bioworks_spec.rb in ms-sequest-0.0.18

- old
+ new

@@ -11,14 +11,14 @@
 describe Bioworks, 'set from an xml file' do
   # NEED TO DEBUG THIS PROB!
   it 'can set one with labeled proteins' do
     file = Tfiles + "/bioworks_with_INV_small.xml"
     obj = Bioworks.new(file)
-    obj.prots.size.should == 19
+    obj.proteins.size.should == 19
     file = Tfiles + '/bioworks_small.xml'
     obj = Bioworks.new(file)
-    obj.prots.size.should == 106
+    obj.proteins.size.should == 106
   end
 
   it 'can parse an xml file NOT derived from multi-concensus' do
     tf_bioworks_single_xml_small = Tfiles + '/bioworks_single_run_small.xml'
     obj = Bioworks.new(tf_bioworks_single_xml_small)
@@ -26,14 +26,14 @@
     origfilename = '5prot_mix_michrom_20fmol_200pmol.RAW'
     origfilepath = 'C:\Xcalibur\sequest'
     obj.global_filename.should == gfn
     obj.origfilename.should == origfilename
     obj.origfilepath.should == origfilepath
-    obj.prots.size.should == 7
-    obj.prots.first.peps.first.base_name.should ==  gfn
-    obj.prots.first.peps.first.file.should ==  "152"
-    obj.prots.first.peps.first.charge.should == 2
+    obj.proteins.size.should == 7
+    obj.proteins.first.peptides.first.base_name.should ==  gfn
+    obj.proteins.first.peptides.first.file.should ==  "152"
+    obj.proteins.first.peptides.first.charge.should == 2
     # @TODO: add more tests here
   end
 
   it 'can output in excel format (**semi-verified right now)' do
     tf_bioworks_to_excel = Tfiles + '/tf_bioworks2excel.bioXML'
@@ -55,11 +55,11 @@
 
   # prot is boolean if this is a protein line!
   def _assert_equal_pieces(exp, act, prot)
     # equal as floats (by delta)
     exp.each_index do |i|
-      if i == 5  # both prots and peps
+      if i == 5  # both proteins and peptides
         act[i].to_f.should be_close(exp[i].to_f, 0.1)
       elsif i == 3 && !prot
         act[i].to_f.should be_close(exp[i].to_f, 0.01)
       elsif i == 6 && !prot
         act[i].to_f.should be_close(exp[i].to_f, 0.01)
@@ -97,20 +97,20 @@
         prot
       end
     end
     exp_peps = exp_peps.zip(exp_prots)
     exp_peps.collect! do |both|
-      both[0].prots = [both[1]]
+      both[0].proteins = [both[1]]
       both[0]
     end
 
     peptides = [%w(2 PEPTIDE), %w(3 PEPTIDE), %w(2 PEPTIDE), %w(3 PEPY), %w(3 PEPTIDE), %w(3 PEPTIDE), %w(2 PEPY)].collect do |arr|
       pep = Bioworks::Pep.new
       pep.charge = arr[0]
       pep.sequence = arr[1]
-      pep.prots = [Bioworks::Prot.new]
-      pep.prots.first.reference = "#{cnt}"
+      pep.proteins = [Bioworks::Prot.new]
+      pep.proteins.first.reference = "#{cnt}"
       cnt += 1
       pep
     end
     peptides, proteins = Bioworks.new._uniq_peps_by_sequence_charge(peptides)
     proteins.size.should == peptides.size
@@ -128,10 +128,10 @@
 
 end
 
 describe Bioworks::Pep do
   it 'can be initialized from a hash' do
-    hash = {:sequence => 0, :mass => 1, :deltamass => 2, :charge => 3, :xcorr => 4, :deltacn => 5, :sp => 6, :rsp => 7, :ions => 8, :count => 9, :tic => 10, :prots => 11, :base_name => 12, :first_scan => 13, :last_scan => 14, :peptide_probability => 15, :file => 16, :_num_prots => 17, :_first_prot => 18}
+    hash = {:sequence => 0, :mass => 1, :deltamass => 2, :charge => 3, :xcorr => 4, :deltacn => 5, :sp => 6, :rsp => 7, :ions => 8, :count => 9, :tic => 10, :proteins => 11, :base_name => 12, :first_scan => 13, :last_scan => 14, :peptide_probability => 15, :file => 16, :_num_proteins => 17, :_first_prot => 18}
     pep = Bioworks::Pep.new(hash)
     hash.each do |k,v|
       pep.send(k).should == v
     end
   end