public void testDebug() {
int POP_SIZE = 50;
int numAlleles = 10;
int numLoci = 10;
POP_MODEL.loadDefaults();
POP_MODEL.setIncParents(true);
POP_MODEL.setAllelicFreqType(ButlerFamilyData.EQUAL_FREQ);
POP_MODEL.setSize(POP_SIZE);
POP_MODEL.setFamilyType(ButlerFamilyData.BUTLER_50x1);
POP_MODEL.setNumLoci(numLoci);
POP_MODEL.setNumAlleles(numAlleles);
KinGroupProjectV1.makeInstance("SimpsPopFactoryTest", "1");
POP_MODEL.setFamilyType(ButlerFamilyData.BUTLER_50x1);
OldAlleleFreq freq = OldAlleleFreqFactory.makeAlleleFreq(POP_MODEL);
freq.normalize(1.0f, false);
GenotypeFactory.init();
POP_MODEL.setIncParents(false);
// POP_MODEL.setIncludeParents(true);
OldPop popA = new ButlerPopBuilder(freq).buildButler(POP_MODEL);
SysPop simsPop = OldPopToSysPopFactory.makePopFrom(popA);
System.out.println(new JWAlg_v2_HapDip(simsPop, freq).makeOutgoingData(new Date()));
}
protected double calcOneDistance(OldPop popA) {
PopToPartitionFactory factory =
PopToPartitionFactory.makeInstance(
popA); // must be called here, since we created a new population
Partition partA = factory.makeFromPopulation(popA);
SysPop pop = OldPopToSysPopFactory.makePopFrom(popA);
SIMPS2Alg method = new SIMPS2Alg(pop, ALG_MODEL);
Partition partB = method.partition();
int dist = new LitowDistance().distance(partA, partB);
// if (dist != 0) {
// LOG.trace(this, "A=", partA);
// LOG.trace(this, "B=", partB);
// LOG.trace(this, "D(A,B)=", Integer.toString(dist));
// }
return dist;
}
public void testSingleTest() {
int POP_SIZE = 50;
int numAlleles = 10;
int numLoci = 10;
POP_MODEL.loadDefaults();
POP_MODEL.setIncParents(true);
POP_MODEL.setAllelicFreqType(ButlerFamilyData.EQUAL_FREQ);
POP_MODEL.setSize(POP_SIZE);
POP_MODEL.setFamilyType(ButlerFamilyData.BUTLER_50x1);
POP_MODEL.setNumLoci(numLoci);
POP_MODEL.setNumAlleles(numAlleles);
KinGroupProjectV1.makeInstance("SimpsPopFactoryTest", "3");
POP_MODEL.setFamilyType(ButlerFamilyData.BUTLER_6x2);
OldAlleleFreq freq = OldAlleleFreqFactory.makeAlleleFreq(POP_MODEL);
freq.normalize(1.0f, false);
GenotypeFactory.init();
POP_MODEL.setIncParents(false);
// POP_MODEL.setIncludeParents(true);
OldPop popA = new ButlerPopBuilder(freq).buildButler(POP_MODEL);
SysPop simsPop = OldPopToSysPopFactory.makePopFrom(popA);
JWAlg_v2_HapDip f = new JWAlg_v2_HapDip(simsPop, freq);
f.setDebug(true);
Partition partB = f.partition();
System.out.println(partB);
PopToPartitionFactory factory =
PopToPartitionFactory.makeInstance(
popA); // must be called here, since we created a new population
Partition partA = factory.makeFromPopulation(popA);
int dist = new LitowDistance().distance(partA, partB);
if (dist != 0) {
LOG.report(this, "A=" + partA);
LOG.report(this, "B=" + partB);
LOG.report(this, "D(A,B)=" + Integer.toString(dist));
dist = new LitowDistance().distance(partA, partB);
}
assertEquals(0, dist);
}