code: private void fillTableWithMatches(VariantGraphRanking ranking, VariantGraph graph, Iterable<Token> witness, Comparator<Token> comparator) {
          Matches matches = Matches.between(graph.vertices(), witness, comparator);
          Set<Token> unique = matches.uniqueInWitness;
          Set<Token> ambiguous = matches.ambiguousInWitness;
          int rowIndex = 0;
          for (Token t : witness) {
              if (unique.contains(t) || ambiguous.contains(t)) {
                  List<VariantGraph.Vertex> matchingVertices = matches.allMatches.getOrDefault(t, Collections.emptyList());
                  for (VariantGraph.Vertex vgv : matchingVertices) {
                      set(rowIndex, ranking.apply(vgv) - 1, t, vgv);
                  }
              }
              rowIndex++;
          }
      }
docs: move parameters into fields?