Class: Bioinform::MotifModel::PPM

Inherits:
PM
  • Object
show all
Defined in:
lib/bioinform/data_models/ppm.rb

Constant Summary collapse

VALIDATOR = 
PM::VALIDATOR * PPM.probability_validator(eps: 1.0e-4).make_strict

Constants inherited from PM

Bioinform::MotifModel::PM::DEFAULT_PARSER, Bioinform::MotifModel::PM::TRIVIAL_VALIDATOR

Instance Attribute Summary

Attributes inherited from PM

#alphabet, #matrix

Class Method Summary collapse

Methods inherited from PM

#==, #complemented, #default_validator, #each_position, from_file, from_string, #initialize, #length, #named, #reverse_complemented, #reversed, #rounded, #to_s

Constructor Details

This class inherits a constructor from Bioinform::MotifModel::PM

Class Method Details

.default_validator ⇒ Object 



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# File 'lib/bioinform/data_models/ppm.rb', line 10

def self.default_validator
  PPM::VALIDATOR
end

.probability_validator(eps: 1.0e-4) ⇒ Object 



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# File 'lib/bioinform/data_models/ppm.rb', line 14

def self.probability_validator(eps: 1.0e-4)
  Validator.new{|matrix, alphabet|
    errors = []
    unless matrix.all?{|pos| pos.all?{|el| el >= 0 } }
      errors << "Elements of PPM should be non-negative."
    end

    warnings = []
    probability_sums = matrix.map{|pos| pos.inject(0.0, &:+) }
    max_discrepancy = probability_sums.map{|sum| (sum - 1.0).abs }.max
    unless max_discrepancy <= eps
      warnings << "PPM should sum up to 1, with discrepancy not greater than #{eps}."
    end

    ValidationResult.new(errors: errors, warnings: warnings)
  }
end