mspire 0.4.9 → 0.5.0

data/specs/spec_id/precision/filter_spec.rb

@@ -1,246 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
-require 'spec_id/srf'
-require 'spec_id/precision/filter'
-
-require File.dirname(__FILE__) + '/../../spec_id_helper'
-
-require 'set'
-require 'set_from_hash'
-
-describe SpecID::Precision::Filter::Peps do
-  it 'does basic top hit filtering with ties=true|false|:as_array' do
-    hashes = [
-      {:aaseq=> 'A', :first_scan => 1, :xcorr => 1.5, :deltacn => 0.1, :ppm => 40, :charge => 2}, # 0
-      {:aaseq=> 'B', :first_scan => 1, :xcorr => 1.5, :deltacn => 0.1, :ppm => 40, :charge => 2}, # 1
-      {:aaseq=> 'C', :first_scan => 1, :xcorr => 1.4, :deltacn => 0.1, :ppm => 40, :charge => 2}, # 2
-      {:aaseq=> 'D', :first_scan => 1, :xcorr => 1.4, :deltacn => 0.2, :ppm => 25, :charge => 2}, # 3
-      {:aaseq=> 'D', :first_scan => 2, :xcorr => 1.9, :deltacn => 0.1, :ppm => 25, :charge => 2}, # 4
-    ]
-    pep_klass = SRF::OUT::Pep
-    @sequest_peps = hashes.map do |hash|
-      hash[:prots] = []
-      pep = pep_klass.new.set_from_hash(hash) 
-    end
-    # no tie:
-    options = { 
-      :per => [:first_scan, :charge], 
-      :by => [:xcorr, {:down => [:xcorr]}], 
-      :ties => false
-    }
-    peps = SpecID::Precision::Filter::Peps.new.top_hit(@sequest_peps, options)
-    peps.size.should == 2
-    set_of_hash_xcorrs = [0,4].map {|i| hashes[i][:xcorr] }.to_set
-    peps.map {|v| v.xcorr }.to_set.should == set_of_hash_xcorrs
-
-    # with tie == true:
-    options[:ties] = true
-    peps = SpecID::Precision::Filter::Peps.new.top_hit(@sequest_peps, options)
-    peps.size.should == 3
-    set_of_hash_xcorrs = [0,1,4].map {|i| hashes[i][:xcorr] }.to_set
-    peps.map{|v| v.xcorr}.to_set.should == set_of_hash_xcorrs
-
-    # with tie == :as_array
-    options[:ties] = :as_array
-    peps = SpecID::Precision::Filter::Peps.new.top_hit(@sequest_peps, options)
-    peps.size.should == 2
-    peps.any? {|v| v.class == Array }.should be_true
-    peps.select {|v| v.is_a? pep_klass }.first.should equal(@sequest_peps[4])
-  end
-end
-
-
-describe 'filtering on a small bioworks file' do
-  before(:each) do
-    @file = Tfiles + '/bioworks_small.xml'
-    @spec_id = SpecID.new(@file)
-  end
-
-  it 'filters with basic sequest filters' do
-    opts = {:sequest => {:xcorr1 => 1.0, :xcorr2 => 1.0, :xcorr3 => 1.0, :deltacn => 0.1, :ppm => 1000.0, :include_deltacnstar => false} }
-    ans = SpecID::Precision::Filter.new.filter_and_validate(@spec_id, opts)
-    
-  
-    ans[:params][:sequest].should == opts[:sequest]
-    # FROZEN:
-    ans[:pephits].size.should == 4
-
-    ans[:pephits].each do |pephit|
-      pephit.pass_filters?(opts[:sequest]).should be_true
-      pephit.fail_filters?(opts[:sequest]).should be_false
-    end
-    before = @spec_id.peps.size
-    ans[:pephits].each do |pephit|
-      @spec_id.peps.delete(pephit)
-    end
-    @spec_id.peps.size.should == before - 4
-    @spec_id.peps.each do |not_passing_pep|
-      not_passing_pep.pass_filters?(opts[:sequest]).should_not be_true
-    end
-    
-    ans[:pephits].map {|v| v.aaseq }.to_set.size == 4
