LPhy argument matching does not handle the array of objects

[walterxie]

To match the argument type, lphy core does not handle the array of types. For example br = localClock(tree=tree, clades=[node1,node2], cladeRates=[0.4,0.1], rootRate=0.2, includeStem=true);, the java is

@ParameterInfo(name = cladeArrayName, description = "...") Value<TimeTreeNode[]> clades,

But in ArgumentUtils.matchingParameterTypes(List<Argument> arguments, ...), that value type is casted to Object[] as we do not have the TimeTreeNodeArrayValue. This value class has to be in the base, so the SPI for ArrayValue will be the general solution.

Alternatively, the easy treatment is to get the Object[] and cast the component during the for loop, such as :

Object[] clades = (Object[]) params.get(cladeArrayName).value();

for (int i = 0; i < clades.length; i++){
            TimeTreeNode clade = (TimeTreeNode) clades[i];