changing namespace to mspire from ms

lib/ms/lipid.rb → lib/mspire/lipid.rb

@@ -1,5 +1,5 @@
 
-module MS
+module Mspire
   class Lipid
     def self.members
       [:lm_id,:common_name,:systematic_name,:formula,:mass,:category,:main_class,:sub_class]

lib/ms/lipid/ion.rb → lib/mspire/lipid/ion.rb

@@ -1,12 +1,12 @@
 
-module MS
+module Mspire
   class Lipid
     # a lipid with modifications (typically the mods give it a charge so that
     # it can be seen in the mass spec)
     class Ion
-      # an MS::Lipid object
+      # an Mspire::Lipid object
       attr_accessor :lipid
-      # an MS::Lipid::Modifications object
+      # an Mspire::Lipid::Modifications object
       attr_accessor :modifications
       # the key attribute of a query
 

lib/ms/lipid/modification.rb → lib/mspire/lipid/modification.rb

@@ -1,6 +1,6 @@
-require 'ms/mass'
+require 'mspire/mass'
 
-module MS
+module Mspire
   class Lipid
 
 
@@ -27,9 +27,9 @@ def self.formula_and_charge(string)
       # electron is added.  If gain is false, then the mass diff will be
       # negative.
       def self.massdiff(formula, charge, gain=true)
-        MS::Mass.formula_to_exact_mass(formula)
-        massdiff = MS::Mass.formula_to_exact_mass(formula)
-        massdiff -= (charge * MS::Mass::ELECTRON) # + charge subtracts, - charge adds
+        Mspire::Mass.formula_to_exact_mass(formula)
+        massdiff = Mspire::Mass.formula_to_exact_mass(formula)
+        massdiff -= (charge * Mspire::Mass::ELECTRON) # + charge subtracts, - charge adds
         massdiff = -massdiff unless gain
         massdiff
       end
@@ -50,7 +50,7 @@ def self.massdiff(formula, charge, gain=true)
         :water => 0,
       }
 
-      # determined by running formulas through MS::Mass.massdiff
+      # determined by running formulas through Mspire::Mass.massdiff
       MASSDIFFS = {}
       FORMULAS.each do |name, formula|
          MASSDIFFS[name] = self.massdiff(formula, CHARGE[name])

lib/ms/lipid/search.rb → lib/mspire/lipid/search.rb

@@ -1,12 +1,12 @@
-require 'ms/spectrum'
+require 'mspire/spectrum'
 require 'rserve/simpler'  # TODO: move to integrated interface with rserve when available
 require 'core_ext/array/in_groups'
-require 'ms/lipid/search/hit'
-require 'ms/lipid/search/bin'
-require 'ms/lipid/modification'
-require 'ms/lipid/search/probability_distribution'
+require 'mspire/lipid/search/hit'
+require 'mspire/lipid/search/bin'
+require 'mspire/lipid/modification'
+require 'mspire/lipid/search/probability_distribution'
 
-module MS
+module Mspire
   class Lipid
     class Search
       STANDARD_MODIFICATIONS = {
@@ -32,11 +32,11 @@ class Search
       # true
       def self.generate_simple_queries(lipids, mods=STANDARD_MODIFICATIONS, gain_and_loss=false)
         possible_lipids = []
-        real_mods_and_cnts = mods.map {|name, cnts| [MS::Lipid::Modification.new(name), cnts] }
+        real_mods_and_cnts = mods.map {|name, cnts| [Mspire::Lipid::Modification.new(name), cnts] }
         # one of each
         real_mods_and_cnts.each do |mod, counts|
           counts.each do |cnt|
-            possible_lipids << MS::Lipid::Search::Query.new(lipid, Array.new(cnt, mod))
+            possible_lipids << Mspire::Lipid::Search::Query.new(lipid, Array.new(cnt, mod))
           end
         end
         if gain_and_loss
@@ -52,7 +52,7 @@ def self.generate_simple_queries(lipids, mods=STANDARD_MODIFICATIONS, gain_and_l
         self.new(possible_lipids)
       end
 
