mspire 0.6.26 → 0.7.2

data/lib/{ms → mspire}/ident/pepxml/msms_pipeline_analysis.rb

@@ -1,12 +1,12 @@
 require 'merge'
 
-require 'ms/ident/pepxml/msms_run_summary'
+require 'mspire/ident/pepxml/msms_run_summary'
 
-module MS ; end
-module MS::Ident ; end
-class MS::Ident::Pepxml; end
+module Mspire ; end
+module Mspire::Ident ; end
+class Mspire::Ident::Pepxml; end
 
-class MS::Ident::Pepxml::MsmsPipelineAnalysis
+class Mspire::Ident::Pepxml::MsmsPipelineAnalysis
   include Merge
   XMLNS = "http://regis-web.systemsbiology.net/pepXML"
   XMLNS_XSI = "http://www.w3.org/2001/XMLSchema-instance"
@@ -32,7 +32,7 @@ class MS::Ident::Pepxml::MsmsPipelineAnalysis
   attr_writer :date
 
   def block_arg 
-    @msms_run_summary = MS::Ident::Pepxml::MsmsRunSummary.new
+    @msms_run_summary = Mspire::Ident::Pepxml::MsmsRunSummary.new
   end
 
   # if block given, yields a new msms_run_summary to return value of block

data/lib/{ms → mspire}/ident/pepxml/msms_run_summary.rb

@@ -1,15 +1,15 @@
 require 'merge'
 require 'nokogiri'
 
-require 'ms/ident/pepxml/sample_enzyme'
-require 'ms/ident/pepxml/search_summary'
-require 'ms/ident/pepxml/spectrum_query'
+require 'mspire/ident/pepxml/sample_enzyme'
+require 'mspire/ident/pepxml/search_summary'
+require 'mspire/ident/pepxml/spectrum_query'
 
-module MS ; end
-module MS::Ident ; end
-class MS::Ident::Pepxml; end
+module Mspire ; end
+module Mspire::Ident ; end
+class Mspire::Ident::Pepxml; end
 
-class MS::Ident::Pepxml::MsmsRunSummary
+class Mspire::Ident::Pepxml::MsmsRunSummary
   include Merge
   # The name of the pep xml file without any extension
   attr_accessor :base_name
@@ -31,8 +31,8 @@ class MS::Ident::Pepxml::MsmsRunSummary
   attr_accessor :spectrum_queries
 
   def block_arg
-    [@sample_enzyme = MS::Ident::Pepxml::SampleEnzyme.new,    
-      @search_summary = MS::Ident::Pepxml::SearchSummary.new,
+    [@sample_enzyme = Mspire::Ident::Pepxml::SampleEnzyme.new,    
+      @search_summary = Mspire::Ident::Pepxml::SearchSummary.new,
       @spectrum_queries ]
   end
 

data/lib/{ms → mspire}/ident/pepxml/parameters.rb

@@ -1,4 +1,4 @@
-module MS
+module Mspire
   module Ident
     class Pepxml
       class Parameters < Hash

data/lib/{ms → mspire}/ident/pepxml/sample_enzyme.rb

@@ -1,11 +1,11 @@
 require 'merge'
 require 'strscan'
 
-module MS ; end
-module MS::Ident ; end
-class MS::Ident::Pepxml ; end
+module Mspire ; end
+module Mspire::Ident ; end
+class Mspire::Ident::Pepxml ; end
 
-class MS::Ident::Pepxml::SampleEnzyme
+class Mspire::Ident::Pepxml::SampleEnzyme
   include Merge
   # an identifier
   attr_accessor :name

data/lib/{ms → mspire}/ident/pepxml/search_database.rb

@@ -1,9 +1,9 @@
-require 'ms/fasta'
+require 'mspire/fasta'
 require 'merge'
-module MS ; end
-module MS::Ident ; end
+module Mspire ; end
+module Mspire::Ident ; end
 
-class MS::Ident::Pepxml
+class Mspire::Ident::Pepxml
   class SearchDatabase
     include Merge
     # required! the local, full path to the protein sequence database
@@ -33,7 +33,7 @@ class MS::Ident::Pepxml
     # returns self for chaining
     def set_size_of_residues!
       @size_of_residues = 0
-      MS::Fasta.foreach(@local_path) do |entry|
+      Mspire::Fasta.foreach(@local_path) do |entry|
         @size_of_residues += entry.sequence.size
       end
       self

data/lib/{ms → mspire}/ident/pepxml/search_hit.rb

@@ -2,13 +2,13 @@ require 'set'
 require 'merge'
 require 'nokogiri'
 
