/**
  * A helper to add a single word to a given dependency tree
  *
  * @param toModify The tree to add the word to.
  * @param root The root of the tree where we should be adding the word.
  * @param rel The relation to add the word with.
  * @param coreLabel The word to add.
  */
 @SuppressWarnings("UnusedDeclaration")
 private static void addWord(
     SemanticGraph toModify, IndexedWord root, String rel, CoreLabel coreLabel) {
   IndexedWord dependent = new IndexedWord(coreLabel);
   toModify.addVertex(dependent);
   toModify.addEdge(
       root,
       dependent,
       GrammaticalRelation.valueOf(Language.English, rel),
       Double.NEGATIVE_INFINITY,
       false);
 }
  /**
   * Parse a CoNLL formatted tree into a SemanticGraph object (along with a list of tokens).
   *
   * @param conll The CoNLL formatted tree.
   * @return A pair of a SemanticGraph and a token list, corresponding to the parse of the sentence
   *     and to tokens in the sentence.
   */
  protected Pair<SemanticGraph, List<CoreLabel>> mkTree(String conll) {
    List<CoreLabel> sentence = new ArrayList<>();
    SemanticGraph tree = new SemanticGraph();
    for (String line : conll.split("\n")) {
      if (line.trim().equals("")) {
        continue;
      }
      String[] fields = line.trim().split("\\s+");
      int index = Integer.parseInt(fields[0]);
      String word = fields[1];
      CoreLabel label = IETestUtils.mkWord(word, index);
      sentence.add(label);
      if (fields[2].equals("0")) {
        tree.addRoot(new IndexedWord(label));
      } else {
        tree.addVertex(new IndexedWord(label));
      }
      if (fields.length > 4) {
        label.setTag(fields[4]);
      }
      if (fields.length > 5) {
        label.setNER(fields[5]);
      }
      if (fields.length > 6) {
        label.setLemma(fields[6]);
      }
    }
    int i = 0;
    for (String line : conll.split("\n")) {
      if (line.trim().equals("")) {
        continue;
      }
      String[] fields = line.trim().split("\\s+");
      int parent = Integer.parseInt(fields[2]);
      String reln = fields[3];
      if (parent > 0) {
        tree.addEdge(
            new IndexedWord(sentence.get(parent - 1)),
            new IndexedWord(sentence.get(i)),
            new GrammaticalRelation(Language.UniversalEnglish, reln, null, null),
            1.0,
            false);
      }
      i += 1;
    }

    return Pair.makePair(tree, sentence);
  }
  /**
   * 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());
    }
  }