-      # ions are MS::Lipid::Ion objects
+      # ions are Mspire::Lipid::Ion objects
       # each one should give a non-nil m/z value
       def initialize(ions=[], opts={})
         @options = STANDARD_SEARCH.merge(opts)
@@ -145,7 +145,7 @@ def create_db_isobar_spectrum(ions)
         mzs = [] ; query_groups = []
         pairs = ions.group_by(&:mz).sort_by(&:first)
         pairs.each {|mz, ar| mzs << mz ; query_groups << ar }
-        MS::Spectrum.new([mzs, query_groups])
+        Mspire::Spectrum.new([mzs, query_groups])
       end
 
       # use_ppm uses ppm or amu if false
@@ -185,15 +185,15 @@ def create_search_bins(db_isobar_spectrum, min_n_per_bin)
           raise 'I think you need some data in your query spectrum!'
         when 1
           group = groups.first
-          [ MS::Lipid::Search::Bin.new( Range.new(group.first.first, group.last.first), db_isobar_spectrum ) ]
+          [ Mspire::Lipid::Search::Bin.new( Range.new(group.first.first, group.last.first), db_isobar_spectrum ) ]
         else
           search_bins = groups.each_cons(2).map do |points1, points2|
-            bin = MS::Lipid::Search::Bin.new( Range.new(points1.first.first, points2.first.first, true), db_isobar_spectrum )
+            bin = Mspire::Lipid::Search::Bin.new( Range.new(points1.first.first, points2.first.first, true), db_isobar_spectrum )
             prev = points2
             bin
           end
           _range = Range.new(prev.first.first, prev.last.first)
-          search_bins << MS::Lipid::Search::Bin.new(_range, db_isobar_spectrum) # inclusive
+          search_bins << Mspire::Lipid::Search::Bin.new(_range, db_isobar_spectrum) # inclusive
         end
       end
     end

lib/ms/lipid/search/bin.rb → lib/mspire/lipid/search/bin.rb

@@ -1,14 +1,14 @@
-require 'bin'
+require 'mspire/bin'
 
-module MS
+module Mspire
   class Lipid
     class Search
 
       # A Search::Bin is a range that contains the *entire* query spectrum
       # (not just the portion covered by the range).  the query spectrum, and
       # a ProbabilityDistribution -- the probability that a peak's delta to
       # nearest peak is that small by chance.
-      class Bin < ::Bin
+      class Bin < Mspire::Bin
         # the intensity value of the query spectrum should be a query
         attr_accessor :db_spectrum
         attr_accessor :probability_distribution
@@ -22,7 +22,7 @@ def <<(query)
           @data << query
         end
 
-        # returns the nearest num_hits MS::Lipid::Search::Hits sorted by delta
+        # returns the nearest num_hits Mspire::Lipid::Search::Hits sorted by delta
         # [with tie going to the lower m/z]
         # searches all queries and removes them from the data queue
         def queries_to_hit_groups!(num_hits=1)

lib/ms/lipid/search/db_isobar_group.rb → lib/mspire/lipid/search/db_isobar_group.rb

@@ -1,5 +1,5 @@
 
-module MS
+module Mspire
   class Lipid
     class Search
       # this is a group of Lipid::Ion objects that all have the same (or

lib/ms/lipid/search/hit.rb → lib/mspire/lipid/search/hit.rb

@@ -1,5 +1,5 @@
 
-module MS
+module Mspire
   class Lipid
     class Search
       class Hit

lib/ms/lipid/search/probability_distribution.rb → lib/mspire/lipid/search/probability_distribution.rb

@@ -1,5 +1,5 @@
 
-module MS
+module Mspire
   class Lipid
     class Search
       class ProbabilityDistribution

lib/ms/lipid/search/query.rb → lib/mspire/lipid/search/query.rb

@@ -1,7 +1,7 @@
 
 
 