-module MS ; end
-module MS::Ident ; end
+module Mspire ; end
+module Mspire::Ident ; end
 
 
-class MS::Ident::Pepxml 
+class Mspire::Ident::Pepxml 
 
-  class MS::Ident::Pepxml::SearchHit 
+  class Mspire::Ident::Pepxml::SearchHit 
     include Merge
 
     DEFAULT_MEMBERS = [:hit_rank, :peptide, :peptide_prev_aa, :peptide_next_aa, :num_matched_ions, :tot_num_ions, :calc_neutral_pep_mass, :massdiff, :num_tol_term, :num_missed_cleavages, :is_rejected, :protein, :num_tot_proteins, :protein_desc, :calc_pI, :protein_mw, :modification_info, :search_scores, :spectrum_query]

data/lib/{ms → mspire}/ident/pepxml/search_hit/modification_info.rb

@@ -1,14 +1,14 @@
 require 'andand'
 require 'nokogiri'
 
-module MS ; end
-module MS::Ident ; end
-class MS::Ident::Pepxml ; end
-class MS::Ident::Pepxml::SearchHit ; end
+module Mspire ; end
+module Mspire::Ident ; end
+class Mspire::Ident::Pepxml ; end
+class Mspire::Ident::Pepxml::SearchHit ; end
 
 
 # Positions and masses of modifications
-MS::Ident::Pepxml::SearchHit::ModificationInfo = Struct.new(:modified_peptide, :mod_aminoacid_masses, :mod_nterm_mass, :mod_cterm_mass) do
+Mspire::Ident::Pepxml::SearchHit::ModificationInfo = Struct.new(:modified_peptide, :mod_aminoacid_masses, :mod_nterm_mass, :mod_cterm_mass) do
   ## Should be something like this:
   # <modification_info mod_nterm_mass=" " mod_nterm_mass=" " modified_peptide=" ">
   #   <mod_aminoacid_mass position=" " mass=" "/>
@@ -64,14 +64,14 @@ MS::Ident::Pepxml::SearchHit::ModificationInfo = Struct.new(:modified_peptide, :
     self[3] = node['mod_cterm_mass']
     _masses = []
     node.children do |mass_n|
-      _masses << MS::Ident::Pepxml::SearchHit::ModificationInfo::ModAminoacidMass.new([mass_n['position'].to_i, mass_n['mass'].to_f])
+      _masses << Mspire::Ident::Pepxml::SearchHit::ModificationInfo::ModAminoacidMass.new([mass_n['position'].to_i, mass_n['mass'].to_f])
     end
     self.mod_aminoacid_masses = _masses
     self 
   end
 end
 
-MS::Ident::Pepxml::SearchHit::ModificationInfo::ModAminoacidMass = Struct.new(:position, :mass) do
+Mspire::Ident::Pepxml::SearchHit::ModificationInfo::ModAminoacidMass = Struct.new(:position, :mass) do
   def to_xml(builder)
     builder.mod_aminoacid_mass(:position => position, :mass => mass)
     builder

data/lib/{ms → mspire}/ident/pepxml/search_result.rb

@@ -1,12 +1,12 @@
 require 'nokogiri'
 
-require 'ms/ident/pepxml/search_hit'
+require 'mspire/ident/pepxml/search_hit'
 
-module MS ; end
-module MS::Ident ; end
-class MS::Ident::Pepxml ; end
+module Mspire ; end
+module Mspire::Ident ; end
+class Mspire::Ident::Pepxml ; end
 
-class MS::Ident::Pepxml::SearchResult
+class Mspire::Ident::Pepxml::SearchResult
   # an array of search_hits
   attr_accessor :search_hits
 

data/lib/{ms → mspire}/ident/pepxml/search_summary.rb

@@ -1,13 +1,13 @@
-require 'ms/ident/pepxml/search_database'
-require 'ms/ident/pepxml/modifications'
-require 'ms/ident/pepxml/parameters'
+require 'mspire/ident/pepxml/search_database'
+require 'mspire/ident/pepxml/modifications'
+require 'mspire/ident/pepxml/parameters'
 
 require 'nokogiri'
 require 'merge'
 
