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)); }