-module MS
+module Mspire
   class Lipid
     class Search
       class Query

lib/ms/lipid_maps.rb → lib/mspire/lipid_maps.rb

@@ -1,7 +1,7 @@
-require 'ms/lipid'
-require 'ms/mass'
+require 'mspire/lipid'
+require 'mspire/mass'
 
-module MS
+module Mspire
   module LipidMaps
     # returns an array of Lipids
     # if high_res_mass is true (default), then the formula is used to calculate a higher
@@ -15,11 +15,11 @@ def self.parse_file(lipidmaps_tsv, high_res_mass=true, skip_clas_defs=true)
           nil
         else
           if seen_first_line
-            pieces[4] = MS::Mass.formula_to_exact_mass(pieces[3]) if high_res_mass
-            l = MS::Lipid.new *pieces
+            pieces[4] = Mspire::Mass.formula_to_exact_mass(pieces[3]) if high_res_mass
+            l = Mspire::Lipid.new *pieces
           else
             seen_first_line = true
-            warn "lipidmaps column headers are not right!" unless pieces.map(&:downcase) == MS::Lipid.members.map(&:to_s)
+            warn "lipidmaps column headers are not right!" unless pieces.map(&:downcase) == Mspire::Lipid.members.map(&:to_s)
             nil
           end
         end

spec/mspire/lipid/ion_spec.rb

@@ -0,0 +1,23 @@
+require 'spec_helper'
+
+
+require 'mspire/lipid'
+require 'mspire/lipid/modification'
+require 'mspire/lipid/ion'
+
+describe Mspire::Lipid::Ion do
+  before do
+    lipid = Mspire::Lipid.new
+    lipid.mass = 300.2
+    proton = Mspire::Lipid::Modification.new(:proton)
+    h2o_loss = Mspire::Lipid::Modification.new(:water, :loss => true)
+    @plus1 = Mspire::Lipid::Ion.new(lipid, [proton, h2o_loss])
+    @plus2 = Mspire::Lipid::Ion.new(lipid, [proton, proton, h2o_loss])
+  end
+
+  it 'calculates the correct m/z' do
+    @plus1.mz.should be_within(1e5).of(283.196711735)
+    @plus2.mz.should be_within(1e5).of(142.101994085)
+  end
+
+end

spec/ms/lipid/modification_spec.rb → spec/mspire/lipid/modification_spec.rb

@@ -1,9 +1,9 @@
 require 'spec_helper'
 
-require 'ms/lipid/modification'
+require 'mspire/lipid/modification'
 
-describe MS::Lipid::Modification do
-  Mod = MS::Lipid::Modification
+describe Mspire::Lipid::Modification do
+  Mod = Mspire::Lipid::Modification
 
   it 'can create common mods easily' do
     # water loss
@@ -35,7 +35,7 @@
 
     mymod.formula = 'CH4'
     mymod.charge = 2
-    mymod.massdiff = MS::Lipid::Modification.massdiff(mymod.formula, mymod.charge)
+    mymod.massdiff = Mspire::Lipid::Modification.massdiff(mymod.formula, mymod.charge)
     mymod.massdiff.should be_within(1e4).of(16.030202)
   end
 end

spec/ms/lipid/search_spec.rb → spec/mspire/lipid/search_spec.rb

@@ -1,21 +1,21 @@
 require 'spec_helper'
 
-require 'ms/lipid_maps'
-require 'ms/lipid/search'
-require 'ms/lipid/search/query'
-require 'ms/lipid/modification'
+require 'mspire/lipid_maps'
+require 'mspire/lipid/search'
+require 'mspire/lipid/search/query'
+require 'mspire/lipid/modification'
 