-module MS ; end
-module MS::Ident ; end
-class MS::Ident::Pepxml ; end
+module Mspire ; end
+module Mspire::Ident ; end
+class Mspire::Ident::Pepxml ; end
 
 
 # requires these keys:  
@@ -15,10 +15,10 @@ class MS::Ident::Pepxml ; end
 #    :enzyme => a valid enzyme name
 #    :max_num_internal_cleavages => max number of internal cleavages allowed
 #    :min_number_termini => minimum number of termini??
-class MS::Ident::Pepxml::EnzymaticSearchConstraint < Hash
+class Mspire::Ident::Pepxml::EnzymaticSearchConstraint < Hash
 end
 
-class MS::Ident::Pepxml::SearchSummary
+class Mspire::Ident::Pepxml::SearchSummary
   include Merge
 
   DEFAULT_SEARCH_ID = '1'
@@ -30,7 +30,7 @@ class MS::Ident::Pepxml::SearchSummary
   attr_accessor :out_data
   # by default, "1"
   attr_accessor :search_id
-  # an array of MS::Ident::Pepxml::Modification objects
+  # an array of Mspire::Ident::Pepxml::Modification objects
   attr_accessor :modifications
   # A SearchDatabase object (responds to :local_path and :type)
   attr_accessor :search_database
@@ -47,10 +47,10 @@ class MS::Ident::Pepxml::SearchSummary
   attr_accessor :enzymatic_search_constraint
 
   def block_arg
-    [@search_database = MS::Ident::Pepxml::SearchDatabase.new,
-      @enzymatic_search_constraint = MS::Ident::Pepxml::EnzymaticSearchConstraint.new,
+    [@search_database = Mspire::Ident::Pepxml::SearchDatabase.new,
+      @enzymatic_search_constraint = Mspire::Ident::Pepxml::EnzymaticSearchConstraint.new,
       @modifications,
-      @parameters = MS::Ident::Pepxml::Parameters.new,
+      @parameters = Mspire::Ident::Pepxml::Parameters.new,
     ]
   end
 

data/lib/{ms → mspire}/ident/pepxml/spectrum_query.rb

@@ -1,15 +1,15 @@
 require 'nokogiri'
-require 'ms/mass'
+require 'mspire/mass'
 require 'merge'
 
-require 'ms/ident/pepxml/search_result'
+require 'mspire/ident/pepxml/search_result'
 
-module MS ; end
-module MS::Ident ; end
-class MS::Ident::Pepxml ; end
+module Mspire ; end
+module Mspire::Ident ; end
+class Mspire::Ident::Pepxml ; end
 
 # search_specification is a search constraint applied specifically to this query (a String)
-class MS::Ident::Pepxml::SpectrumQuery
+class Mspire::Ident::Pepxml::SpectrumQuery
   include Merge
   DEFAULT_MEMBERS = [:spectrum, :start_scan, :end_scan, :precursor_neutral_mass, :index, :assumed_charge, :retention_time_sec, :search_specification, :search_results, :pepxml_version]
   
@@ -77,7 +77,7 @@ class MS::Ident::Pepxml::SpectrumQuery
     self
   end
 
-  def self.calc_precursor_neutral_mass(m_plus_h, deltamass, h_plus=MS::Mass::H_PLUS)
+  def self.calc_precursor_neutral_mass(m_plus_h, deltamass, h_plus=Mspire::Mass::H_PLUS)
     m_plus_h - h_plus + deltamass
   end
 end

data/lib/{ms → mspire}/ident/protein.rb

@@ -1,7 +1,7 @@
 require 'andand'
 
-module MS ; end
-module MS::Ident
+module Mspire ; end
+module Mspire::Ident
   module ProteinLike
     # an id for the protein
     attr_accessor :id

data/lib/{ms → mspire}/ident/protein_group.rb

@@ -1,6 +1,6 @@
 require 'set'
 
