/FileExtraction/Java_unseen/slavpetrov_berkeleyparser/src/edu/berkeley/nlp/PCFGLA/ArrayParser.java
package edu.berkeley.nlp.PCFGLA;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;

import edu.berkeley.nlp.discPCFG.Linearizer;
import edu.berkeley.nlp.math.DoubleArrays;
import edu.berkeley.nlp.syntax.StateSet;
import edu.berkeley.nlp.syntax.Tree;
import edu.berkeley.nlp.util.ArrayUtil;
import edu.berkeley.nlp.util.Numberer;
import edu.berkeley.nlp.util.ScalingTools;

/**
 * Simple mixture parser.
 */
public class ArrayParser implements Parser {
	// i dont know how to initialize shorts...
	short zero = 0, one = 1;
	protected Numberer tagNumberer = Numberer.getGlobalNumberer("tags");

	// inside scores
	protected double[][][] iScore; // start idx, end idx, state -> logProb

	// outside scores
	protected double[][][] oScore; // start idx, end idx, state -> logProb

	protected int[][] narrowLExtent = null; // the rightmost left extent of
											// state
											// s ending at position i

	protected int[][] wideLExtent = null; // the leftmost left extent of state s
											// ending at position i

	protected int[][] narrowRExtent = null; // the leftmost right extent of
											// state
											// s starting at position i

	protected int[][] wideRExtent = null; // the rightmost right extent of state
											// s
											// starting at position i

	protected short length;

	protected int arraySize = 0;

	protected int myMaxLength = 200;

	Lexicon lexicon;

	int numStates;
	int maxNSubStates;
	int[] idxC;
	double[] scoresToAdd;
	int touchedRules;
	double[] tmpCountsArray;
	Grammar grammar;
	int[] stateClass;

	public ArrayParser() {
	}

	public ArrayParser(Grammar gr, Lexicon lex) {
		this.touchedRules = 0;
		this.grammar = gr;
		this.lexicon = lex;
		this.tagNumberer = Numberer.getGlobalNumberer("tags");
		this.numStates = gr.numStates;
		this.maxNSubStates = maxSubStates(gr);
		this.idxC = new int[maxNSubStates];
		this.scoresToAdd = new double[maxNSubStates];
		tmpCountsArray = new double[scoresToAdd.length * scoresToAdd.length
				* scoresToAdd.length];

		// System.out.println("This grammar has " + numStates
		// + " states and a total of " + grammar.totalSubStates() +
		// " substates.");
	}

	@SuppressWarnings("unchecked")
	public List<Integer>[][] getPossibleStates(List<String> sentence,
			double logThreshold) {
		length = (short) sentence.size();
		initializeArrays();
		initializeChart(sentence, false);

		doInsideScores();
		double score = iScore[0][length][0];
		if (score > Double.NEGATIVE_INFINITY) {
			System.out.println("\nFound a parse for sentence with length "
					+ length + ". The LL is " + score + ".");
		} else {
			System.out.println("Did NOT find a parse for sentence with length "
					+ length + ".");
		}
		oScore[0][length][tagNumberer.number("ROOT")] = 0.0;
		doOutsideScores();

		List<Integer>[][] possibleStates = new ArrayList[length + 1][length + 1];

		int unprunedStates = 0;
		int prunedStates = 0;

		double sentenceProb = iScore[0][length][0];
		for (int diff = 1; diff <= length; diff++) {
			for (int start = 0; start < (length - diff + 1); start++) {
				int end = start + diff;
				possibleStates[start][end] = new ArrayList<Integer>();
				for (int state = 0; state < numStates; state++) {
					double viterbiPosterior = iScore[start][end][state]
							+ oScore[start][end][state] - sentenceProb;

					if (!Double.isInfinite(viterbiPosterior)) {
						unprunedStates++;
					}
					if (viterbiPosterior > logThreshold) {
						possibleStates[start][end].add(new Integer(state));
						prunedStates++;
						// if ((start==0)&&(end==length)
						// )System.out.println(start+" "+end+"
						// "+state);
						// System.out.println("i "+iScore[start][end][state]+" o
						// "+oScore[start][end][state]+" v-pos:
						// "+viterbiPosterior);
					}
				}
			}
		}
		System.out.print("Down to " + prunedStates + " states from "
				+ unprunedStates + ". ");
		return possibleStates;

	}

	// belongs in the grammar but i didnt want to change the signature for
	// now...
	public int maxSubStates(Grammar grammar) {
		int max = 0;
		for (int i = 0; i < numStates; i++) {
			if (grammar.numSubStates[i] > max)
				max = grammar.numSubStates[i];
		}
		return max;
	}

	public Tree<String> getBestParse(List<String> sentence) {
		System.out
				.println("This parser assumes an unsplit grammar (= split grammar with 1 substate)");
		length = (short) sentence.size();
		initializeArrays();
		initializeChart(sentence, false);

		doInsideScores();
		/*
		 * for (int i = 0; i < numStates; i++) { // if (iScore[15][16][i] !=
		 * null){ if (iScore[12][13][i] > -30) {// !=
		 * Double.NEGATIVE_INFINITY){// System.out.println(i + " " + (String)
		 * tagNumberer.object(i) + " " + iScore[12][13][i]); } }
		 */
		// for (int i =0; i<numStates; i++){
		// if (iScore[0][1][i] != Double.NEGATIVE_INFINITY){
		// System.out.println(i + " " + (String) tagNumberer.object(i) + "
		// "+iScore[0][1][i]);}
		// }

		// oScore[0][length][tagNumberer.number("ROOT")] = 0.0f;
		// doOutsideScores();

