matlab.unittest.constraints.Tolerance - Fundamental interface for tolerances - MATLAB (original) (raw)

Namespace: matlab.unittest.constraints

Fundamental interface for tolerances

Description

The matlab.unittest.constraints.Tolerance class provides an interface for tolerances. Tolerances define a notion of approximate equality for given data types and can be applied to the IsEqualTo constraint as well as certain comparators using the Within name-value argument.

The class has three abstract methods. To create a custom tolerance class, derive your class from matlab.unittest.constraints.Tolerance and implement all the abstract methods.

Methods

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Examples

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Determine if two DNA sequences have a Hamming distance within a specified tolerance. For two DNA sequences of the same length, the Hamming distance is the number of positions in which the nucleotides (letters) of one sequence differ from the other.

Create DNA Class

To represent DNA sequences, create the DNA class in a file named DNA.m in your current folder.

classdef DNA properties (SetAccess=immutable) Sequence char {mustHaveValidLetters} end

methods
    function dna = DNA(sequence)
        dna.Sequence = sequence;
    end
end

end

function mustHaveValidLetters(sequence) validLetters = ... sequence == 'A' | ... sequence == 'C' | ... sequence == 'T' | ... sequence == 'G';

if ~all(validLetters,"all") error("Sequence contains one or more invalid letters.") end end

Create HammingDistance Class

In a file named HammingDistance.m in your current folder, create the HammingDistance class by subclassing matlab.unittest.constraints.Tolerance. Add a property Value so that you can specify the maximum allowable Hamming distance.

Classes that derive from the Tolerance class must implement the supports, satisfiedBy, and getDiagnosticFor methods:

• supports method — Specify that the tolerance must support objects of the DNA class.
• satisfiedBy method — Specify that for the actual and expected values to be within the tolerance, they must be the same size and their Hamming distance must be less than or equal to the tolerance value.
• getDiagosticFor method — Create and return a StringDiagnostic object that contains diagnostic information about the comparison.

classdef HammingDistance < matlab.unittest.constraints.Tolerance properties Value end

methods
    function tolerance = HammingDistance(value)
        tolerance.Value = value;
    end

    function tf = supports(~,expected)
        tf = isa(expected,"DNA");
    end

    function tf = satisfiedBy(tolerance,actual,expected)
        if ~isSameSize(actual.Sequence,expected.Sequence)
            tf = false;
            return
        end
        tf = hammingDistance(actual.Sequence,expected.Sequence) <= ...
            tolerance.Value;
    end

    function diagnostic = getDiagnosticFor(tolerance,actual,expected)
        import matlab.automation.diagnostics.StringDiagnostic
        if ~isSameSize(actual.Sequence,expected.Sequence)
            str = "The DNA sequences have different lengths.";
        else
            str = "The DNA sequences have a Hamming distance of " ...
                + hammingDistance(actual.Sequence,expected.Sequence) ...
                + "." + newline + "The allowable distance is " ...
                + tolerance.Value + ".";
        end
        diagnostic = StringDiagnostic(str);
    end
end

end

function tf = isSameSize(str1,str2) tf = isequal(size(str1),size(str2)); end

function distance = hammingDistance(str1,str2) distance = nnz(str1 ~= str2); end

Compare DNA Sequences

To compare DNA sequences using a tolerance, first import the necessary classes and create a test case for interactive testing.

import matlab.unittest.TestCase import matlab.unittest.constraints.IsEqualTo testCase = TestCase.forInteractiveUse;

Create two DNA objects and compare them without specifying a tolerance. The test fails because the objects are not equal.

sampleA = DNA("ACCTGAGTA"); sampleB = DNA("ACCACAGTA"); testCase.verifyThat(sampleA,IsEqualTo(sampleB))

Verification failed. --------------------- Framework Diagnostic: --------------------- IsEqualTo failed. --> ObjectComparator failed. --> The objects are not equal using "isequaln".

    Actual Value:
      DNA with properties:
    
        Sequence: 'ACCTGAGTA'
    Expected Value:
      DNA with properties:
    
        Sequence: 'ACCACAGTA'
------------------
Stack Information:
------------------
In C:\work\CreateCustomToleranceExample.m (CreateCustomToleranceExample) at 45

Verify that the DNA sequences are equal within a Hamming distance of 1. The test fails and the testing framework displays additional diagnostic information produced by the getDiagnosticFor method.

testCase.verifyThat(sampleA,IsEqualTo(sampleB,"Within",HammingDistance(1)))

Verification failed. --------------------- Framework Diagnostic: --------------------- IsEqualTo failed. --> ObjectComparator failed. --> The objects are not equal using "isequaln". --> The DNA sequences have a Hamming distance of 2. The allowable distance is 1.

    Actual Value:
      DNA with properties:
    
        Sequence: 'ACCTGAGTA'
    Expected Value:
      DNA with properties:
    
        Sequence: 'ACCACAGTA'
------------------
Stack Information:
------------------
In C:\work\CreateCustomToleranceExample.m (CreateCustomToleranceExample) at 51

Verify that the DNA sequences are equal within a Hamming distance of 2. The test passes.

testCase.verifyThat(sampleA,IsEqualTo(sampleB,"Within",HammingDistance(2)))

Version History

Introduced in R2013a