.new(xml[:id])
@@ -77,8 +81,21 @@ module MS
         spec.centroided = !params.key?("MS:1000128") # profile spectrum 
         # centroid -> "MS:1000127"
 
+        # this is a quick hack to get retention time, implement fully as shown
+        # below!
+        cv_param = xml.xpath("./scanList/scan/cvParam[@accession='MS:1000016']").first
+        retention_time = cv_param && cv_param['value'].to_f
+
+        # this is roughly how the scan list stuff should be implemented:
+=begin
+        sl_obj = MS::Mzml::ScanList.new
+
         # TODO: need to slot in all the other info in reasonable ways
         # TODO: need to make sure we deal with referencable params
+        scan_list = xml.xpath('.scanList/scan').each do |scan_n|
+          sl_obj << MS::Mzml::Scan.from_xml(scan_n)
+        end
+=end
 
         data_arrays = xml.xpath('./binaryDataArrayList/binaryDataArray').map do |binary_data_array_n|
           accessions = binary_data_array_n.xpath('./cvParam').map {|node| node['accession'] }
@@ -89,6 +106,7 @@ module MS
         # just has no mzs or intensities
         data_arrays = [MS::Mzml::DataArray.new, MS::Mzml::DataArray.new] if data_arrays.size == 0
         spec.data_arrays = data_arrays
+        spec.retention_time = retention_time
         spec
       end
 

data/mspire.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "mspire"
-  s.version = "0.6.25"
+  s.version = "0.6.26"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["John T. Prince", "Simon Chiang"]
-  s.date = "2012-03-13"
+  s.date = "2012-03-15"
   s.description = "mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire, merging of ms-* gems"
   s.email = "jtprince@gmail.com"
   s.extra_rdoc_files = [
@@ -177,7 +177,7 @@ Gem::Specification.new do |s|
   s.homepage = "http://github.com/princelab/mspire"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.15"
+  s.rubygems_version = "1.8.18"
   s.summary = "mass spectrometry proteomics, lipidomics, and tools"
 
   if s.respond_to? :specification_version then

data/spec/ms/mzml_spec.rb

@@ -38,6 +38,12 @@ describe MS::Mzml do
         spectrum.should be_a(MS::Mzml::Spectrum)
       end
 
+      it 'each spectrum knows its retention_time' do
+        spec = @mzml[1]
+        rt = @mzml[1].retention_time
+        rt.should == 33.035128333333333
+      end
+
       it 'goes through spectrum with #each or #each_spectrum' do
         mz_sizes = [20168, 315, 634]
         centroided = [false, true, true]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.6.25
+  version: 0.6.26
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-13 00:00:00.000000000 Z
+date: 2012-03-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &13676060 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,15 @@ dependencies:
         version: '1.5'
   type: :runtime
   prerelease: false
-  version_requirements: *13676060
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.5'
 - !ruby/object:Gem::Dependency
   name: bsearch
-  requirement: &13674700 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +38,15 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *13674700
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.0
 - !ruby/object:Gem::Dependency
   name: andand
-  requirement: &13673200 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +54,15 @@ dependencies:
         version: 1.3.1
   type: :runtime
   prerelease: false
-  version_requirements: *13673200
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.3.1
 - !ruby/object:Gem::Dependency
   name: obo
-  requirement: &13672440 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +70,15 @@ dependencies:
         version: 0.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *13672440
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.0
 - !ruby/object:Gem::Dependency
   name: builder
-  requirement: &13671860 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -66,10 +86,15 @@ dependencies:
         version: 3.0.0
   type: :runtime
   prerelease: false
-  version_requirements: *13671860
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.0.0
 - !ruby/object:Gem::Dependency
   name: trollop
-  requirement: &13687020 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,10 +102,15 @@ dependencies:
         version: 1.16.2
   type: :runtime
   prerelease: false
-  version_requirements: *13687020
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.16.2
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &13685880 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +118,15 @@ dependencies:
         version: '2.6'
   type: :development
   prerelease: false
-  version_requirements: *13685880
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.6'
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &13684660 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -99,10 +134,15 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *13684660
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.5.2
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &13683500 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,7 +150,12 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *13683500
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
   merging of ms-* gems
 email: jtprince@gmail.com
@@ -297,7 +342,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.15
+rubygems_version: 1.8.18
 signing_key: 
 specification_version: 3
 summary: mass spectrometry proteomics, lipidomics, and tools