Class: MS::Sequest::Srf::Out

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

Overview

0=first_scan, 1=last_scan, 2=charge, 3=num_hits, 4=computer, 5=date_time, 6=hits, 7=total_inten, 8=lowest_sp, 9=num_matched_peptides, 10=db_locus_count

Defined Under Namespace

Classes: Peptide, Protein

Constant Summary collapse

Unpack_32 = 
'@36vx2Z*@60Z*'
Unpack_35 = 
'@36vx4Z*@62Z*'

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.from_io(fh, unpack_35, dup_refs_gt_0) ⇒ Object

returns an MS::Sequest::Srf::Out object



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# File 'lib/ms/sequest/srf.rb', line 548

def self.from_io(fh, unpack_35, dup_refs_gt_0)
  ## EMPTY out file is 96 bytes
  ## each hit is 320 bytes
  ## num_hits and charge:
  st = fh.read(96)

  # num_hits computer date_time
  initial_vals = st.unpack( (unpack_35 ? Unpack_35 : Unpack_32) )
  # total_inten lowest_sp num_matched_peptides db_locus_count
  initial_vals.push( *st.unpack('@8eex4Ix4I') )
  out_obj = self.new( *initial_vals )

  _num_hits = out_obj.num_hits

  ar = Array.new(_num_hits)
  if ar.size > 0
    num_extra_references = 0
    _num_hits.times do |i|
      ar[i] = MS::Sequest::Srf::Out::Peptide.from_io(fh, unpack_35)
      num_extra_references += ar[i].num_other_loci
    end
    if dup_refs_gt_0
      MS::Sequest::Srf::Out::Peptide.read_extra_references(fh, num_extra_references, ar)
    end
    ## The xcorrs are already ordered by best to worst hit
    ## ADJUST the deltacn's to be meaningful for the top hit:
    ## (the same as bioworks and prophet)
    MS::Sequest::Srf::Out::Peptide.set_deltacn_from_deltacn_orig(ar)
  end
  out_obj.hits = ar
  out_obj[1].chomp! # computer
  out_obj
end

Instance Method Details

#inspect ⇒ Object 



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# File 'lib/ms/sequest/srf.rb', line 537

def inspect
  hits_s = 
    if self.hits
      ", @hits(#)=#{hits.size}"
    else
      ''
    end
  "<MS::Sequest::Srf::Out  first_scan=#{first_scan}, last_scan=#{last_scan}, charge=#{charge}, num_hits=#{num_hits}, computer=#{computer}, date_time=#{date_time}#{hits_s}>"
end