-  end
-
-   it 'can exclude deltacnstar' do
-    opts = {:sequest => {:xcorr1 => 1.0, :xcorr2 => 1.0, :xcorr3 => 1.0, :deltacn => 0.1, :ppm => 1000.0, :include_deltacnstar => false} }
-    # make two hits have the deltacnstar deltacn of 1.1
-    sorted = @spec_id.peps.sort_by {|pep| [pep.xcorr, pep.deltacn, 1.0/pep.ppm, pep.first_scan, pep.aaseq] }
-    # for two of these indices:
-    [286, 287].each do |index| 
-      sorted[index].deltacn = 1.1
-      sorted[index].deltacn.should == 1.1
-    end
-    ans = SpecID::Precision::Filter.new.filter_and_validate(@spec_id, opts)
-  
-    ans[:params][:sequest].should == opts[:sequest]
-    # FROZEN:
-    ans[:pephits].size.should == 2
-  end
- 
-end
-
-describe 'filtering on small bioworks file with inverse prots' do
-  before(:each) do
-    @regexp = /^INV_/o
-    @file = Tfiles + '/bioworks_with_INV_small.xml'
-    @spec_id = SpecID.new(@file)
-    vals = [Validator::Decoy.new(:constraint => @regexp)]
-    @opts = {:sequest => {:xcorr1 => 1.0, :xcorr2 => 1.0, :xcorr3 => 1.0, :deltacn => 0.1, :ppm => 1000.0, :include_deltacnstar=> false}, :validators => vals}
-  end
-
-  it 'gets decoy precision' do
-    ans = SpecID::Precision::Filter.new.filter_and_validate(@spec_id, @opts)
-    peps = ans[:pephits]
-    vals = ans[:pephits_precision]
-    # FROZEN:
-    peps.size.should == 150
-    peps.hash_by(:aaseq).size.should == 74
-    vals.first.should == 149.0/150
-  end
-
-  it 'gets cys precision with freq' do
-    # this does a minimal test to see if this functions properly
-    # (not for accuracy, which is done in validator_spec)
-    ## WITH FASTA FILE:
-    val1 = Validator::AAEst.new('C').set_frequency(Fasta.new(Tfiles + '/small.fasta').prots)
-    @opts[:validators] << val1   # obviously this guy is not his
-    ans1 = SpecID::Precision::Filter.new.filter_and_validate(@spec_id, @opts)
-    peps = ans1[:pephits]
-    vals1 = ans1[:pephits_precision]
-    # FROZEN:
-    vals1.last.should be_close(0.84432189117806, 0.0000000001)
-
-    ## WITH A CYSTEINE BACKGROUND:
-    background_cys = 0.0172
-    val3 = Validator::AAEst.new('C', :background => background_cys).set_frequency(Fasta.new(Tfiles + '/small.fasta').prots)
-    @opts[:validators][1] = val3
-    ans3 = SpecID::Precision::Filter.new.filter_and_validate(@spec_id, @opts)
-    peps = ans3[:pephits]
-    vals3 = ans3[:pephits_precision]
-    # FROZEN:
-    vals3.last.should be_close(0.944734271368211, 0.00000000001)
-  end
-end
-
-describe 'filtering on a real srf file' do
-
-  spec_large do
-    it 'does tmm with a toppred file on srf' do
-      opts = {:sequest => {:xcorr1 => 1.0, :xcorr2 => 1.0, :xcorr3 => 1.0, :deltacn => 0.1, :ppm => 1000.0, :include_deltacnstar => false}}
-      dir = Tfiles_l + '/opd1_2runs_2mods/sequest33'
-      tmm_file = dir + '/ecoli_K12_ncbi_20060321.toppred.xml'
-      fasta_file = dir + '/ecoli_K12_ncbi_20060321.fasta'
-      sequest_file = dir + '/ecoli.params'
-      srf_file = dir + '/020.srf'
-      spec_id = SpecID.new(srf_file)
-      #   :tmm   -> [transmembrane file,min_tm_seqs=1,expect_soluble=true,correct_wins=true,no_include_tm_peps=0.8, bkg=0]  # a toppred.out file
