Class: Ms::Sequest::SrfGroup

Inherits:
Object
  • Object
show all
Includes:
Ident::SearchGroup
Defined in:
lib/ms/sequest/srf.rb

Instance Method Summary collapse

Constructor Details

#initialize(arg, opts = {}, &block) ⇒ SrfGroup

see Ms::Id::Search for acceptable arguments (filename, filenames, array of objects) opts =

:filter_by_precursor_mass_tolerance => true | false (default true)



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# File 'lib/ms/sequest/srf.rb', line 762

def initialize(arg, opts={}, &block)
  orig_opts = opts.dup
  indiv_opts = { :link_protein_hits => false }
  super(arg, opts.merge(indiv_opts)) do
    unless orig_opts[:link_protein_hits] == false
      (@peptides, @proteins) = merge!(@searches.map {|v| v.peptides }) do |_prot, _peps|
        Ms::Sequest::Srf::Out::Protein.new(_prot.reference, _peps)
      end
    end
  end
  block.call(self) if block_given?
end

Instance Method Details

#search_class ⇒ Object 



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# File 'lib/ms/sequest/srf.rb', line 775

def search_class
  Ms::Sequest::Srf
end

#to_srg(srg_filename = 'bioworks.srg') ⇒ Object

returns the filename used if the file exists, the name will be expanded to full path, otherwise just what is given



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# File 'lib/ms/sequest/srf.rb', line 782

def to_srg(srg_filename='bioworks.srg')
  File.open(srg_filename, 'w') do |v|
    @filenames.each do |srf_file|
      if File.exist? srf_file
        v.puts File.expand_path(srf_file)
      else
        v.puts srf_file
      end
    end
  end
  srg_filename
end