		Tree<String> bestTree = new Tree<String>("ROOT");
		double score = iScore[0][length][tagNumberer.number("ROOT")];
		if (score > Double.NEGATIVE_INFINITY) {
			System.out.println("\nFound a parse for sentence with length "
					+ length + ". The LL is " + score + ".");
			bestTree = extractBestParse(tagNumberer.number("ROOT"), 0, length,
					sentence);
			restoreUnaries(bestTree);
		} else {
			System.out.println("Did NOT find a parse for sentence with length "
					+ length + ".");
		}

		return bestTree;
	}

	public boolean hasParse() {
		if (length > arraySize) {
			return false;
		}
		return (iScore[0][length][tagNumberer.number("ROOT")] > Double.NEGATIVE_INFINITY);
	}

	void initializeArrays() {
		if (length > arraySize) {
			if (length > myMaxLength) {
				throw new OutOfMemoryError(
						"Refusal to create such large arrays.");
			} else {
				try {
					createArrays(length + 1);
				} catch (OutOfMemoryError e) {
					myMaxLength = length;
					if (arraySize > 0) {
						try {
							createArrays(arraySize);
						} catch (OutOfMemoryError e2) {
							throw new RuntimeException(
									"CANNOT EVEN CREATE ARRAYS OF ORIGINAL SIZE!!!");
						}
					}
					throw e;
				}
			}
			arraySize = length + 1;
		}
		for (int start = 0; start < length; start++) {
			for (int end = start + 1; end <= length; end++) {
				Arrays.fill(iScore[start][end], Double.NEGATIVE_INFINITY);
				Arrays.fill(oScore[start][end], Double.NEGATIVE_INFINITY);
			}
		}
		for (int loc = 0; loc <= length; loc++) {
			Arrays.fill(narrowLExtent[loc], -1); // the rightmost left with
													// state s
													// ending at i that we can
													// get is
													// the beginning
			Arrays.fill(wideLExtent[loc], length + 1); // the leftmost left with
														// state s ending at i
														// that we
														// can get is the end
			Arrays.fill(narrowRExtent[loc], length + 1); // the leftmost right
															// with
															// state s starting
															// at i
															// that we can get
															// is the
															// end
			Arrays.fill(wideRExtent[loc], -1); // the rightmost right with state
												// s
												// starting at i that we can get
												// is
												// the beginning
		}

	}

	void initializeChart(List<String> sentence, boolean noSmoothing) {
		// for simplicity the lexicon will store words and tags as strings,
		// while the grammar will be using integers -> Numberer()
		int start = 0;
		int end = start + 1;
		for (String word : sentence) {
			end = start + 1;
			// for (short tag : lexicon.getAllTags()) {
			for (short tag = 0; tag < numStates; tag++) {
				if (grammar.isGrammarTag[tag])
					continue;
				double prob = lexicon.score(word, tag, start, noSmoothing,
						false)[0];
				iScore[start][end][tag] = prob;
				narrowRExtent[start][tag] = end;
				narrowLExtent[end][tag] = start;
				wideRExtent[start][tag] = end;
				wideLExtent[end][tag] = start;
				/*
				 * UnaryRule[] unaries =
				 * grammar.getClosedUnaryRulesByChild(state); for (int r = 0; r
				 * < unaries.length; r++) { UnaryRule ur = unaries[r]; int
				 * parentState = ur.parent; double pS = (double) ur.score;
				 * double tot = prob + pS; if (tot >
				 * iScore[start][end][parentState]) {
				 * iScore[start][end][parentState] = tot;
				 * narrowRExtent[start][parentState] = end;
				 * narrowLExtent[end][parentState] = start;
				 * wideRExtent[start][parentState] = end;
				 * wideLExtent[end][parentState] = start; } }
				 */
			}
			// scaleIScores(start,end,0);
			start++;
		}
	}

	/**
	 * Fills in the iScore array of each category over each span of length 2 or
	 * more.
	 * 
	 * Note: This places the grammar and lexicon into logarithm mode!
	 */

	void doInsideScores() {
		grammar.logarithmMode();
		lexicon.logarithmMode();
		// for all symbol lengths
		for (int diff = 1; diff <= length; diff++) {
			// for all symbol starting positions
			for (int start = 0; start < (length - diff + 1); start++) {
				int end = start + diff;
				// for all symbols, calculate the inside score without unaries
				for (int pparentState = 0; pparentState < numStates; pparentState++) {
					BinaryRule[] parentRules = grammar
							.splitRulesWithP(pparentState);
					// for all rules with this parent symbol
					for (int i = 0; i < parentRules.length; i++) {
						BinaryRule r = parentRules[i];
						int leftState = r.leftChildState;
						int parentState = r.parentState;

						int narrowR = narrowRExtent[start][leftState];
						boolean iPossibleL = (narrowR < end); // can this left
																// constituent
						// leave space for a right
						// constituent?
						if (!iPossibleL) {
							continue;
						}

						int narrowL = narrowLExtent[end][r.rightChildState];
						boolean iPossibleR = (narrowL >= narrowR); // can this
																	// right
						// constituent fit next
						// to the left
						// constituent?
						if (!iPossibleR) {
							continue;
						}

						int min1 = narrowR;
						int min2 = wideLExtent[end][r.rightChildState];
						int min = (min1 > min2 ? min1 : min2); // can this right
						// constituent stretch far
						// enough to reach the left
						// constituent?
						if (min > narrowL) {
							continue;
						}

						int max1 = wideRExtent[start][leftState];
						int max2 = narrowL;
						int max = (max1 < max2 ? max1 : max2); // can this left
																// constituent
						// stretch far enough to
						// reach the right
						// constituent?
						if (min > max) {
							continue;
						}

						double pS = r.getScore(0, 0, 0);
						double oldIScore = iScore[start][end][parentState];
						double bestIScore = oldIScore;
						boolean foundBetter; // always set below for this rule

						for (int split = min; split <= max; split++) {
							double lS = iScore[start][split][leftState];
							if (Double.isInfinite(lS)) {
								continue;
							}
							double rS = iScore[split][end][r.rightChildState];
							if (Double.isInfinite(rS)) {
								continue;
							}
							touchedRules++;
							double tot = pS + lS + rS;