-      
-      regexp = /FAKINGIT_OUT/
-      opts[:decoy] = regexp
-      decoy_val = Validator::Decoy.new(:constraint => regexp) # this is not real, just to test
-      cys_val = Validator::AAEst.new('C').set_frequency(Fasta.new(fasta_file).prots)
-      tmm_val = Validator::Transmem::Protein.new(tmm_file, :min_num_tms => 1, :soluble_fraction => true, :correct_wins => true, :no_include_tm_peps => false, :background => 0.0).set_false_to_total_ratio( Digestor.digest( Fasta.new(fasta_file), Sequest::Params.new(sequest_file) ) )
-      opts[:validators] = [decoy_val, cys_val, tmm_val]
-      ans = SpecID::Precision::Filter.new.filter_and_validate(spec_id, opts)
-      peps = ans[:pephits]
-      vals = ans[:pephits_precision]
-
-      # frozen:
-      vals[0].should == 1.0 
-      vals[1].should be_close(0.366612274427855, 0.00000001)
-      #vals[2].should be_close(0.396396396396396, 0.00000001)
-      # if the srf file is not 'filtered' by proper sequest vals, should give
-      # this:
-      #vals[2].should be_close(-0.204031426241371, 0.00000001)
-      vals[2].should be_close(-0.199538771665843, 0.00000001)
-      peps.size.should == 444
-    end
-  end
-
-    # This is what I was doing before.  I think I may have been forgetting to
-    # remove the INV_ peptide from these counts!
-    # or more likely, the peptide hits were pep+prot hits!
-    #  SpecID::Filterer.run_from_argv([@small_inv].push( *(%w(-1 1.0 -2 1.0 -3 1.0 -c 0.1 --ppm 1000 -f INV_))) )
-    ### FROZEN:
-    #assert_match(/pep_hits\s+151/, output)
-    #assert_match(/uniq_aa_hits\s+75/, output)
-    #assert_match(/prot_hits\s+13/, output)
-
-end
-
-describe SpecID::Precision::Filter::Peps do
-
-  before(:all) do
-    hashes = [
-      {:xcorr => 1.2, :deltacn => 0.1, :ppm => 40, :charge => 2},
-      {:xcorr => 1.3, :deltacn => 0.1, :ppm => 50, :charge => 3},
-      {:xcorr => 1.4, :deltacn => 0.1, :ppm => 50, :charge => 1},
-      {:xcorr => 1.5, :deltacn => 1.1, :ppm => 20, :charge => 2},
-      {:xcorr => 1.3, :deltacn => 0.1, :ppm => 20, :charge => 2},
-      {:xcorr => 1.3, :deltacn => 0.1, :ppm => 40, :charge => 2},
-    ]
-    @sequest_peps = hashes.map do |hash|
-      pep = SRF::OUT::Pep.new.set_from_hash(hash) 
-    end
-    #sp = GenericSpecID.new.set_from_hash({:peps => peps})
-
-  end
-
-  it 'filters sequest peptides' do
-    args_and_expected = {
-      #deltacnstar false
-      [1.2, 1.2, 1.2, 0.1, 50, false] => 5, # "all passing"
-      [1.6, 1.6, 1.6, 0.1, 50, false] => 0, # "xcorrs too high"
-      [1.6, 1.0, 1.0, 0.1, 50, false] => 4, # "one xcorr too high"
-      [1.0, 1.6, 1.0, 0.1, 50, false] => 2, # "one xcorr too high"
-      [1.0, 1.0, 1.6, 0.1, 50, false] => 4, # "one xcorr too high"
-      [1.2, 1.2, 1.2, 0.2, 50, false] => 0, # "high deltacn"
-
-      ## includedeltcnstars :
-      [1.2, 1.2, 1.2, 0.1, 50, true] => 6, # "all passing"
-      [1.2, 1.2, 1.2, 0.2, 50, true] => 1, # "high deltacn"
-      [1.0, 1.0, 1.6, 0.1, 50, true] => 5, # "one xcorr too high"
-      ## 
-      [1.0, 1.0, 1.0, 0.05, 60, true] => 6,  ## testing ppm filtering:
-      [1.0, 1.0, 1.0, 0.05, 10, true] => 0,
