/** Constructor */
public SampleStateAndCategoryModel(
Parameter muParameter, Parameter categoriesParameter, Vector substitutionModels) {
super(SampleStateAndCategoryModelParser.SAMPLE_STATE_AND_CATEGORY_MODEL);
this.substitutionModels = substitutionModels;
for (int i = 0; i < substitutionModels.size(); i++) {
addModel((SubstitutionModel) substitutionModels.elementAt(i));
}
this.categoryCount = substitutionModels.size();
sitesInCategory = new int[categoryCount];
// stateCount =
// ((SubstitutionModel)substitutionModels.elementAt(0)).getDataType().getStateCount();
this.muParameter = muParameter;
addVariable(muParameter);
muParameter.addBounds(new Parameter.DefaultBounds(1000.0, 0.0, 1));
this.categoriesParameter = categoriesParameter;
addVariable(categoriesParameter);
if (categoryCount > 1) {
for (int i = 0; i < categoryCount; i++) {
Parameter p = (Parameter) ((YangCodonModel) substitutionModels.elementAt(i)).getVariable(0);
Parameter lower = null;
Parameter upper = null;
if (i == 0) {
upper = (Parameter) ((YangCodonModel) substitutionModels.elementAt(i + 1)).getVariable(0);
p.addBounds(new omegaBounds(lower, upper));
} else {
if (i == (categoryCount - 1)) {
lower =
(Parameter) ((YangCodonModel) substitutionModels.elementAt(i - 1)).getVariable(0);
p.addBounds(new omegaBounds(lower, upper));
} else {
upper =
(Parameter) ((YangCodonModel) substitutionModels.elementAt(i + 1)).getVariable(0);
lower =
(Parameter) ((YangCodonModel) substitutionModels.elementAt(i - 1)).getVariable(0);
p.addBounds(new omegaBounds(lower, upper));
}
}
}
}
}
public MixtureModelBranchRates(
TreeModel tree,
Parameter rateCategoryQuantilesParameter,
ParametricDistributionModel[] models,
Parameter distributionIndexParameter,
boolean useQuantilesForRates,
boolean normalize,
double normalizeBranchRateTo) {
super(MixtureModelBranchRatesParser.MIXTURE_MODEL_BRANCH_RATES);
this.useQuantilesForRates = useQuantilesForRates;
this.rateCategoryQuantiles =
new TreeParameterModel(tree, rateCategoryQuantilesParameter, false);
rates = new double[tree.getNodeCount()];
this.normalize = normalize;
this.treeModel = tree;
this.distributionModels = models;
this.normalizeBranchRateTo = normalizeBranchRateTo;
this.tree = new SimpleTree(tree);
this.distributionIndexParameter = distributionIndexParameter;
addVariable(this.distributionIndexParameter);
// Force the boundaries of rateCategoryParameter to match the category count
// d Parameter.DefaultBounds bound = new Parameter.DefaultBounds(categoryCount - 1, 0,
// rateCategoryParameter.getDimension());
// d rateCategoryParameter.addBounds(bound);
// rateCategoryQuantilesParameter.;
Parameter.DefaultBounds bound =
new Parameter.DefaultBounds(1.0, 0.0, rateCategoryQuantilesParameter.getDimension());
rateCategoryQuantilesParameter.addBounds(bound);
Parameter.DefaultBounds bound2 = new Parameter.DefaultBounds(models.length, 0.0, 1);
distributionIndexParameter.addBounds(bound2);
distributionIndexParameter.setParameterValue(0, 0);
// Parameter distributionIndexParameter;
for (ParametricDistributionModel distributionModel : distributionModels) {
addModel(distributionModel);
}
// AR - commented out: changes to the tree are handled by model changed events fired by
// rateCategories
// addModel(tree);
// d addModel(rateCategories);
addModel(rateCategoryQuantiles);
// addModel(treeModel); // Maybe
// AR - commented out: changes to rateCategoryParameter are handled by model changed events
// fired by rateCategories
// addVariable(rateCategoryParameter);
if (normalize) {
tree.addModelListener(
new ModelListener() {
public void modelChangedEvent(Model model, Object object, int index) {
computeFactor();
}
public void modelRestored(Model model) {
computeFactor();
}
});
}
setupRates();
}