/**
* Creates a new {@code DuoBaum} instance.
*
* @param dag the directed acyclic graph that determines the transition probabilities.
* @param gl the emission probabilities.
* @param seed the initial random seed.
* @param nCopies the number of haplotype pairs that will be sampled for each individual in a
* parent-offspring duo.
* @throws IllegalArgumentException if {@code nCopies<1 ||
* dag.markers().equals(gl.markers())==false}
* @throws NullPointerException if {@code dag==null || gl==null}
*/
public DuoBaum(Dag dag, GL gl, long seed, int nCopies) {
if (dag.markers().equals(gl.markers()) == false) {
throw new IllegalArgumentException("inconsistent markers");
}
if (nCopies < 1) {
throw new IllegalArgumentException("nCopies<1: " + nCopies);
}
this.dag = dag;
this.gl = gl;
this.nMarkers = dag.nMarkers();
this.nCopies = nCopies;
this.seed = seed;
this.random = new Random(seed);
this.nodeAB1 = new int[nCopies];
this.nodeA2 = new int[nCopies];
this.nodeB2 = new int[nCopies];
this.nodeValue = new double[nCopies];
this.allelesAB1 = new byte[nCopies][gl.nMarkers()];
this.allelesA2 = new byte[nCopies][gl.nMarkers()];
this.allelesB2 = new byte[nCopies][gl.nMarkers()];
int size = (int) Math.ceil(Math.sqrt(1 + 8 * dag.nMarkers()) / 2.0) + 1;
this.levels = new DuoBaumLevel[size];
for (int j = 0; j < levels.length; ++j) {
levels[j] = new DuoBaumLevel(dag, gl);
}
this.fwdNodes = new DuoNodes();
this.bwdNodes = new DuoNodes();
}
private double parentSum(DuoBaumLevel level, int sampleA, int sampleB, int state) {
int marker = level.marker();
double fwdValue = level.forwardValuesSum() * level.forwardValue(state);
int edgeAB1 = level.edgeAB1(state);
int edgeA2 = level.edgeA2(state);
int edgeB2 = level.edgeB2(state);
double tpAB1 = dag.condEdgeProb(marker, edgeAB1);
double tpA2 = dag.condEdgeProb(marker, edgeA2);
double tpB2 = dag.condEdgeProb(marker, edgeB2);
byte symbolAB1 = dag.symbol(marker, edgeAB1);
byte symbolA2 = dag.symbol(marker, edgeA2);
byte symbolB2 = dag.symbol(marker, edgeB2);
double epA = gl.gl(marker, sampleA, symbolAB1, symbolA2);
double epB = gl.gl(marker, sampleB, symbolAB1, symbolB2);
return fwdValue / ((epA * epB) * (tpAB1 * tpA2 * tpB2));
}