Class: Proph::PepSummary

Inherits:
Object
  • Object
show all
Includes:
SpecID
Defined in:
lib/ms/ident/pepxml/pep_summary.rb

Defined Under Namespace

Classes: Pep, Prot

Constant Summary collapse

Filetype_and_version_re_new = 
/version="PeptideProphet v([\d\.]+) /

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(file = nil) ⇒ PepSummary

Returns a new instance of PepSummary.



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# File 'lib/ms/ident/pepxml/pep_summary.rb', line 54

def initialize(file=nil)
  if file
    @version = get_version(file)
    spec_id = SpecID::Parser::PepProph.new(:spec_id).parse(file, :spec_id => self)
  end
end

Instance Attribute Details

#msms_run_summaries ⇒ Object

Returns the value of attribute msms_run_summaries.



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# File 'lib/ms/ident/pepxml/pep_summary.rb', line 29

def msms_run_summaries
  @msms_run_summaries
end

#peptideprophet_summary ⇒ Object

the protein groups currently these are just xml nodes returned!



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# File 'lib/ms/ident/pepxml/pep_summary.rb', line 28

def peptideprophet_summary
  @peptideprophet_summary
end

#version ⇒ Object

Returns the value of attribute version.



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# File 'lib/ms/ident/pepxml/pep_summary.rb', line 30

def version
  @version
end

Instance Method Details

#get_version(file) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/ms/ident/pepxml/pep_summary.rb', line 34

def get_version(file)
  answer = nil
  File.open(file) do |fh|
    8.times do
      line = fh.gets
      answer = 
        if line =~ Filetype_and_version_re_new
          $1.dup
        end
      break if answer
    end
  end
  raise(ArgumentError, "couldn't detect version in #{file}") unless answer
  answer
end

#hi_prob_best ⇒ Object 



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# File 'lib/ms/ident/pepxml/pep_summary.rb', line 32

def hi_prob_best ; true end

#search_hit_class ⇒ Object 



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# File 'lib/ms/ident/pepxml/pep_summary.rb', line 50

def search_hit_class
  PepSummary::Pep
end