private void setup() { DataType dataType = baseSubstitutionModel.getDataType(); FrequencyModel freqModel = baseSubstitutionModel.getFrequencyModel(); Parameter kappaParameter = new Parameter.Default("kappa", 1, baseSubstitutionModel.getKappa()); substitutionModels = new LinkedList<SubstitutionModel>(); branchAssignmentMap = new LinkedHashMap<NodeRef, Integer>(); int branchClass = 0; for (NodeRef node : treeModel.getNodes()) { if (!treeModel.isRoot(node)) { double nodeHeight = treeModel.getNodeHeight(node); double parentHeight = treeModel.getNodeHeight(treeModel.getParent(node)); double time = 0.5 * (parentHeight + nodeHeight); double baseOmega = baseSubstitutionModel.getOmega(); double fixed = baseOmega * time; double epsilon = (Math.log(1 - random.nextDouble()) / (-rate)); // Math.exp((random.nextGaussian() * stdev + mean)); double value = fixed + epsilon; Parameter omegaParameter = new Parameter.Default("omega", 1, value); GY94CodonModel gy94 = new GY94CodonModel((Codons) dataType, omegaParameter, kappaParameter, freqModel); substitutionModels.add(gy94); branchAssignmentMap.put(node, branchClass); branchClass++; } // END: root check } // END: nodes loop } // END: setup