Class: Sequest::PepXML::SearchHit

Inherits:
Object
  • Object
show all
Includes:
SpecID::Pep, SpecIDXML
Defined in:
lib/ms/sequest/pepxml.rb

Overview

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

Defined Under Namespace

Classes: ModificationInfo

Constant Summary collapse

Non_standard_amino_acid_char_re = 
/[^A-Z\.\-]/

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(hash = nil) ⇒ SearchHit

Returns a new instance of SearchHit.



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# File 'lib/ms/sequest/pepxml.rb', line 1314

def initialize(hash=nil)
  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

Class Method Details

.split_ions(ions) ⇒ Object

Takes ions in the form XX/YY and returns [XX.to_i, YY.to_i]



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# File 'lib/ms/sequest/pepxml.rb', line 1330

def self.split_ions(ions)
  ions.split("/").map {|ion| ion.to_i }
end

Instance Method Details

#aaseq ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 1305

def aaseq ; self[1] end

#aaseq=(arg) ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 1306

def aaseq=(arg) ; self[1] = arg end

#from_pepxml_node(node) ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 1362

def from_pepxml_node(node)
  self[0] = node['hit_rank'].to_i
  self[1] = node['peptide']
  self[2] = node['peptide_prev_aa']
  self[3] = node['peptide_next_aa']
  self[4] = node['protein']  ## will this be the string?? (yes, for now)
  self[5] = node['num_tot_proteins'].to_i
  self[6] = node['num_matched_ions'].to_i
  self[7] = node['tot_num_ions'].to_i
  self[8] = node['calc_neutral_pep_mass'].to_f
  self[9] = node['massdiff'].to_f
  self[10] = node['num_tol_term'].to_i
  self[11] = node['num_missed_cleavages'].to_i
  self[12] = node['is_rejected'].to_i
  self
end

#inspect ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 1324

def inspect
  var = @@attributes.map do |m| "#{m}:#{self.send(m)}" end.join(" ")
  "#<SearchHit #{var}>"
end

#search_score_xml(symbol) ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 1334

def search_score_xml(symbol)
  "#{tabs}<search_score name=\"#{symbol}\" value=\"#{send(symbol)}\"/>"
end

#search_scores_xml(*symbol_list) ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 1338

def search_scores_xml(*symbol_list)
  symbol_list.collect do |sy|
    search_score_xml(sy)
  end.join("\n") + "\n"
end

#to_pepxml ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 1344

def to_pepxml
  mod_pepxml = 
    if self[18]
      self[18].to_pepxml
    else
      ''
    end

  #string = element_xml_and_att_string("search_hit", [:hit_rank, :peptide, :peptide_prev_aa, :peptide_next_aa, :protein, :num_tot_proteins, :num_matched_ions, :tot_num_ions, :calc_neutral_pep_mass, :massdiff_as_string, :num_tol_term, :num_missed_cleavages, :is_rejected]) do
  # note the to_plus_minus_string
  #puts "MASSDIFF:"
  #p massdiff
  element_xml_and_att_string("search_hit", "hit_rank=\"#{hit_rank}\" peptide=\"#{peptide}\" peptide_prev_aa=\"#{peptide_prev_aa}\" peptide_next_aa=\"#{peptide_next_aa}\" protein=\"#{protein}\" num_tot_proteins=\"#{num_tot_proteins}\" num_matched_ions=\"#{num_matched_ions}\" tot_num_ions=\"#{tot_num_ions}\" calc_neutral_pep_mass=\"#{calc_neutral_pep_mass}\" massdiff=\"#{massdiff.to_plus_minus_string}\" num_tol_term=\"#{num_tol_term}\" num_missed_cleavages=\"#{num_missed_cleavages}\" is_rejected=\"#{is_rejected}\"") do
    mod_pepxml +
      search_scores_xml(:xcorr, :deltacn, :deltacnstar, :spscore, :sprank)
  end
end