Class: MzID::ParserSax::SpectraIDHandler

Inherits:
Ox::Sax
  • Object
show all
Defined in:
lib/mzid/parser_sax.rb

Overview

handler for SpectrumIDItem elements

Constant Summary collapse

ATTR = 
[:SpectrumIdentificationItem, :PeptideEvidenceRef]
SPEC_ATTR_MAP = 
[:peptide_ref, :id, :passThreshold]
SPEC_PROB_ATTR_MAP = 
[:accession, :value]
SPEC_PROB_ACC =

code for spec-prob

"MS:1002052"

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(dbseq_h, pep_h, pep_ev_h, block, num_spec = nil) ⇒ SpectraIDHandler

Returns a new instance of SpectraIDHandler.



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# File 'lib/mzid/parser_sax.rb', line 161

def initialize(dbseq_h, pep_h, pep_ev_h, block, num_spec=nil)
  @yield_to = block
  @dbseq_h = dbseq_h
  @pep_h = pep_h
  @pep_ev_h = pep_ev_h
  @spec_h = Hash.new
  @pbar = num_spec.nil? ? nil : ProgressBar.new("Spectra", num_spec)
end

Instance Attribute Details

#pbar ⇒ Object

Returns the value of attribute pbar.



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# File 'lib/mzid/parser_sax.rb', line 170

def pbar
  @pbar
end

#spec_h ⇒ Object

Returns the value of attribute spec_h.



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# File 'lib/mzid/parser_sax.rb', line 170

def spec_h
  @spec_h
end

Instance Method Details

#attr(name, value) ⇒ Object 



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# File 'lib/mzid/parser_sax.rb', line 178

def attr(name, value)
  return unless ATTR.include?(@curr_node) || 
    (@curr_node == :cvParam && SPEC_PROB_ATTR_MAP.include?(name))
  
  @h_param[name] = value if !@h_param.nil?
  @h_param = {} if name == :accession && value == SPEC_PROB_ACC    
  if name == :peptideEvidence_ref then # if peptideEvidence, force into list
    @h[name].nil? ? @h[name] = [value.to_sym] : @h[name].push(value.to_sym)
  end 
  @h[name] = value.to_sym if SPEC_ATTR_MAP.include?(name)
  @h[name] = value.split("_")[1].to_i if name == :id
end

#attrs_done ⇒ Object 



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# File 'lib/mzid/parser_sax.rb', line 191

def attrs_done()
  return unless (!@h_param.nil? && !@h.nil?)
  @h[:spec_prob] = @h_param[:value].to_f 
end

#end_element(name) ⇒ Object 



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# File 'lib/mzid/parser_sax.rb', line 196

def end_element(name)
  return unless name == :SpectrumIdentificationItem
  @yield_to.call(@h)
  @pbar.inc if !@pbar.nil?
end

#start_element(name) ⇒ Object 



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# File 'lib/mzid/parser_sax.rb', line 172

def start_element(name)
  @h = {} if name == :SpectrumIdentificationItem
  @curr_node = name
  @h_param = nil if name == :cvParam
end