SequencePhenotype.java

I wrote a very rough draft of SequencePhenotype.java.

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On Monday's meeting, Erick said something about Strings and a Wrapper class. I think he meant generic class, since String is not a primitive type. At first, I tried including a type parameter, S, but it got too complex for an outline. A few String methods are used in the class, and public class SequencePhenotype<S extends String> seems a little silly.

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constants
public final String[] NUCLEOBASES = new String[]{"A", "C", "G", "T"};

• Not entirely sure if these are the letters we should be using

fields
private String sequence;

• No longer a double.
• Always this 1 field (unlike number of traits in GeometricPhenotype.java and GeometricPhenotype3D.java).

distance
public double distance(Phenotype p) {

• Only works for sequences of the same length. Should we use something like this to include sequences of different lengths?
• The parameter Phenotype p must be an instance of SequencePhenotype since hamming distance is a metric for comparing Strings. It is not enough to be an instance of Phenotype.

mutate
public Phenotype mutate() {

• Naïve implementation of mutate. Currently, all this method does is add one randomly chosen nucleobase to the current sequence. It's possible to mutate a sequence without increasing its length if that's what we want (as well). In other words, we can change the sequence at one index instead of adding.

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Here's a trivial static method if you would like to try out the class:

    public static void main(String[] args) {
        System.out.print("SequencePhenotype(): ");
        SequencePhenotype emptyConstructor = new SequencePhenotype();
        System.out.println(emptyConstructor);
        System.out.println("After mutate(): " + emptyConstructor.mutate());
        System.out.println();

        System.out.print("SequencePhenotype(\"AGTCTTCCG\"): ");
        SequencePhenotype constructor = new SequencePhenotype("AGTCTTCCG");
        System.out.println(constructor);

        SequencePhenotype seq1 = (SequencePhenotype) constructor.mutate();
        SequencePhenotype seq2 = (SequencePhenotype) constructor.mutate();
        System.out.println("(1) AGTCTTCCG after mutate(): " + seq1);
        System.out.println("(2) AGTCTTCCG after mutate(): " + seq2);
        System.out.println();

        System.out.println("Distance: " + constructor.distance(seq1));
        System.out.println("Distance: " + constructor.distance(seq2));
        System.out.println("Distance: " + seq1.distance(seq2));
    }

Note, your output will be different, since the nucleobases are randomly chosen in the empty constructor and mutate.

    SequencePhenotype(): C
    After mutate(): CA

    SequencePhenotype("AGTCTTCCG"): AGTCTTCCG
    (1) AGTCTTCCG after mutate(): AGTCTTCCGA
    (2) AGTCTTCCG after mutate(): AGTCTTCCGC

    Distance: 1.0