Class: Sequest::PepXML::MSMSRunSummary

Inherits:
Object
  • Object
show all
Includes:
SpecIDXML
Defined in:
lib/spec_id/sequest.rb

Constant Summary

Constants included from SpecIDXML

SpecIDXML::Special_chrs_hash

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from SpecIDXML

#attr_xml, #attrs_xml, #element_xml, #element_xml_and_att_string, #element_xml_no_atts, #escape_special_chars, #param_xml, #params_xml, #short_element_xml, #short_element_xml_and_att_string, #short_element_xml_from_instance_vars, #tabs

Constructor Details

#initialize(hash = nil) ⇒ MSMSRunSummary

takes a hash of name, value pairs if block given, spectrum_queries (should be array of spectrum queries) is set to the return value of the block



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# File 'lib/spec_id/sequest.rb', line 179

def initialize(hash=nil)
  @spectrum_queries = []
  if hash
    instance_var_set_from_hash(hash)
  end
  if block_given? ; @spectrum_queries = yield end
end

Instance Attribute Details

#base_name ⇒ Object

the version of TPP you are using (determines xml output) The name of the pep xml file (without extension) (but this is a long filename!!!)



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# File 'lib/spec_id/sequest.rb', line 158

def base_name
  @base_name
end

#ms_detector ⇒ Object

Returns the value of attribute ms_detector.



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# File 'lib/spec_id/sequest.rb', line 163

def ms_detector
  @ms_detector
end

#ms_ionization ⇒ Object

Returns the value of attribute ms_ionization.



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# File 'lib/spec_id/sequest.rb', line 166

def ms_ionization
  @ms_ionization
end

#ms_manufacturer ⇒ Object

The name of the mass spec manufacturer



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# File 'lib/spec_id/sequest.rb', line 160

def ms_manufacturer
  @ms_manufacturer
end

#ms_mass_analyzer ⇒ Object

Returns the value of attribute ms_mass_analyzer.



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# File 'lib/spec_id/sequest.rb', line 162

def ms_mass_analyzer
  @ms_mass_analyzer
end

#ms_model ⇒ Object

Returns the value of attribute ms_model.



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# File 'lib/spec_id/sequest.rb', line 161

def ms_model
  @ms_model
end

#pepxml_version ⇒ Object

Returns the value of attribute pepxml_version.



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# File 'lib/spec_id/sequest.rb', line 167

def pepxml_version
  @pepxml_version
end

#raw_data ⇒ Object

Returns the value of attribute raw_data.



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# File 'lib/spec_id/sequest.rb', line 165

def raw_data
  @raw_data
end

#raw_data_type ⇒ Object

Returns the value of attribute raw_data_type.



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# File 'lib/spec_id/sequest.rb', line 164

def raw_data_type
  @raw_data_type
end

#sample_enzyme ⇒ Object

A SampleEnzyme object (responds to: name, cut, no_cut, sense)



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# File 'lib/spec_id/sequest.rb', line 170

def sample_enzyme
  @sample_enzyme
end

#search_summary ⇒ Object

A SearchSummary object



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# File 'lib/spec_id/sequest.rb', line 172

def search_summary
  @search_summary
end

#spectrum_queries ⇒ Object

An array of spectrum_queries



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# File 'lib/spec_id/sequest.rb', line 174

def spectrum_queries
  @spectrum_queries
end

Instance Method Details

#to_pepxml ⇒ Object 



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# File 'lib/spec_id/sequest.rb', line 187

def to_pepxml
  case Sequest::PepXML.pepxml_version
  when 18
    element_xml_and_att_string(:msms_run_summary, "base_name=\"#{base_name}\" msManufacturer=\"#{ms_manufacturer}\" msModel=\"#{ms_model}\" msIonization=\"#{ms_ionization}\" msMassAnalyzer=\"#{ms_mass_analyzer}\" msDetector=\"#{ms_detector}\" raw_data_type=\"#{raw_data_type}\" raw_data=\"#{raw_data}\"") do
      sample_enzyme.to_pepxml +
        search_summary.to_pepxml +
        spectrum_queries.map {|sq| sq.to_pepxml }.join
    end
  when 0
    #      element_xml(:msms_run_summary, [:base_name, :search_engine, :database, :raw_data_type, :raw_data, :out_data_type, :out_data, :sample_enzyme]) do
    #        element_xml(:search_summary, [:base_name, :search_engine, :precursor_mass_type, :fragment_mass_type]) do
    #          [
    #            @params.short_element_xml(:enzymatic_search_constraint, [:enzyme, :max_num_internal_cleavages, :min_number_termini]),
    #            @params.short_element_xml(:sequence_search_constraint, [:sequence]),
    #            @params.short_element_xml(:sequence_search_constraint, [:sequence]),
    #            @params.pepxml_parameters(:peptide_mass_tol, :fragment_ion_tol, :ion_series, :max_num_differential_AA_per_mod, :nucleotide_reading_frame, :num_output_lines, :remove_precursor_peak, :ion_cutoff_percentage, :match_peak_count, :match_peak_allowed_error, :match_peak_tolerance, :protein_mass_filter, :sequence_header_filter)
    #          ].join("\n")
    #        end  + "\n" +
    #          @spectrum_queries.collect {|result| result.to_pepxml }.join("\n")
    #      end
  end
end