							if (tot > bestIScore) {
								bestIScore = tot;
							}
						}
						foundBetter = bestIScore > oldIScore;
						if (foundBetter) { // this way of making "parentState"
											// is better
							// than previous
							iScore[start][end][parentState] = bestIScore;
							if (Double.isInfinite(oldIScore)) {
								if (start > narrowLExtent[end][parentState]) {
									narrowLExtent[end][parentState] = start;
									wideLExtent[end][parentState] = start;
								} else {
									if (start < wideLExtent[end][parentState]) {
										wideLExtent[end][parentState] = start;
									}
								}
								if (end < narrowRExtent[start][parentState]) {
									narrowRExtent[start][parentState] = end;
									wideRExtent[start][parentState] = end;
								} else {
									if (end > wideRExtent[start][parentState]) {
										wideRExtent[start][parentState] = end;
									}
								}
							}
						}
					}
				}
				// for all symbols, close all unary productions
				for (int pState = 0; pState < numStates; pState++) {
					UnaryRule[] unaries = grammar
							.getClosedViterbiUnaryRulesByParent(pState);
					double cur = iScore[start][end][pState];
					double best = cur;
					for (int r = 0; r < unaries.length; r++) {
						UnaryRule ur = unaries[r];
						int cState = ur.childState;
						if (pState == cState)
							continue;

						double pS = ur.getScore(0, 0);
						double iS = iScore[start][end][cState];
						if (Double.isInfinite(iS)) {
							continue;
						}

						double tot = iS + pS;
						touchedRules++;
						if (tot > best) {
							best = tot;
						}
					}
					if (best > cur) {
						iScore[start][end][pState] = best;
						if (cur == Double.NEGATIVE_INFINITY) {
							if (start > narrowLExtent[end][pState]) {
								narrowLExtent[end][pState] = start;
								wideLExtent[end][pState] = start;
							} else {
								if (start < wideLExtent[end][pState]) {
									wideLExtent[end][pState] = start;
								}
							}
							if (end < narrowRExtent[start][pState]) {
								narrowRExtent[start][pState] = end;
								wideRExtent[start][pState] = end;
							} else {
								if (end > wideRExtent[start][pState]) {
									wideRExtent[start][pState] = end;
								}
							}
						}
					}
				}// ~ for all symbols
			}// ~for all symbol starting positions
		}// ~for all symbol lengths
	}

	/**
	 * Calculate outside scores using internal arrays.
	 * 
	 * Note: This places the grammar and lexicon into logarithm mode!
	 */
	private void doOutsideScores() {
		grammar.logarithmMode();
		lexicon.logarithmMode();
		// TODO: this almost certainly underflows!
		for (int diff = length; diff >= 1; diff--) {
			for (int start = 0; start + diff <= length; start++) {
				int end = start + diff;
				// do unaries
				for (int s = 0; s < numStates; s++) {
					double oS = oScore[start][end][s];
					if (Double.isInfinite(oS)) {
						continue;
					}
					UnaryRule[] rules = grammar
							.getClosedViterbiUnaryRulesByParent(s);
					for (int r = 0; r < rules.length; r++) {
						UnaryRule ur = rules[r];
						double pS = ur.getScore(0, 0);
						double tot = oS + pS;
						touchedRules++;
						if (tot > oScore[start][end][ur.childState]
								&& iScore[start][end][ur.childState] > Double.NEGATIVE_INFINITY) {
							oScore[start][end][ur.childState] = tot;
						}
					}
				}
				// do binaries
				for (int s = 0; s < numStates; s++) {
					BinaryRule[] rules = grammar.splitRulesWithP(s);
					for (int r = 0; r < rules.length; r++) {
						BinaryRule br = rules[r];
						double oS = oScore[start][end][br.parentState];
						if (Double.isInfinite(oS)) {
							continue;
						}
						int min1 = narrowRExtent[start][br.leftChildState];
						if (end < min1) {
							continue;
						}
						int max1 = narrowLExtent[end][br.rightChildState];
						if (max1 < min1) {
							continue;
						}
						int min = min1;
						int max = max1;
						if (max - min > 2) {
							int min2 = wideLExtent[end][br.rightChildState];
							min = (min1 > min2 ? min1 : min2);
							if (max1 < min) {
								continue;
							}
							int max2 = wideRExtent[start][br.leftChildState];
							max = (max1 < max2 ? max1 : max2);
							if (max < min) {
								continue;
							}
						}
						double pS = br.getScore(0, 0, 0);
						for (int split = min; split <= max; split++) {
							double lS = iScore[start][split][br.leftChildState];
							if (Double.isInfinite(lS)) {
								continue;
							}
							double rS = iScore[split][end][br.rightChildState];
							if (Double.isInfinite(rS)) {
								continue;
							}
							double totL = pS + rS + oS;
							touchedRules++;
							if (totL > oScore[start][split][br.leftChildState]) {
								oScore[start][split][br.leftChildState] = totL;
							}
							double totR = pS + lS + oS;
							if (totR > oScore[split][end][br.rightChildState]) {
								oScore[split][end][br.rightChildState] = totR;
							}
						}
					}
				}
				/*
				 * for (int s = 0; s < numStates; s++) { int max1 =
				 * narrowLExtent[end][s]; if (max1 < start) { continue; }
				 * BinaryRule[] rules = grammar.splitRulesWithRC(s); for (int r
				 * = 0; r < rules.length; r++) { BinaryRule br = rules[r];
				 * double oS = oScore[start][end][br.parentState]; if
				 * (Double.isInfinite(oS)) { continue; } int min1 =
				 * narrowRExtent[start][br.leftChildState]; if (max1 < min1) {
				 * continue; } int min = min1; int max = max1; if (max - min >
				 * 2) { int min2 = wideLExtent[end][br.rightChildState]; min =
				 * (min1 > min2 ? min1 : min2); if (max1 < min) { continue; }
				 * int max2 = wideRExtent[start][br.leftChildState]; max = (max1
				 * < max2 ? max1 : max2); if (max < min) { continue; } } double
				 * pS = br.getScore(0, 0, 0); for (int split = min; split <=
				 * max; split++) { double lS =
				 * iScore[start][split][br.leftChildState]; if
				 * (Double.isInfinite(lS)) { continue; } double rS =
				 * iScore[split][end][br.rightChildState]; if
				 * (Double.isInfinite(rS)) { continue; } double totL = pS + rS +
				 * oS; if (totL > oScore[start][split][br.leftChildState]) {
				 * oScore[start][split][br.leftChildState] = totL; } double totR
				 * = pS + lS + oS; if (totR >
				 * oScore[split][end][br.rightChildState]) {
				 * oScore[split][end][br.rightChildState] = totR; } } } }
				 */
			}
		}
	}