-    }
-    args_and_expected.each do |args,exp|
-      filt = SpecID::Precision::Filter::Peps.new(:standard_sequest_filter, *args)
-      filt.filter(@sequest_peps).size.should == exp
-    end
-  end
-
-  it 'can change the pep array permanently' do
-    args_and_expected = {[1.2, 1.2, 1.2, 0.2, 50, true] => 1} # "high deltacn"
-    array_to_change = @sequest_peps.dup
-    array_to_change.size.should == @sequest_peps.size
-    args_and_expected.each do |args,exp|
-      filt = SpecID::Precision::Filter::Peps.new(:standard_sequest_filter, *args)
-      filt.filter!(array_to_change)
-    end
-    array_to_change.size.should_not == @sequest_peps.size
-  end
-
-end
-
-
-

data/specs/spec_id/precision/prob_spec.rb

@@ -1,44 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
-
-require 'spec_id/precision/prob'
-require 'spec_id'
-require 'spec_id/proph'
-require 'validator'
-require 'fasta'
-require 'spec_id/sequest/params'
-
-
-describe 'finding precision Proph::Prot::Pep objects' do
-  before(:each) do
-    @spec_id = GenericSpecID.new
-    # actual sort order: 3, 0, 4, 1, 2
-    peps = [
-      # 0: canonical
-      {:peptide_sequence => '0', :initial_probability => 0.63, :nsp_adjusted_probability => 0.62, :weight => 1.0, :is_nondegenerate_evidence => true, :n_enzymatic_termini => 2, :n_sibling_peptides => 0.0, :n_instances => 1, :is_contributing_evidence => true}, 
-      # 1: lower init prob
-      {:peptide_sequence => '1', :initial_probability => 0.60, :nsp_adjusted_probability => 0.62, :weight => 1.0, :is_nondegenerate_evidence => true, :n_enzymatic_termini => 2, :n_sibling_peptides => 0.0, :n_instances => 1, :is_contributing_evidence => true}, 
-      # 2: lower nsp prob
-      {:peptide_sequence => '2', :initial_probability => 0.63, :nsp_adjusted_probability => 0.52, :weight => 1.0, :is_nondegenerate_evidence => true, :n_enzymatic_termini => 2, :n_sibling_peptides => 0.0, :n_instances => 1, :is_contributing_evidence => true}, 
-      # extra instances! (best hit)
-      {:peptide_sequence => '3', :initial_probability => 0.63, :nsp_adjusted_probability => 0.62, :weight => 1.0, :is_nondegenerate_evidence => true, :n_enzymatic_termini => 2, :n_sibling_peptides => 0.0, :n_instances => 5, :is_contributing_evidence => true}, 
-      # is nondegen = false 
-      {:peptide_sequence => '4', :initial_probability => 0.63, :nsp_adjusted_probability => 0.62, :weight => 1.0, :is_nondegenerate_evidence => false, :n_enzymatic_termini => 2, :n_sibling_peptides => 0.0, :n_instances => 1, :is_contributing_evidence => true},].map {|v| Proph::Prot::Pep.new(v) }
-      @spec_id.peps = peps
-  end
-
-  it 'runs without any validator' do
-    answer = SpecID::Precision::Prob.new.precision_vs_num_hits(@spec_id) 
-    answer.keys.map {|v| v.to_s }.sort.should == ["aaseqs", "charges", "count", "params", "pephits", "pephits_precision", "probabilities"]
-    answer[:aaseqs].should == %w(3 0 4 1 2)
-  end
-
-  it 'returns modified peptides if any modified peptides' do
-    @spec_id.peps[1].mod_info = Sequest::PepXML::SearchHit::ModificationInfo.new(['MODIFIED', []])
-    answer = SpecID::Precision::Prob.new.precision_vs_num_hits(@spec_id) 
