PhenotypeFactory.java

/* Acts as constructor for Phenotype objects */
/* A completely static class */

public class PhenotypeFactory {

	public static String GEOMETRIC = "geometric";
	public static String GEOMETRIC3D = "geometric3d";
	public static String GEOMETRIC10D = "geometric10d";
	public static String SEQUENCE = "sequence";
	public static String GEOMETRIC_SEQ = "geometricSeq";

	// returns newly instantiated Phenotype objects of type according to Parameters.phenotypeSpace
	public static Phenotype makeVirusPhenotype() {

		Phenotype p = null;
		if (GEOMETRIC.equals(Parameters.phenotypeSpace)) { p = new GeometricPhenotype(); }
		if (GEOMETRIC3D.equals(Parameters.phenotypeSpace)) { p = new GeometricPhenotype3D(); }
		if (GEOMETRIC10D.equals(Parameters.phenotypeSpace)) { p = new GeometricPhenotype10D(); }
		if (GEOMETRIC_SEQ.equals(Parameters.phenotypeSpace)) { p = new GeometricSeqPhenotype(); }
		return p;

	}

	// returns newly instantiated Phenotype objects of type according to Parameters.phenotypeSpace
	public static Phenotype makeHostPhenotype() {

		Phenotype p = null;
		if (GEOMETRIC.equals(Parameters.phenotypeSpace)) {
			p = new GeometricPhenotype(Parameters.initialTraitA, 0);
		}
		if (GEOMETRIC3D.equals(Parameters.phenotypeSpace)) {
			p = new GeometricPhenotype3D(Parameters.initialTraitA, 0, 0);
		}
		if (GEOMETRIC10D.equals(Parameters.phenotypeSpace)) {
			double[] traits = {Parameters.initialTraitA, 0, 0, 0, 0, 0, 0, 0, 0, 0};
			p = new GeometricPhenotype10D(traits);
		}
		if (GEOMETRIC_SEQ.equals(Parameters.phenotypeSpace)) {
			String startingSequence = Parameters.startingSequence;
			if (startingSequence == null) {
				p = new GeometricSeqPhenotype(Parameters.initialTraitA, 0);
			} else {
				p = new GeometricSeqPhenotype(Parameters.initialTraitA, 0, Parameters.startingSequence.toCharArray());
			}
		}
		return p;

	}

	// returns newly instantiated Phenotype objects of type according to Parameters.phenotypeSpace
	public static Phenotype makeArbitaryPhenotype(double x, double y) {

		Phenotype p = null;
		if (GEOMETRIC.equals(Parameters.phenotypeSpace)) { p = new GeometricPhenotype(x, y); }
		if (GEOMETRIC_SEQ.equals(Parameters.phenotypeSpace)) { p = new GeometricSeqPhenotype(x, y); }
		return p;

	}

}