	/**
	 * Calculate the inside scores, P(words_i,j|nonterminal_i,j) of a tree given
	 * the string if words it should parse to.
	 * 
	 * @param tree
	 * @param sentence
	 */
	void doInsideScores(Tree<StateSet> tree, boolean noSmoothing,
			boolean debugOutput, double[][][] spanScores) {
		if (grammar.isLogarithmMode() || lexicon.isLogarithmMode())
			throw new Error(
					"Grammar in logarithm mode!  Cannot do inside scores!");
		if (tree.isLeaf()) {
			return;
		}
		List<Tree<StateSet>> children = tree.getChildren();
		for (Tree<StateSet> child : children) {
			if (!child.isLeaf())
				doInsideScores(child, noSmoothing, debugOutput, spanScores);
		}
		StateSet parent = tree.getLabel();
		short pState = parent.getState();
		int nParentStates = parent.numSubStates();
		if (tree.isPreTerminal()) {
			// Plays a role similar to initializeChart()
			StateSet wordStateSet = tree.getChildren().get(0).getLabel();
			double[] lexiconScores = lexicon.score(wordStateSet, pState,
					noSmoothing, false);
			if (lexiconScores.length != nParentStates) {
				System.out.println("Have more scores than substates!"
						+ lexiconScores.length + " " + nParentStates);// truncate
																		// the
																		// array
			}
			parent.setIScores(lexiconScores);
			parent.scaleIScores(0);
		} else {
			switch (children.size()) {
			case 0:
				break;
			case 1:
				StateSet child = children.get(0).getLabel();
				short cState = child.getState();
				int nChildStates = child.numSubStates();
				double[][] uscores = grammar.getUnaryScore(pState, cState);
				double[] iScores = new double[nParentStates];
				boolean foundOne = false;
				for (int j = 0; j < nChildStates; j++) {
					if (uscores[j] != null) { // check whether one of the
												// parents can produce this
												// child
						double cS = child.getIScore(j);
						if (cS == 0)
							continue;
						for (int i = 0; i < nParentStates; i++) {
							double rS = uscores[j][i]; // rule score
							if (rS == 0)
								continue;
							double res = rS * cS;
							/*
							 * if (res == 0) {
							 * System.out.println("Prevented an underflow: rS "
							 * +rS+" cS "+cS); res = Double.MIN_VALUE; }
							 */
							iScores[i] += res;
							foundOne = true;
						}
					}
				}
				if (debugOutput && !foundOne) {
					System.out.println("iscore reached zero!");
					System.out.println(grammar.getUnaryRule(pState, cState));
					System.out.println(Arrays.toString(iScores));
					System.out.println(ArrayUtil.toString(uscores));
					System.out.println(Arrays.toString(child.getIScores()));
				}
				parent.setIScores(iScores);
				parent.scaleIScores(child.getIScale());
				break;
			case 2:
				StateSet leftChild = children.get(0).getLabel();
				StateSet rightChild = children.get(1).getLabel();
				int nLeftChildStates = leftChild.numSubStates();
				int nRightChildStates = rightChild.numSubStates();
				short lState = leftChild.getState();
				short rState = rightChild.getState();
				double[][][] bscores = grammar.getBinaryScore(pState, lState,
						rState);
				double[] iScores2 = new double[nParentStates];
				boolean foundOne2 = false;
				for (int j = 0; j < nLeftChildStates; j++) {
					double lcS = leftChild.getIScore(j);
					if (lcS == 0)
						continue;
					for (int k = 0; k < nRightChildStates; k++) {
						double rcS = rightChild.getIScore(k);
						if (rcS == 0)
							continue;
						if (bscores[j][k] != null) { // check whether one of the
														// parents can produce
														// these kids
							for (int i = 0; i < nParentStates; i++) {
								double rS = bscores[j][k][i];
								if (rS == 0)
									continue;
								double res = rS * lcS * rcS;
								/*
								 * if (res == 0) {
								 * System.out.println("Prevented an underflow: rS "
								 * +rS+" lcS "+lcS+" rcS "+rcS); res =
								 * Double.MIN_VALUE; }
								 */
								iScores2[i] += res;
								foundOne2 = true;
							}
						}
					}
				}
				if (spanScores != null) {
					for (int i = 0; i < nParentStates; i++) {
						iScores2[i] *= spanScores[parent.from][parent.to][stateClass[pState]];
					}
				}

				// if (!foundOne2)
				// System.out.println("Did not find a way to build binary transition from "+pState+" to "+lState+" and "+rState+" "+ArrayUtil.toString(bscores));
				if (debugOutput && !foundOne2) {
					System.out.println("iscore reached zero!");
					System.out.println(grammar.getBinaryRule(pState, lState,
							rState));
					System.out.println(Arrays.toString(iScores2));
					System.out.println(Arrays.toString(bscores));
					System.out.println(Arrays.toString(leftChild.getIScores()));
					System.out
							.println(Arrays.toString(rightChild.getIScores()));
				}
				parent.setIScores(iScores2);
				parent.scaleIScores(leftChild.getIScale()
						+ rightChild.getIScale());
				break;
			default:
				throw new Error("Malformed tree: more than two children");
			}
		}
	}

