private static MatchTableImpl createEmptyTable(
VariantGraphRanking ranking, VariantGraph graph, Iterable<Token> witness) {
// -2 === ignore the start and the end vertex
return new MatchTableImpl(
StreamSupport.stream(witness.spliterator(), false).toArray(Token[]::new),
IntStream.range(0, Math.max(0, ranking.apply(graph.getEnd()) - 1)).toArray());
}
// move parameters into fields?
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.<VariantGraph.Vertex>emptyList());
for (VariantGraph.Vertex vgv : matchingVertices) {
set(rowIndex, ranking.apply(vgv) - 1, t, vgv);
}
}
rowIndex++;
}
}