NetTrainer

public List<Double> trainNet(List<Double> input, List<Double> expectedOutput, GeneticAlgorithm<Double> ga, int gens) {

    ga.setFitnessFunction( genes -> {
        assert output.sizeWithoutBias() == expectedOutput.size();
        setWeights( genes.getSequence() );

        //"Fire" net
        List<Double> output = update();

        int fitness = Integer.MAX_VALUE;
        for (int i = 0; i < output.size(); i++) {
            fitness -= 100 * Math.abs( output.get(i) - expectedOutput.get(i) );
        }

        return fitness;
    } );

    resetInput(input);

    ga.simNGens(gens);

    return output.getActivationsWithoutBias();
 }