	/**
	 * Set the outside score of the root node to P=1.
	 * 
	 * @param tree
	 */
	void setRootOutsideScore(Tree<StateSet> tree) {
		tree.getLabel().setOScore(0, 1);
		tree.getLabel().setOScale(0);
	}

	/**
	 * Calculate the outside scores of a tree; that is,
	 * P(nonterminal_i,j|words_0,i; words_j,end). It is calculate from the
	 * inside scores of the tree.
	 * 
	 * <p>
	 * Note: when calling this, call setRootOutsideScore() first.
	 * 
	 * @param tree
	 */
	void doOutsideScores(Tree<StateSet> tree, boolean unaryAbove,
			double[][][] spanScores) {
		if (grammar.isLogarithmMode() || lexicon.isLogarithmMode())
			throw new Error(
					"Grammar in logarithm mode!  Cannot do inside scores!");
		if (tree.isLeaf())
			return;
		List<Tree<StateSet>> children = tree.getChildren();
		StateSet parent = tree.getLabel();
		short pState = parent.getState();
		int nParentStates = parent.numSubStates();
		// this sets the outside scores for the children
		if (tree.isPreTerminal()) {

		} else {
			double[] parentScores = parent.getOScores();
			if (spanScores != null && !unaryAbove) {
				for (int i = 0; i < nParentStates; i++) {
					parentScores[i] *= spanScores[parent.from][parent.to][stateClass[pState]];
				}
			}
			switch (children.size()) {
			case 0:
				// Nothing to do
				break;
			case 1:
				StateSet child = children.get(0).getLabel();
				short cState = child.getState();
				int nChildStates = child.numSubStates();
				// UnaryRule uR = new UnaryRule(pState,cState);
				double[][] uscores = grammar.getUnaryScore(pState, cState);
				double[] oScores = new double[nChildStates];
				for (int j = 0; j < nChildStates; j++) {
					if (uscores[j] != null) {
						double childScore = 0;
						for (int i = 0; i < nParentStates; i++) {
							double pS = parentScores[i];
							if (pS == 0)
								continue;
							double rS = uscores[j][i]; // rule score
							if (rS == 0)
								continue;
							childScore += pS * rS;
						}
						oScores[j] = childScore;
					}
				}
				child.setOScores(oScores);
				child.scaleOScores(parent.getOScale());
				unaryAbove = true;
				break;
			case 2:
				StateSet leftChild = children.get(0).getLabel();
				StateSet rightChild = children.get(1).getLabel();
				int nLeftChildStates = leftChild.numSubStates();
				int nRightChildStates = rightChild.numSubStates();
				short lState = leftChild.getState();
				short rState = rightChild.getState();
				// double[] leftScoresToAdd -> use childScores array instead =
				// new double[nRightChildStates * nParentStates];
				// double[][] rightScoresToAdd -> use binaryScores array instead
				// = new double[nRightChildStates][nLeftChildStates *
				// nParentStates];
				double[][][] bscores = grammar.getBinaryScore(pState, lState,
						rState);
				double[] lOScores = new double[nLeftChildStates];
				double[] rOScores = new double[nRightChildStates];
				for (int j = 0; j < nLeftChildStates; j++) {
					double lcS = leftChild.getIScore(j);
					double leftScore = 0;
					for (int k = 0; k < nRightChildStates; k++) {
						double rcS = rightChild.getIScore(k);
						if (bscores[j][k] != null) {
							for (int i = 0; i < nParentStates; i++) {
								double pS = parentScores[i];
								if (pS == 0)
									continue;
								double rS = bscores[j][k][i];
								if (rS == 0)
									continue;
								leftScore += pS * rS * rcS;
								rOScores[k] += pS * rS * lcS;
							}
						}
						lOScores[j] = leftScore;
					}
				}
				leftChild.setOScores(lOScores);
				leftChild.scaleOScores(parent.getOScale()
						+ rightChild.getIScale());
				rightChild.setOScores(rOScores);
				rightChild.scaleOScores(parent.getOScale()
						+ leftChild.getIScale());
				unaryAbove = false;
				break;
			default:
				throw new Error("Malformed tree: more than two children");
			}
			for (Tree<StateSet> child : children) {
				doOutsideScores(child, unaryAbove, spanScores);
			}
		}
	}

	public double doInsideOutsideScores(Tree<StateSet> tree,
			boolean noSmoothing, boolean debugOutput, double[][][] spanScores) {
		doInsideScores(tree, noSmoothing, debugOutput, spanScores);
		setRootOutsideScore(tree);
		doOutsideScores(tree, false, spanScores);
		double tree_score = tree.getLabel().getIScore(0);
		int tree_scale = tree.getLabel().getIScale();
		return Math.log(tree_score) + (ScalingTools.LOGSCALE * tree_scale);
	}

	public void doInsideOutsideScores(Tree<StateSet> tree, boolean noSmoothing,
			boolean debugOutput) {
		doInsideScores(tree, noSmoothing, debugOutput, null);
		setRootOutsideScore(tree);
		doOutsideScores(tree, false, null);
	}

	private void createArrays(int length) {

		// zero out some stuff first in case we recently ran out of memory and
		// are
		// reallocating
		clearArrays();

		// allocate just the parts of iScore and oScore used (end > start, etc.)
		// System.out.println("initializing iScore arrays with length " + length
		// + "
		// and numStates " + numStates);
		iScore = new double[length][length + 1][];
		for (int start = 0; start < length; start++) {
			for (int end = start + 1; end <= length; end++) {
				iScore[start][end] = new double[numStates];
			}
		}
		// System.out.println("finished initializing iScore arrays");
		// System.out.println("initializing oScore arrays with length " + length
		// + "
		// and numStates " + numStates);
		oScore = new double[length][length + 1][];
		for (int start = 0; start < length; start++) {
			for (int end = start + 1; end <= length; end++) {
				oScore[start][end] = new double[numStates];
			}
		}
		// System.out.println("finished initializing oScore arrays");

