/**
* create new instance of src object, connecting all inputs from src object Note if input is a
* SubstModel, it is duplicated as well.
*
* @param src object to be copied
* @param i index used to extend ID with.
* @return copy of src object
*/
private Object duplicate(BEASTInterface src, int i) {
if (src == null) {
return null;
}
BEASTInterface copy;
try {
copy = src.getClass().newInstance();
copy.setID(src.getID() + "_" + i);
} catch (InstantiationException | IllegalAccessException e) {
e.printStackTrace();
throw new RuntimeException(
"Programmer error: every object in the model should have a default constructor that is publicly accessible: "
+ src.getClass().getName());
}
for (Input<?> input : src.listInputs()) {
if (input.get() != null) {
if (input.get() instanceof List) {
// handle lists
// ((List)copy.getInput(input.getName())).clear();
for (Object o : (List<?>) input.get()) {
if (o instanceof BEASTInterface) {
// make sure it is not already in the list
copy.setInputValue(input.getName(), o);
}
}
} else if (input.get() instanceof SubstitutionModel) {
// duplicate subst models
BEASTInterface substModel = (BEASTInterface) duplicate((BEASTInterface) input.get(), i);
copy.setInputValue(input.getName(), substModel);
} else {
// it is some other value
copy.setInputValue(input.getName(), input.get());
}
}
}
copy.initAndValidate();
return copy;
}
