Class Validator
In: lib/validator.rb
lib/validator/aa_est.rb
lib/validator/background.rb
Parent: Object

Methods

adjust_fps_for_background   increment_pephits_precision   initialize_increment   requires_pephits?   sample_stats   sensible_validator_hashes  

Classes and Modules

Module Validator::Transmem
Class Validator::AA
Class Validator::AAEst
Class Validator::Background
Class Validator::Bias
Class Validator::Cmdline
Class Validator::Decoy
Class Validator::DigestionBased
Class Validator::Probability
Class Validator::ProtFromPep
Class Validator::QValue
Class Validator::TruePos

Constants

Validator_to_string = { 'Validator::AA' => 'badAA', 'Validator::AAEst' => 'badAAEst', 'Validator::Decoy' => 'decoy', 'Validator::Transmem::Protein' => 'tmm', 'Validator::TruePos' => 'tps', 'Validator::Bias' => 'bias', 'Validator::Probability' => 'prob', 'Validator::QValue' => 'qval', :bad_aa => 'badAA', :bad_aa_est => 'badAAEst', :decoy => 'decoy', :tmm => 'tmm', :tps => 'tps', :bias => 'bias', :prob => 'prob', :qval => 'qval', }

Public Class methods

requires_pephits?(spec_id_obj)

in the absence of digestion, does the spec_id type requires pephits for validation?

sensible_validator_hashes(validators)

takes an array of validators and returns a fresh array where each has been turned into a sensible hash (with symbols as the keys!)

Public Instance methods

adjust_fps_for_background(num_tps, num_fps, background)

returns an adjusted false positive rate (a float not to drop below 0.0) based on a background of ‘false’-false positive hits to total hits. Also sets the @calculated_background attribute. Accepts floats or ints

increment_pephits_precision(peps)

if adding pephits in groups at a time, the entire group does not need to be queried, just the individual hit. Use this OR pephits_precision (NOT both). The initial query to this method will begin a running tally that is saved by the validator. takes either an array or a single pephit (determined by if it is a SpecID::Pep)

sample_stats(array)

copied from libjtp: vec returns the mean and std_dev

[Validate]