-module MS
+module Mspire
   module Ident
     # represents a group of proteins, typically indistinguishable in the
     # experiment.
@@ -47,7 +47,7 @@ module MS
           peptides_to_protein_group[peptide_set] << protein
         end
         peptides_to_protein_group.each do |pephits,ar_of_prots| 
-          pg = MS::Ident::ProteinGroup.new(ar_of_prots)
+          pg = Mspire::Ident::ProteinGroup.new(ar_of_prots)
           pg.peptide_hits = pephits
           peptides_to_protein_group[pephits] = pg
         end

data/lib/{ms → mspire}/ident/search.rb

@@ -1,5 +1,5 @@
 
-module MS
+module Mspire
   module Ident
 
     module SearchLike

data/lib/{ms → mspire}/isotope.rb

@@ -1,6 +1,6 @@
 require 'yaml'
 
-module MS
+module Mspire
   class Isotope
     MEMBERS = [:atomic_number, :element, :mass_number, :atomic_mass, :relative_abundance, :average_mass, :mono]
     MEMBERS.each {|key| attr_accessor key }
@@ -30,7 +30,7 @@ module MS
 
     if File.exist?(INFO_FILE_FULL_PATH)
 
-      ISOTOPES = YAML.load_file(INFO_FILE_FULL_PATH).map {|ar| MS::Isotope.new *ar }
+      ISOTOPES = YAML.load_file(INFO_FILE_FULL_PATH).map {|ar| Mspire::Isotope.new *ar }
       BY_ELEMENT = ISOTOPES.group_by(&:element)
 
     else
@@ -89,5 +89,5 @@ module MS
 end
 
 if __FILE__ == $0
-  MS::Isotope::Updater.write_nist_info(MS::Isotope::INFO_FILE_FULL_PATH)
+  Mspire::Isotope::Updater.write_nist_info(Mspire::Isotope::INFO_FILE_FULL_PATH)
 end

data/lib/{ms → mspire}/isotope/aa.rb

@@ -1,5 +1,5 @@
 
-module MS
+module Mspire
   class Isotope
     module AA
       # These represent counts for the individual residues (i.e., no extra H

data/lib/{ms → mspire}/isotope/distribution.rb

@@ -1,12 +1,12 @@
 
-require 'ms/mass'
-require 'ms/isotope'
-require 'ms/molecular_formula'
-require 'ms/spectrum'
+require 'mspire/mass'
+require 'mspire/isotope'
+require 'mspire/molecular_formula'
+require 'mspire/spectrum'
 
 require 'fftw3'
 
-module MS
+module Mspire
   class Isotope
     module Distribution
       NORMALIZE = :total
@@ -15,7 +15,7 @@ module MS
   end
 end
 
-module MS
+module Mspire
   class MolecularFormula < Hash
 
     # takes any element composition (see any_to_num_elements).
@@ -30,7 +30,7 @@ module MS
     #     :max     normalize to the highest peak intensity
     #     :low     normalize to the intensity of the lowest m/z peak 
     #             (this is typically the monoisotopic peak)
-    def isotope_distribution(normalize=MS::Isotope::Distribution::NORMALIZE, percent_cutoff=MS::Isotope::Distribution::PERCENT_CUTOFF)
+    def isotope_distribution(normalize=Mspire::Isotope::Distribution::NORMALIZE, percent_cutoff=Mspire::Isotope::Distribution::PERCENT_CUTOFF)
       mono_dist = raw_isotope_distribution
       # percent_cutoff:
       final_output = []
@@ -58,12 +58,12 @@ module MS
     # Arguments are passed directly to isotope_distribution.
     def isotope_distribution_spectrum(*args)
       intensities = isotope_distribution(*args)
-      mono = self.map {|el,cnt| MS::Mass::MONO[el]*cnt }.reduce(:+)
+      mono = self.map {|el,cnt| Mspire::Mass::MONO[el]*cnt }.reduce(:+)
       masses = Array.new(intensities.size)
-      neutron = MS::Mass::NEUTRON
+      neutron = Mspire::Mass::NEUTRON
       masses[0] = mono
       (1...masses.size).each {|i| masses[i] = masses[i-1] + neutron }
-      MS::Spectrum.new [masses, intensities]
+      Mspire::Spectrum.new [masses, intensities]
     end
 