		// iPossibleByL = new boolean[length + 1][numStates];
		// iPossibleByR = new boolean[length + 1][numStates];
		narrowRExtent = new int[length + 1][numStates];
		wideRExtent = new int[length + 1][numStates];
		narrowLExtent = new int[length + 1][numStates];
		wideLExtent = new int[length + 1][numStates];
		/*
		 * (op.doDep) { oPossibleByL = new boolean[length + 1][numStates];
		 * oPossibleByR = new boolean[length + 1][numStates];
		 * 
		 * oFilteredStart = new boolean[length + 1][numStates]; oFilteredEnd =
		 * new boolean[length + 1][numStates]; } tags = new boolean[length +
		 * 1][numTags];
		 * 
		 * if (Test.lengthNormalization) { wordsInSpan = new int[length +
		 * 1][length + 1][]; for (int start = 0; start <= length; start++) { for
		 * (int end = start + 1; end <= length; end++) { wordsInSpan[start][end]
		 * = new int[numStates]; } } }
		 */// System.out.println("ExhaustivePCFGParser constructor finished.");
	}

	protected void clearArrays() {
		iScore = oScore = null;
		// iPossibleByL = iPossibleByR = oFilteredEnd = oFilteredStart =
		// oPossibleByL = oPossibleByR = tags = null;
		narrowRExtent = wideRExtent = narrowLExtent = wideLExtent = null;
	}

	// borrowed from the stanford parser
	/**
	 * Return all best parses (except no ties allowed on POS tags?). Note that
	 * the returned tree may be missing intermediate nodes in a unary chain
	 * because it parses with a unary-closed grammar.
	 */
	public Tree<String> extractBestParse(int goal, int start, int end,
			List<String> sentence) {
		grammar.logarithmMode();
		lexicon.logarithmMode();
		// find sources of inside score
		// no backtraces so we can speed up the parsing for its primary use
		double bestScore = iScore[start][end][goal];
		String goalStr = (String) tagNumberer.object(goal);
		// System.out.println("Looking for " + goalStr + " from " + start +
		// " to " + end + " with score " + bestScore + ".");
		if (end - start == 1) {
			// handle the (pre)terminal nodes differently
			// System.out.println("Tag node: "+goalStr);
			// check whether there is a rewrite that is actually better

			// if the lexicon contains the goal, then we're already at
			// the preterminal level, so we don't need to try to find any
			// unary rules to get to a preterminal tag
			if (!grammar.isGrammarTag[goal]) {
				// if (lexicon.getAllTags().contains(goal)) {
				List<Tree<String>> child = new ArrayList<Tree<String>>();
				child.add(new Tree<String>(sentence.get(start)));
				return new Tree<String>(goalStr, child);
			}
			// if the lexicon does not contain the goal, then we must find
			// the best way to get from the goal tag to a preterminal tag
			else {
				double veryBestScore = Double.NEGATIVE_INFINITY;
				int newIndex = -1;
				UnaryRule[] unaries = grammar
						.getClosedViterbiUnaryRulesByParent(goal);
				for (int r = 0; r < unaries.length; r++) {
					UnaryRule ur = unaries[r];
					double ruleScore = iScore[start][end][ur.childState]
							+ grammar.getUnaryScore(ur)[0][0];
					if ((ruleScore > veryBestScore) && (goal != ur.childState)
							&& (!grammar.isGrammarTag[ur.getChildState()])) {
						// if ((ruleScore > veryBestScore) && (goal !=
						// ur.childState)
						// && lexicon.getAllTags().contains(ur.getChildState()))
						// {
						veryBestScore = ruleScore;
						newIndex = ur.childState;
					}
				}

				// insert the nonterminal tag into the tree
				List<Tree<String>> child1 = new ArrayList<Tree<String>>();
				child1.add(new Tree<String>(sentence.get(start)));
				String goalStr1 = (String) tagNumberer.object(newIndex);

				List<Tree<String>> child = new ArrayList<Tree<String>>();
				child.add(new Tree<String>(goalStr1, child1));
				return new Tree<String>(goalStr, child);
			}
			/*
			 * IntTaggedWord tagging = new IntTaggedWord(words[start],
			 * tagNumberer.number(goalStr)); double tagScore =
			 * lex.score(tagging, start); if (tagScore >
			 * Double.NEGATIVE_INFINITY || floodTags) { // return a pre-terminal
			 * tree String wordStr = (String) wordNumberer.object(words[start]);
			 * Tree wordNode = tf.newLeaf(new StringLabel(wordStr)); List
			 * childList = new ArrayList(); childList.add(wordNode); Tree
			 * tagNode = tf.newTreeNode(new StringLabel(goalStr), childList);
			 * //System.out.println("Tag node: "+tagNode); return
			 * Collections.singletonList(tagNode); }
			 */
		}
		// check binaries first
		for (int split = start + 1; split < end; split++) {
			BinaryRule[] parentRules = grammar.splitRulesWithP(goal);
			for (int i = 0; i < parentRules.length; i++) {
				BinaryRule br = parentRules[i];
				double score = br.getScore(0, 0, 0)
						+ iScore[start][split][br.leftChildState]
						+ iScore[split][end][br.rightChildState];
				if (matches(score, bestScore)) {
					// build binary split
					Tree<String> leftChildTree = extractBestParse(
							br.leftChildState, start, split, sentence);
					Tree<String> rightChildTree = extractBestParse(
							br.rightChildState, split, end, sentence);
					List<Tree<String>> children = new ArrayList<Tree<String>>();
					children.add(leftChildTree);
					children.add(rightChildTree);
					Tree<String> result = new Tree<String>(goalStr, children);
					// System.out.println("Binary node: "+result);
					// result.setScore(score);
					return result;
				}
			}
		}
		// check unaries
		UnaryRule[] unaries = grammar.getClosedViterbiUnaryRulesByParent(goal);
		for (int r = 0; r < unaries.length; r++) {
			UnaryRule ur = unaries[r];
			double score = ur.getScore(0, 0)
					+ iScore[start][end][ur.childState];
			if (ur.childState != ur.parentState && matches(score, bestScore)) {
				// build unary
				Tree<String> childTree = extractBestParse(ur.childState, start,
						end, sentence);
				List<Tree<String>> children = new ArrayList<Tree<String>>();
				children.add(childTree);
				Tree<String> result = new Tree<String>(goalStr, children);
				// System.out.println("Unary node: "+result);
				// result.setScore(score);
				return result;
			}
		}
		System.err.println("Warning: no parse found");
		return null;
	}

