Class: Ms::Sequest::SrfGroup
- Inherits:
-
Object
- Object
- Ms::Sequest::SrfGroup
- Includes:
- Id::SearchGroup
- Defined in:
- lib/ms/sequest/srf.rb
Instance Method Summary collapse
-
#initialize(arg, opts = {}, &block) ⇒ SrfGroup
constructor
see Ms::Id::Search for acceptable arguments (filename, filenames, array of objects) opts = :filter_by_precursor_mass_tolerance => true | false (default true).
- #search_class ⇒ Object
-
#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.
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 743 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 (@peps, @prots) = merge!(@searches.map {|v| v.peps }) do |_prot, _peps| Ms::Sequest::Srf::Out::Prot.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 756 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 763 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.(srf_file) else v.puts srf_file end end end srg_filename end |