-describe MS::Lipid::Search do
+describe Mspire::Lipid::Search do
   before do
-    @proton = MS::Lipid::Modification.new(:proton)
-    @h2o_loss = MS::Lipid::Modification.new(:water, :loss => true)
+    @proton = Mspire::Lipid::Modification.new(:proton)
+    @h2o_loss = Mspire::Lipid::Modification.new(:water, :loss => true)
   end
   describe 'searching a section of lipid maps' do
     before do
-      @lipids = MS::LipidMaps.parse_file(TESTFILES + '/lipidmaps_short.tsv')
+      @lipids = Mspire::LipidMaps.parse_file(TESTFILES + '/lipidmaps_short.tsv')
       @ions = @lipids.map do |lipid| 
         [[@proton], [@proton, @h2o_loss]].map do |mods|
-          MS::Lipid::Ion.new(lipid, mods)
+          Mspire::Lipid::Ion.new(lipid, mods)
         end
       end.flatten(1)
       @samples = Hash[ {
@@ -27,7 +27,7 @@
           [120, 220, 120, 220, 120]],
         :sample4 => [[187.157, 396.20, 244.30, 618.22, 933.01],
           [30, 33, 38, 99, 22]],
-      }.map {|key,data| [key, MS::Spectrum.new(data)] } ]
+      }.map {|key,data| [key, Mspire::Spectrum.new(data)] } ]
       @pretend_search_mzs = [187.157, 396.20, 244.30, 618.22, 933.01]
     end
 
@@ -44,7 +44,7 @@
     end
 
     xit 'searches mz values' do
-      searcher = MS::Lipid::Search.new(@ions, :query_min_count_per_bin => 8, :num_rand_samples_per_bin => 1000, :ppm => false)
+      searcher = Mspire::Lipid::Search.new(@ions, :query_min_count_per_bin => 8, :num_rand_samples_per_bin => 1000, :ppm => false)
       num_nearest_hits = 3
       (hit_groups, qvals) = searcher.search(@pretend_search_mzs, 3)
       p hit_groups.map(&:first).map(&:pvalue)
@@ -56,17 +56,17 @@
     before do
       # this will be specific to your install since it's not part of install
       path_to_lipidmaps_db = "#{ENV['HOME']}/tmp/tamil/lipidmaps_20120103_classes_1_2_3_4_5_6_7_8.exact_mass.tsv"
-      @lipids = MS::LipidMaps.parse_file(path_to_lipidmaps_db)
+      @lipids = Mspire::LipidMaps.parse_file(path_to_lipidmaps_db)
       @ions = @lipids.map do |lipid| 
         [[@proton], [@proton, @proton], [@proton, @h2o_loss]].map do |mods|
-          MS::Lipid::Search::Query.new(lipid, mods)
+          Mspire::Lipid::Search::Query.new(lipid, mods)
         end
       end.flatten(1)
       @pretend_search_mzs = [187.157, 396.20, 244.30, 618.22, 933.01]
     end
 
     it 'returns hit groups parallel with input m/zs' do
-      searcher = MS::Lipid::Search.new(@ions, :query_min_count_per_bin => 1000, :ppm => false)
+      searcher = Mspire::Lipid::Search.new(@ions, :query_min_count_per_bin => 1000, :ppm => false)
       hit_groups = searcher.search(@pretend_search_mzs, 3)
       best_hits = hit_groups.map(&:best_hit)
       best_hits.map {|hit| hit.observed_mz }.should == @pretend_search_mzs

spec/ms/lipid_spec.rb → spec/mspire/lipid_spec.rb

@@ -1,15 +1,15 @@
 require 'spec_helper'
 
-require 'ms/lipid'
+require 'mspire/lipid'
 
-describe MS::Lipid do
+describe Mspire::Lipid do
 
   before do
     @data = ['LMFA00000007', 'n-decanohydroxamic acid', 'N-hydroxydecanamide', 'C10H21NO2', 187.16, 'Fatty Acyls [FA]', 'Other Fatty Acyls [FA00]']
   end
 
   it 'can be initialized with an array' do
-    lipid = MS::Lipid.new(*@data)
+    lipid = Mspire::Lipid.new(*@data)
     lipid.mass.should == @data[4]
     lipid.sub_class.should == nil
   end