public void initAndValidate() {
paramList = paramListInput.get();
modelList = modelListInput.get();
freqsList = freqsListInput.get();
ratesList = ratesListInput.get();
paramPointers = paramPointersInput.get();
modelPointers = modelPointersInput.get();
freqsPointers = freqsPointersInput.get();
ratesPointers = ratesPointersInput.get();
pointerCount = paramPointers.getDimension();
dp = dpInput.get();
List<ParametricDistribution> distrs = dp.getBaseDistributions();
paramBaseDistr = paramDistrInput.get();
// paramBaseDistr = distrs.get(0);
modelBaseDistr = distrs.get(1);
// modelBaseDistr = modelDistrInput.get();
freqsBaseDistr = distrs.get(2);
// ratesBaseDistr = distrs.get(3);
ratesBaseDistr = rateDistrInput.get();
tempLikelihood = tempLikelihoodInput.get();
dpTreeLikelihood = dpTreeLikelihoodInput.get();
modelNetworkMap.put(1.0, new double[] {3.0});
modelNetworkMap.put(2.0, new double[] {3.0});
modelNetworkMap.put(3.0, new double[] {1.0, 2.0, 4.0});
modelNetworkMap.put(4.0, new double[] {3.0, 5.0});
modelNetworkMap.put(5.0, new double[] {4.0});
// System.out.println("is null? "+(modelNetworkMap.get(5.0) == null));
}
public void initAndValidate() {
testCorrect = testCorrectInput.get();
ratesList = ratesListInput.get();
alphaList = alphaListInput.get();
invPrList = invPrListInput.get();
siteModelList = siteModelListInput.get();
ratesPointers = ratesPointersInput.get();
pointerCount = ratesPointers.getDimension();
ratesBaseDistr = ratesDistrInput.get();
alphaBaseDistr = alphaDistrInput.get();
invPrBaseDistr = invPrDistrInput.get();
siteModelBaseDistr = siteModelDistrInput.get();
tempLikelihood = tempLikelihoodInput.get();
dpTreeLikelihood = dpTreeLikelihoodInput.get();
modelNetworkMap.put(1.0, new double[] {3.0});
modelNetworkMap.put(2.0, new double[] {3.0});
modelNetworkMap.put(3.0, new double[] {1.0, 2.0, 4.0});
modelNetworkMap.put(4.0, new double[] {3.0, 5.0});
modelNetworkMap.put(5.0, new double[] {4.0});
// System.out.println("is null? "+(modelNetworkMap.get(5.0) == null));
}
