lib/validator/decoy.rb in mspire-0.4.5 vs lib/validator/decoy.rb in mspire-0.4.7

- old
+ new

@@ -7,14 +7,15 @@ attr_accessor :constraint attr_accessor :decoy_on_match attr_accessor :correct_wins # This is the the number of incorrect target hits over the total decoy hits - # The very rough, conservative ballpark estimate is the ratio of target hits - # to decoy hits. This can be refined by removing the number of true target + # The percent incorrect targets (PIT) expressed as a fraction (== 1 - PI_0). + # The rough, conservative ballpark estimate is the ratio of target hits to + # decoy hits. This can be refined by removing the number of true target # hits from the targets used to calculate it. - attr_accessor :pi_zero + attr_accessor :frit attr_accessor :last_pep_was_decoy attr_accessor :increment_normal attr_accessor :increment_decoy @@ -23,16 +24,16 @@ attr_reader :normal_peps_just_submitted DEFAULTS = { :decoy_on_match => true, :correct_wins => true, - :pi_zero => 1.0, + :frit => 1.0, } def initialize(opts={}) merged = DEFAULTS.merge(opts) - @constraint, @decoy_on_match, @correct_wins, @pi_zero = merged.values_at(:constraint, :decoy_on_match, :correct_wins, :pi_zero) + @constraint, @decoy_on_match, @correct_wins, @frit = merged.values_at(:constraint, :decoy_on_match, :correct_wins, :frit) end # returns [normal, decoy] (?? I think ??) # reads the full protein reference def partition(peps) @@ -84,18 +85,18 @@ @increment_total_submitted += to_submit.size (normal, decoy) = partition(to_submit) @normal_peps_just_submitted = normal @increment_normal += normal.size @increment_decoy += decoy.size - calc_precision(@increment_normal, @increment_decoy, @pi_zero) + calc_precision(@increment_normal, @increment_decoy, @frit) end def pephit_precision(peps, separate_peps=nil) if separate_peps - calc_precision(peps.size, separate_peps.size, @pi_zero) + calc_precision(peps.size, separate_peps.size, @frit) else (norm, decoy) = partition(peps) - calc_precision(norm.size, decoy.size, @pi_zero) + calc_precision(norm.size, decoy.size, @frit) end end def to_param_string "decoy="+ ["{constraint=#{(constraint ? constraint.inspect : '')}", "decoy_on_match=#{@decoy_on_match}", "correct_wins=#{@correct_wins}}"].join(", ")