Reduction of biojava/biojava#354 into a form suitable for asking at http://stackoverflow.com/questions/40598972/java-two-level-parameterized-type-inference

GenericsHell.java

package demo;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Set;
 
public class GenericsHell {

	static class NumberLists<L extends List<T>,T extends Number> extends ArrayList<L> {}
	
	static <L extends List<T>,T extends Number>
	Set<NumberLists<L,T>> useList(L list) {
		NumberLists<L,T> nl = new NumberLists<L, T>();
		nl.add(list);
		return Collections.singleton(nl);
	}
	
	// Note that this is not assignable to List<Number>
	static List<? extends Number> makeList() {
		if(Math.random()<.5) {
			return new ArrayList<Integer>();
		} else {
			return new ArrayList<Double>();
		}
	}
	
	static <L extends List<T>,T extends Number>
	NumberLists<L,T> createAndAdd(L list) {
		NumberLists<L,T> paraNL = new NumberLists<>();
		paraNL.add(list);
		return paraNL;
	}

	public static void main(String[] args) {
		// Everything works with a concrete class
		List<Integer> intList = new ArrayList<Integer>();
		// Use with parametric functions
		Set<NumberLists<List<Integer>,Integer>> concreteSet = useList(intList);
		// Create related class of the same type
		NumberLists<List<Integer>,Integer> concreteNL = concreteSet.iterator().next();
		concreteNL.add(intList);
		
		// But now I need to handle the case where the input is also parametric
		List<? extends Number> numList = makeList();
		
		// What is the type here? This is obviously an error
		Set<NumberLists<? extends List<? extends Number>>,? extends Number> paramSet = useList(numList);
		// Type should ideally be compatible with numList still
		NumberLists<?,?> paraNL1 = paramSet.iterator().next();
		// Captures don't match
		paraNL1.add(numList);
		
		// Can't even add numList to a NumberLists, since clusters don't match
		NumberLists<?,?> paraNL2 = new NumberLists<>();
		paraNL2.add(numList);
		// Have to work around this with a parametric method that does both steps
		NumberLists<?,?> paraNL3 = createAndAdd(numList);
	}
	
}