	protected void restoreUnaries(Tree<String> t) {
		// System.out.println("In restoreUnaries...");
		for (Iterator nodeI = t.subTreeList().iterator(); nodeI.hasNext();) {
			Tree<String> node = (Tree<String>) nodeI.next();
			// System.out.println("Doing node: "+node.getLabel());
			if (node.isLeaf() || node.isPreTerminal()
					|| node.getChildren().size() != 1) {
				// System.out.println("Skipping node: "+node.getLabel());
				continue;
			}
			// System.out.println("Not skipping node: "+node.getLabel());
			Tree<String> parent = node;
			// Tree<String> child = node.getChildren().get(0);
			short pLabel = (short) tagNumberer.number(parent.getLabel());
			short cLabel = (short) tagNumberer.number(node.getChildren().get(0)
					.getLabel());
			// List path =
			// grammar.getBestPath(stateNumberer.number(parent.getLabel().value()),
			// stateNumberer.number(child.label().value().toString()));
			// if (grammar.getUnaryScore(new UnaryRule(pLabel,cLabel))[0][0] ==
			// 0){
			// continue; }// means the rule was already in grammar
			List<short[]> path = grammar.getBestViterbiPath(pLabel, (short) 0,
					cLabel, (short) 0);
			// System.out.println("Got path for "+pLabel + " to " + cLabel +
			// " via " +
			// path);
			for (int pos = 1; pos < path.size() - 1; pos++) {
				int tmp = path.get(pos)[0];
				int interState = tmp;
				Tree<String> intermediate = new Tree<String>(
						(String) tagNumberer.object(interState),
						parent.getChildren());
				List<Tree<String>> children = new ArrayList<Tree<String>>();
				children.add(intermediate);
				parent.setChildren(children);
				parent = intermediate;
			}
		}
	}

	private static final double TOL = 1e-5;

	protected boolean matches(double x, double y) {
		return (Math.abs(x - y) / (Math.abs(x) + Math.abs(y) + 1e-10) < TOL);
	}

	/**
	 * @param stateSetTree
	 * @return
	 */
	public void doViterbiInsideScores(Tree<StateSet> tree) {
		if (tree.isLeaf()) {
			return;
		}
		List<Tree<StateSet>> children = tree.getChildren();
		for (Tree<StateSet> child : children) {
			if (tree.isLeaf())
				continue;
			doViterbiInsideScores(child);// newChildren.add(getBestViterbiDerivation(child));
		}
		StateSet parent = tree.getLabel();
		short pState = parent.getState();
		int nParentStates = grammar.numSubStates[pState];// parent.numSubStates();
		double[] iScores = new double[nParentStates];
		if (tree.isPreTerminal()) {
			// Plays a role similar to initializeChart()
			String word = tree.getChildren().get(0).getLabel().getWord();
			int pos = tree.getChildren().get(0).getLabel().from;
			iScores = lexicon.score(word, pState, pos, false, false);
			// parent.scaleIScores(0);
		} else {
			Arrays.fill(iScores, Double.NEGATIVE_INFINITY);
			switch (children.size()) {
			case 0:
				break;
			case 1:
				StateSet child = children.get(0).getLabel();
				short cState = child.getState();
				int nChildStates = child.numSubStates();
				double[][] uscores = grammar.getUnaryScore(pState, cState);
				for (int j = 0; j < nChildStates; j++) {
					if (uscores[j] != null) { // check whether one of the
												// parents can produce this
												// child
						double cS = child.getIScore(j);
						if (cS == Double.NEGATIVE_INFINITY)
							continue;
						for (int i = 0; i < nParentStates; i++) {
							double rS = uscores[j][i]; // rule score
							if (rS == Double.NEGATIVE_INFINITY)
								continue;
							double res = rS + cS;
							iScores[i] = Math.max(iScores[i], res);
						}
					}
				}
				// parent.scaleIScores(child.getIScale());
				break;
			case 2:
				StateSet leftChild = children.get(0).getLabel();
				StateSet rightChild = children.get(1).getLabel();
				int nLeftChildStates = grammar.numSubStates[leftChild
						.getState()];// leftChild.numSubStates();
				int nRightChildStates = grammar.numSubStates[rightChild
						.getState()];// rightChild.numSubStates();
				short lState = leftChild.getState();
				short rState = rightChild.getState();
				double[][][] bscores = grammar.getBinaryScore(pState, lState,
						rState);
				for (BinaryRule br : grammar.splitRulesWithP(pState)) {
					if (br.leftChildState != lState)
						continue;
					if (br.rightChildState != rState)
						continue;
					bscores = br.getScores2();
				}

				for (int j = 0; j < nLeftChildStates; j++) {
					double lcS = leftChild.getIScore(j);
					if (lcS == Double.NEGATIVE_INFINITY)
						continue;
					for (int k = 0; k < nRightChildStates; k++) {
						double rcS = rightChild.getIScore(k);
						if (rcS == Double.NEGATIVE_INFINITY)
							continue;
						if (bscores[j][k] != null) { // check whether one of the
														// parents can produce
														// these kids
							for (int i = 0; i < nParentStates; i++) {
								double rS = bscores[j][k][i];
								if (rS == Double.NEGATIVE_INFINITY)
									continue;
								double res = rS + lcS + rcS;
								iScores[i] = Math.max(iScores[i], res);
							}
						}
					}
				}
				// parent.scaleIScores(leftChild.getIScale()+rightChild.getIScale());
				break;
			default:
				throw new Error("Malformed tree: more than two children");
			}
		}
		parent.setIScores(iScores);
	}

