pepxml.rb in mspire-0.4.2

- old
+ new

@@ -1204,11 +1204,11 @@
     short_element_xml_and_att_string(:search_database, "local_path=\"#{local_path}\" type=\"#{seq_type}\"")
   end
 
 end
 
-Sequest::PepXML::SpectrumQuery = ArrayClass.new(%w(spectrum start_scan end_scan precursor_neutral_mass index assumed_charge search_results pepxml_version))
+Sequest::PepXML::SpectrumQuery = Arrayclass.new(%w(spectrum start_scan end_scan precursor_neutral_mass index assumed_charge search_results pepxml_version))
 
 class Sequest::PepXML::SpectrumQuery
   include SpecIDXML
 
   ############################################################
@@ -1290,11 +1290,11 @@
   end
 
 end
 
 
-Sequest::PepXML::SearchHit = ArrayClass.new( %w( hit_rank peptide peptide_prev_aa peptide_next_aa protein num_tot_proteins num_matched_ions tot_num_ions calc_neutral_pep_mass massdiff num_tol_term num_missed_cleavages is_rejected deltacnstar xcorr deltacn spscore sprank modification_info spectrum_query) )
+Sequest::PepXML::SearchHit = Arrayclass.new( %w( hit_rank peptide peptide_prev_aa peptide_next_aa protein num_tot_proteins num_matched_ions tot_num_ions calc_neutral_pep_mass massdiff num_tol_term num_missed_cleavages is_rejected deltacnstar xcorr deltacn spscore sprank modification_info spectrum_query) )
 
 # 0=hit_rank 1=peptide 2=peptide_prev_aa 3=peptide_next_aa 4=protein 5=num_tot_proteins 6=num_matched_ions 7=tot_num_ions 8=calc_neutral_pep_mass 9=massdiff 10=num_tol_term 11=num_missed_cleavages 12=is_rejected 13=deltacnstar 14=xcorr 15=deltacn 16=spscore 17=sprank 18=modification_info 19=spectrum_query
 
 class Sequest::PepXML::SearchHit
   include SpecID::Pep
@@ -1310,11 +1310,11 @@
   # 1 if there is no second ranked hit, 0 otherwise
 
   tmp_verb = $VERBOSE
   $VERBOSE = nil
   def initialize(hash=nil)
-    super(@@arr_size)
+    super(self.class.size)
     if hash
       self[0,20] = [hash[:hit_rank], hash[:peptide], hash[:peptide_prev_aa], hash[:peptide_next_aa], hash[:protein], hash[:num_tot_proteins], hash[:num_matched_ions], hash[:tot_num_ions], hash[:calc_neutral_pep_mass], hash[:massdiff], hash[:num_tol_term], hash[:num_missed_cleavages], hash[:is_rejected], hash[:deltacnstar], hash[:xcorr], hash[:deltacn], hash[:spscore], hash[:sprank], hash[:modification_info], hash[:spectrum_query]]
     end
     self
   end
@@ -1377,11 +1377,11 @@
   end
 
 end
 
 
-Sequest::PepXML::SearchHit::ModificationInfo = ArrayClass.new(%w(modified_peptide mod_aminoacid_masses mod_nterm_mass mod_cterm_mass))
+Sequest::PepXML::SearchHit::ModificationInfo = Arrayclass.new(%w(modified_peptide mod_aminoacid_masses mod_nterm_mass mod_cterm_mass))
 
 # Positions and masses of modifications
 class Sequest::PepXML::SearchHit::ModificationInfo
   include SpecIDXML
 
@@ -1453,6 +1453,6 @@
   # <mod_aminoacid_mass position="2" mass="545.7160"/>
   # <mod_aminoacid_mass position="3" mass="147.1926"/>
   # </modification_info>
 end
 
-Sequest::PepXML::SearchHit::ModificationInfo::ModAminoacidMass = ArrayClass.new(%w(position mass))
+Sequest::PepXML::SearchHit::ModificationInfo::ModAminoacidMass = Arrayclass.new(%w(position mass))