-    answer.keys.map {|v| v.to_s }.sort.should == ["aaseqs", "charges", "count", "modified_peptides", "params", "pephits", "pephits_precision", "probabilities"]
-  end
-
-end
-
-
-

data/specs/spec_id/proph/pep_summary_spec.rb

@@ -1,98 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
-
-require 'spec_id/proph/pep_summary'
-
-ToCheck = {
-  :spectrum_query => {:first => {:spectrum => "020.42.42.3", :start_scan=>42, :end_scan=>42, :precursor_neutral_mass=>1015.77285654469, :assumed_charge=>3, :index=>1 },
-    :last => {:spectrum=>"020.344.344.3", :start_scan=>344, :end_scan=>344, :precursor_neutral_mass=>1447.6040333025, :assumed_charge=>3, :index=>18 },
-},
-
-:search_hit => {:first => {:hit_rank=>1, :peptide=>"GTGVSVTR", :peptide_prev_aa=>"R", :peptide_next_aa=>"S", :protein=>"gi|49176370|ref|YP_026228.1|", :num_tot_proteins=>1, :num_matched_ions=>10, :tot_num_ions=>70, :calc_neutral_pep_mass=>1015.79382542, :massdiff=>-0.0209688753124055, :num_tol_term=>2, :num_missed_cleavages=>0, :is_rejected=>0, :xcorr=>1.06543827056885, :deltacn => 0.192325830459595, :deltacnstar=>0, :spscore=>77.8397979736328, :sprank=>3, :probability=>0.07881571, :fval=>0.1592, :ntt=>2, :nmc=> 0, :massd=>-0.021}, 
-  :last => { :hit_rank=>1, :peptide=>"VAALRVPGGASLTR", :peptide_prev_aa=>"R", :peptide_next_aa=>"K", :protein=>"gi|16129819|ref|NP_416380.1|", :num_tot_proteins=>1, :num_matched_ions=>16, :tot_num_ions=>78, :calc_neutral_pep_mass=>1447.58289842, :massdiff=> 0.0211348825000641, :num_tol_term=>2, :num_missed_cleavages=>1, :is_rejected=>0, :xcorr=>1.3090912103653, :deltacn => 0.259967535734177, :deltacnstar => 0, :spscore => 118.513412475586, :sprank => 4, :probability=>0.27738378, :fval=>1.3810, :ntt=>2, :nmc=>1, :massd=>0.021 },
-}
-}
-
-
-describe Proph::PepSummary, "reading a small .xml file" do
-  before(:each) do
-    file = Tfiles + '/opd1_2runs_2mods/interact-opd1_mods__small.xml'
-    @obj = Proph::PepSummary.new(file)
-  end
-
-  it 'should raise an error if not a peptide prophet file' do
-    lambda { Proph::PepSummary.new(Tfiles + '/opd1/000.tpp_2.9.2.first10.xml')}.should raise_error(ArgumentError)
-  end
-
-  it 'has msms_run_summary objects with spectrum_queries' do
-    @obj.msms_run_summaries.size.should == 1
-    sqs = @obj.msms_run_summaries.first.spectrum_queries
-    sqs.size.should == 18
-
-    [:first, :last].each do |mth|
-      ToCheck[:spectrum_query][mth].each do |k,v|
-        if v.is_a? Float
-          sqs.send(mth).send(k).should be_close(v, 0.0000000001)
-        else
-          sqs.send(mth).send(k).should == v
-        end
-      end
-      ToCheck[:search_hit][mth].each do |k,v|
-        if v.is_a? Float
-          sqs.send(mth).search_results.first.search_hits.first.send(k).should be_close(v, 0.0000000001)
-        else
-          sqs.send(mth).search_results.first.search_hits.first.send(k).should == v
-        end
-      end
-    end
-  end
-
-  it 'has pephits (which are descended from SearchHit)' do
-    @obj.peps.size.should == 18
-    [:hit_rank, :probability, :fval, :ntt, :nmc, :massd].each do |guy|
-      @obj.peps.first.should respond_to(guy)