     # returns relative ratios from low nominal mass to high nominal mass.
@@ -72,14 +72,14 @@ module MS
       low_nominal = 0
       high_nominal = 0
       self.each do |el,cnt|
-        isotopes = MS::Isotope::BY_ELEMENT[el]
+        isotopes = Mspire::Isotope::BY_ELEMENT[el]
         low_nominal += (isotopes.first.mass_number * cnt)
         high_nominal += (isotopes.last.mass_number * cnt)
       end
 
       ffts = self.map do |el, cnt|
-        isotope_el_ar = NArray.float(high_nominal)
-        MS::Isotope::BY_ELEMENT[el].each do |isotope|
+        isotope_el_ar = NArray.float(high_nominal+1)
+        Mspire::Isotope::BY_ELEMENT[el].each do |isotope|
           isotope_el_ar[isotope.mass_number] = isotope.relative_abundance
         end
         FFTW3.fft(isotope_el_ar)**cnt
@@ -92,12 +92,12 @@ module MS
 
   class Isotope
     module Distribution
-      def self.calculate(molecular_formula_like, normalize=MS::Isotope::Distribution::NORMALIZE, percent_cutoff=MS::Isotope::Distribution::PERCENT_CUTOFF)
-        MS::MolecularFormula.new(molecular_formula_like).isotope_distribution(normalize, percent_cutoff)
+      def self.calculate(molecular_formula_like, normalize=Mspire::Isotope::Distribution::NORMALIZE, percent_cutoff=Mspire::Isotope::Distribution::PERCENT_CUTOFF)
+        Mspire::MolecularFormula.new(molecular_formula_like).isotope_distribution(normalize, percent_cutoff)
       end
 
-      def self.spectrum(molecular_formula_like, normalize=MS::Isotope::Distribution::NORMALIZE, percent_cutoff=MS::Isotope::Distribution::PERCENT_CUTOFF)
-        MS::MolecularFormula.new(molecular_formula_like).isotope_distribution_spectrum(normalize, percent_cutoff)
+      def self.spectrum(molecular_formula_like, normalize=Mspire::Isotope::Distribution::NORMALIZE, percent_cutoff=Mspire::Isotope::Distribution::PERCENT_CUTOFF)
+        Mspire::MolecularFormula.new(molecular_formula_like).isotope_distribution_spectrum(normalize, percent_cutoff)
       end
     end
   end

data/lib/{ms → mspire}/mascot.rb

@@ -1,5 +1,5 @@
 
-module MS
+module Mspire
   module Mascot
     H_PLUS = 1.007276
   end

data/lib/{ms → mspire}/mass.rb

@@ -1,12 +1,12 @@
-require 'ms/isotope'
-require 'ms/molecular_formula'
+require 'mspire/isotope'
+require 'mspire/molecular_formula'
 
-module MS
+module Mspire
   module Mass
 
     # takes a molecular formula in this format: C2BrH12O
     def self.formula_to_exact_mass(formula)
-      MS::MolecularFormula.new(formula).map do |el,cnt|
+      Mspire::MolecularFormula.new(formula).map do |el,cnt|
         MONO[el] * cnt
       end.reduce(:+)
     end
@@ -16,20 +16,20 @@ module MS
       'e' => 0.0005486,   # www.mikeblaber.org/oldwine/chm1045/notes/Atoms/.../Atoms03.htm
       'neutron' => 1.0086649156,
     }
-    MS::Isotope::BY_ELEMENT.each do |el, isotopes|
+    Mspire::Isotope::BY_ELEMENT.each do |el, isotopes|
       MONO_STR[el.to_s] = isotopes.find {|iso| iso.mono }.atomic_mass
     end
     MONO_STR['h2o'] = %w(h h o).map {|el| MONO_STR[el] }.reduce(:+)
     MONO_STR['oh'] = %w(o h).map {|el| MONO_STR[el] }.reduce(:+)
     # add on deuterium
-    MONO_STR['d'] = MS::Isotope::BY_ELEMENT[:h].find {|iso| iso.element == :h && iso.mass_number == 2 }.atomic_mass
+    MONO_STR['d'] = Mspire::Isotope::BY_ELEMENT[:h].find {|iso| iso.element == :h && iso.mass_number == 2 }.atomic_mass
 
     AVG_STR = {
       'h+' => 1.007276, # using Mascot_H_plus mass (is this right for AVG??)
       'e' => 0.0005486,
       'neutron' => 1.0086649156,
     }
-    MS::Isotope::BY_ELEMENT.each do |el, isotopes|
+    Mspire::Isotope::BY_ELEMENT.each do |el, isotopes|
       AVG_STR[el.to_s] = isotopes.first.average_mass
     end
     AVG_STR['h2o'] = %w(h h o).map {|el| AVG_STR[el] }.reduce(:+)