/**
   * The basic method for splitting off a clause of a tree. This modifies the tree in place. This
   * method addtionally follows ref edges.
   *
   * @param tree The tree to split a clause from.
   * @param toKeep The edge representing the clause to keep.
   */
  @SuppressWarnings("unchecked")
  private void simpleClause(SemanticGraph tree, SemanticGraphEdge toKeep) {
    splitToChildOfEdge(tree, toKeep);

    // Follow 'ref' edges
    Map<IndexedWord, IndexedWord> refReplaceMap = new HashMap<>();
    // (find replacements)
    for (IndexedWord vertex : tree.vertexSet()) {
      for (SemanticGraphEdge edge : extraEdgesByDependent.get(vertex)) {
        if ("ref".equals(edge.getRelation().toString())
            && // it's a ref edge...
            !tree.containsVertex(
                edge.getGovernor())) { // ...that doesn't already exist in the tree.
          refReplaceMap.put(vertex, edge.getGovernor());
        }
      }
    }
    // (do replacements)
    for (Map.Entry<IndexedWord, IndexedWord> entry : refReplaceMap.entrySet()) {
      Iterator<SemanticGraphEdge> iter = tree.incomingEdgeIterator(entry.getKey());
      if (!iter.hasNext()) {
        continue;
      }
      SemanticGraphEdge incomingEdge = iter.next();
      IndexedWord governor = incomingEdge.getGovernor();
      tree.removeVertex(entry.getKey());
      addSubtree(
          tree,
          governor,
          incomingEdge.getRelation().toString(),
          this.tree,
          entry.getValue(),
          this.tree.incomingEdgeList(tree.getFirstRoot()));
    }
  }
  /**
   * A helper to add an entire subtree to a given dependency tree.
   *
   * @param toModify The tree to add the subtree to.
   * @param root The root of the tree where we should be adding the subtree.
   * @param rel The relation to add the subtree with.
   * @param originalTree The orignal tree (i.e., {@link ClauseSplitterSearchProblem#tree}).
   * @param subject The root of the clause to add.
   * @param ignoredEdges The edges to ignore adding when adding this subtree.
   */
  private static void addSubtree(
      SemanticGraph toModify,
      IndexedWord root,
      String rel,
      SemanticGraph originalTree,
      IndexedWord subject,
      Collection<SemanticGraphEdge> ignoredEdges) {
    if (toModify.containsVertex(subject)) {
      return; // This subtree already exists.
    }
    Queue<IndexedWord> fringe = new LinkedList<>();
    Collection<IndexedWord> wordsToAdd = new ArrayList<>();
    Collection<SemanticGraphEdge> edgesToAdd = new ArrayList<>();
    // Search for subtree to add
    for (SemanticGraphEdge edge : originalTree.outgoingEdgeIterable(subject)) {
      if (!ignoredEdges.contains(edge)) {
        if (toModify.containsVertex(edge.getDependent())) {
          // Case: we're adding a subtree that's not disjoint from toModify. This is bad news.
          return;
        }
        edgesToAdd.add(edge);
        fringe.add(edge.getDependent());
      }
    }
    while (!fringe.isEmpty()) {
      IndexedWord node = fringe.poll();
      wordsToAdd.add(node);
      for (SemanticGraphEdge edge : originalTree.outgoingEdgeIterable(node)) {
        if (!ignoredEdges.contains(edge)) {
          if (toModify.containsVertex(edge.getDependent())) {
            // Case: we're adding a subtree that's not disjoint from toModify. This is bad news.
            return;
          }
          edgesToAdd.add(edge);
          fringe.add(edge.getDependent());
        }
      }
    }
    // Add subtree
    // (add subject)
    toModify.addVertex(subject);
    toModify.addEdge(
        root,
        subject,
        GrammaticalRelation.valueOf(Language.English, rel),
        Double.NEGATIVE_INFINITY,
        false);

    // (add nodes)
    wordsToAdd.forEach(toModify::addVertex);
    // (add edges)
    for (SemanticGraphEdge edge : edgesToAdd) {
      assert !toModify.incomingEdgeIterator(edge.getDependent()).hasNext();
      toModify.addEdge(
          edge.getGovernor(),
          edge.getDependent(),
          edge.getRelation(),
          edge.getWeight(),
          edge.isExtra());
    }
  }