-    end
-
-    [:first, :last].each do |mth|
-      ToCheck[:search_hit][mth].each do |k,v|
-        if v.is_a? Float
-          @obj.peps.send(mth).send(k).should be_close(v, 0.0000000001)
-        else
-          @obj.peps.send(mth).send(k).should == v
-        end
-      end
-    end
-
-  end
-
-end
-
-describe Proph::PepSummary, 'reading a large .xml file' do 
-  spec_large do 
-    before(:all) do 
-      file = Tfiles_l + '/opd1_2runs_2mods/prophet/interact-opd1_mods.xml'
-      @obj = Proph::PepSummary.new(file) 
-    end
-
-    it 'has peps of class Proph::PepSummary::Pep' do
-      @obj.peps.first.class.to_s.should == 'Proph::PepSummary::Pep'
-      @obj.peps.size.should == 1643
-    end
-
-    it 'contains peps that respond_to :aaseq' do
-      @obj.peps.first.should respond_to(:aaseq)
-    end
-
-    it 'has prots (also callable from peps)' do
-      (@obj.prots.size > 0).should be_true
-      @obj.peps.all? {|v| v.prots.size > 0 }.should be_true 
-      peps_with_prots = @obj.peps.select {|v| v.prots.size > 1 }
-      # frozen:
-      peps_with_prots.first.prots.size.should == 3
-      peps_with_prots.first.prots.first.name.should == "gi|16128676|ref|NP_415229.1|"
-      peps_with_prots.first.prots.first.protein_descr.should == "RhsC protein in RhsC element [Escherichia coli K12]"
-      peps_with_prots.first.prots.first.reference.should == "gi|16128676|ref|NP_415229.1| RhsC protein in RhsC element [Escherichia coli K12]"
-      peps_with_prots.first.prots.last.protein_descr.should == "RhsA protein in RhsA element [Escherichia coli K12]"
-    end
-  end
-end
-

data/specs/spec_id/proph/prot_summary_spec.rb

@@ -1,128 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
-
-require 'spec_id/proph/prot_summary'
-
-describe Proph::ProtSummary, "reading a -prot.xml file" do
-  before(:each) do
-    file = Tfiles + '/opd1/000_020_3prots-prot.xml'
-    @obj = Proph::ProtSummary.new(file)
-  end
-
-  it 'extracts protein groups with probabilities' do
-    @obj.prot_groups.size.should == 3
-    @obj.prot_groups.first.probability.should == 1.0
-    @obj.prot_groups[2].probability == 0.98
-  end
-
-  it 'extracts protein hit attributes' do
-    prot = @obj.prot_groups[1].prots.first
-    %w(protein_name n_indistinguishable_proteins probability percent_coverage unique_stripped_peptides group_sibling_id total_number_peptides pct_spectrum_ids).zip(["gi|16132019|ref|NP_418618.1|", 1, 1.0, 13.0, "FRDGLK+AIQFAQDVGIRVIQLAGYDVYYQEANNETRR".split('+'), "a", 2, 0.41]) do |name, val|
-      prot.send(name).should == val
-    end
-  end
-
-  it 'can detect -prot.xml version' do
-    answer = ['1.9', '4']
-    files = ['/yeast_gly_small-prot.xml', '/interact-opd1_mods_small-prot.xml'].map {|v| Tfiles + v}
-    files.zip(answer) do |file,answ|
-      Proph::ProtSummary.new.get_version(file).should == answ 
-    end
-  end
-
-  it 'has prots, peps, and prot_groups ' do
-    @obj.peps.should_not be_nil
-    @obj.prots.should_not be_nil
-    @obj.prot_groups.should_not be_nil
-  end
-
-end
-
-####################################################
-# OTHER TESTS NOT IMPLEMENTED (do we need these??)
