class MzID::ParserSax::SpectraIDHandler
handler for SpectrumIDItem elements
Constants
- ATTR
- SPEC_ATTR_MAP
- SPEC_PROB_ACC
- SPEC_PROB_ATTR_MAP
Attributes
pbar[RW]
spec_h[RW]
Public Class Methods
new(dbseq_h, pep_h, pep_ev_h, block, num_spec=nil)
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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
Public Instance Methods
attr(name, value)
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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()
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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)
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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)
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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