proph.rb in mspire-0.2.0

- old
+ new

@@ -3,11 +3,10 @@
 require 'hash_by'
 require 'instance_var_set_from_hash'
 require 'axml'
 require 'spec_id'
 
-class SpecID
 class Proph
 
 
 ################ --BEGIN
 
@@ -18,10 +17,12 @@
   end
 end
 
 
 class ProtSummary
+  include SpecID
+
   attr_writer :prots
   attr_accessor :prot_groups
   
   def hi_prob_best ; true end
 
@@ -100,11 +101,12 @@
       @prots = yield
     end
   end
 end
 
-class Prot < SpecID::Prot
+class Prot 
+  include SpecID::Prot
 
   ## probability and reference accessors are inherited
   attr_accessor :peps, :protein_name, :cutoff, :group_sibling_id, :n_indistinguishable_proteins, :percent_coverage, :unique_stripped_peptides, :total_number_peptides, :pct_spectrum_ids, :description
 
   # returns protein_name
@@ -135,10 +137,11 @@
   end
 
 end # class Prot
 
 class Pep
+  include SpecID::Pep
 
   attr_accessor :sequence, :probability, :filenames, :charge, :precursor_neutral_mass, :nsp_cutoff, :scans
   attr_writer :arithmetic_avg_scan_by_parent_time
 
   def initialize(args=nil)
@@ -456,6 +459,5 @@
 end  # Prot::Parser
 
 ################ --END
 
 end  # Proph
-end  # SpecID