-####################################################
-
-=begin
-
-require 'test/unit'
-require 'spec_id'
-require 'ms/scan'
-
-class ProphTest < Test::Unit::TestCase
-
-  def initialize(arg)
-    super(arg)
-    @tfiles = File.dirname(__FILE__) + '/tfiles/'
-    @pepproph_xml = @tfiles + 'pepproph_small.xml'
-  end
-
-  def Xtest_filter_by_min_pep_prob
-    obj = Proph::Pep::Parser.new
-    new_file = "tfiles/tmp.xml"
-    assert_match(/peptideprophet_result probability="0.[0-5]/, IO.read(@pepproph_xml))
-    obj.filter_by_min_pep_prob(@pepproph_xml, new_file, 0.50)
-    assert_no_match(/peptideprophet_result probability="0.[0-5]/, IO.read(new_file))
-    assert_match(/<peptideprophet_result[^>]*probability="0.[6-9][^>]*>/, IO.read(new_file))
-    File.unlink new_file
-  end
-
-  def Xtest_uniq_by_seqcharge
-    cls = Proph::Pep
-    p1 = cls.new({ :charge => '2', :sequence => 'PEPTIDE' })
-    p2 = cls.new({ :charge => '3', :sequence => 'PEPTIDE' })
-    p3 = cls.new({ :charge => '2', :sequence => 'PEPTIDE' })
-    p4 = cls.new({ :charge => '2', :sequence => 'APEPTIDE' })
-    p5 = cls.new({ :charge => '2', :sequence => 'APEPTIDE' })
-    un_peps = cls.uniq_by_seqcharge([p1,p2,p3,p4,p5])
-    ## WHY ISn't that working? below!
-    ##assert_equal([p1,p2,p4].to_set, un_peps.to_set)
-    assert(equal_sets([p1,p2,p4], un_peps))
-  end
-
-  def Xequal_sets(arr1, arr2)
-    c1 = arr1.dup
-    c2 = arr2.dup
-    arr1.each do |c|
-      arr2.each do |d|
-        if c == d
-          c1.delete c
-          c2.delete d
-        end
-      end
-    end
-    if (c1.size == c2.size) && (c1.size == 0)
-      true
-    else
-      false
-    end
-  end
-
-  def Xtest_arithmetic_avg_scan_by_parent_time
-    i1 = 100015.0
-    i2 = 30000.0
-    i3 = 100.0
-    t1 = 0.13
-    t2 = 0.23
-    t3 = 0.33
-    p1 = MS::Scan.new(1,1, t1)
-    p2 = MS::Scan.new(2,1, t2)
-    p3 = MS::Scan.new(3,1, t3)
-    s1 = MS::Scan.new(1,2,0.10, 300.2, i1, p1)
-    s2 = MS::Scan.new(2,2,0.20, 301.1, i2, p2)
-    s3 = MS::Scan.new(3,2,0.30, 302.0, i3, p3)
-    scan = Proph::Pep.new({:scans => [s1,s2,s3]}).arithmetic_avg_scan_by_parent_time
-    tot_inten = i1 + i2 + i3
-    tm = ( t1 * (i1/tot_inten) + t2 * (i2/tot_inten) + t3 * (i3/tot_inten) )
-    {:ms_level => 2, :prec_inten => 130115.0/3, :num => nil, :prec_mz => 301.1.to_f, :time => tm }.each do |k,v|
-      if k == :prec_mz  # not sure why this is bugging out, but..
-        assert_equal(v.to_s, scan.send(k).to_s)
-      else
-        assert_equal(v, scan.send(k))
-      end
-    end
-
-  end
-
-
-end
-
-=end