	Tree<String> extractBestViterbiDerivation(Tree<StateSet> tree,
			int substate, boolean outputScore, boolean labelOnlyPOS) {
		if (tree.isLeaf())
			return new Tree<String>(tree.getLabel().getWord());
		if (substate == -1)
			substate = 0;
		if (tree.isPreTerminal()) {
			ArrayList<Tree<String>> child = new ArrayList<Tree<String>>();
			child.add(extractBestViterbiDerivation(tree.getChildren().get(0),
					-1, outputScore, labelOnlyPOS));
			String goalStr = tagNumberer.object(tree.getLabel().getState())
					+ "-" + substate;
			if (outputScore)
				goalStr = goalStr + " " + tree.getLabel().getIScore(substate);
			return new Tree<String>(goalStr, child);
		}

		StateSet node = tree.getLabel();
		short pState = node.getState();

		ArrayList<Tree<String>> newChildren = new ArrayList<Tree<String>>();
		List<Tree<StateSet>> children = tree.getChildren();

		double myScore = node.getIScore(substate);
		if (myScore == Double.NEGATIVE_INFINITY) {
			myScore = DoubleArrays.max(node.getIScores());
			substate = DoubleArrays.argMax(node.getIScores());
		}
		switch (children.size()) {
		case 1:
			StateSet child = children.get(0).getLabel();
			short cState = child.getState();
			int nChildStates = child.numSubStates();
			double[][] uscores = grammar.getUnaryScore(pState, cState);
			int childIndex = -1;
			for (int j = 0; j < nChildStates; j++) {
				if (childIndex != -1)
					break;
				if (uscores[j] != null) {
					double cS = child.getIScore(j);
					if (cS == Double.NEGATIVE_INFINITY)
						continue;
					double rS = uscores[j][substate]; // rule score
					if (rS == Double.NEGATIVE_INFINITY)
						continue;
					double res = rS + cS;
					if (matches(res, myScore))
						childIndex = j;
				}
			}
			newChildren.add(extractBestViterbiDerivation(children.get(0),
					childIndex, outputScore, labelOnlyPOS));
			break;
		case 2:
			StateSet leftChild = children.get(0).getLabel();
			StateSet rightChild = children.get(1).getLabel();
			int nLeftChildStates = leftChild.numSubStates();
			int nRightChildStates = rightChild.numSubStates();
			short lState = leftChild.getState();
			short rState = rightChild.getState();
			double[][][] bscores = grammar.getBinaryScore(pState, lState,
					rState);
			int lChildIndex = -1,
			rChildIndex = -1;
			for (int j = 0; j < nLeftChildStates; j++) {
				if (lChildIndex != -1 && rChildIndex != -1)
					break;
				double lcS = leftChild.getIScore(j);
				if (lcS == Double.NEGATIVE_INFINITY)
					continue;
				for (int k = 0; k < nRightChildStates; k++) {
					if (lChildIndex != -1 && rChildIndex != -1)
						break;
					double rcS = rightChild.getIScore(k);
					if (rcS == Double.NEGATIVE_INFINITY)
						continue;
					if (bscores[j][k] != null) { // check whether one of the
													// parents can produce these
													// kids
						double rS = bscores[j][k][substate];
						if (rS == Double.NEGATIVE_INFINITY)
							continue;
						double res = rS + lcS + rcS;
						if (matches(myScore, res)) {
							lChildIndex = j;
							rChildIndex = k;
						}
					}
				}
			}
			newChildren.add(extractBestViterbiDerivation(children.get(0),
					lChildIndex, outputScore, labelOnlyPOS));
			newChildren.add(extractBestViterbiDerivation(children.get(1),
					rChildIndex, outputScore, labelOnlyPOS));
			break;
		default:
			throw new Error("Malformed tree: more than two children");
		}
		String parentString = (String) tagNumberer.object(node.getState());
		if (parentString.endsWith("^g"))
			parentString = parentString.substring(0, parentString.length() - 2);
		if (!labelOnlyPOS)
			parentString = parentString + "-" + substate;
		if (outputScore)
			parentString = parentString + " " + myScore;

		return new Tree<String>(parentString, newChildren);
	}

	public Tree<String> getBestViterbiDerivation(Tree<StateSet> tree,
			boolean outputScore, boolean labelOnlyPOS) {
		doViterbiInsideScores(tree);
		if (tree.getLabel().getIScore(0) == Double.NEGATIVE_INFINITY) {
			// System.out.println("Tree is unparsable!");
			return null;
		}
		return extractBestViterbiDerivation(tree, 0, outputScore, labelOnlyPOS);
	}

	public void incrementExpectedGoldCounts(Linearizer linearizer,
			double[] probs, Tree<StateSet> tree) {
		double tree_score = tree.getLabel().getIScore(0);
		int tree_scale = tree.getLabel().getIScale();
		incrementExpectedGoldCounts(linearizer, probs, tree, tree_score,
				tree_scale);
	}

	public void incrementExpectedGoldCounts(Linearizer linearizer,
			double[] probs, Tree<StateSet> tree, double tree_score,
			int tree_scale) {

		if (tree.isLeaf())
			return;
		if (tree.isPreTerminal()) {
			StateSet parent = tree.getLabel();
			StateSet child = tree.getChildren().get(0).getLabel();

			// String word = child.getWord();
			short tag = tree.getLabel().getState();

			final int nSubStates = grammar.numSubStates[tag];
			double scalingFactor = ScalingTools.calcScaleFactor(parent
					.getOScale() + parent.getIScale() - tree_scale);

			// if (!combinedLexicon){
			for (short substate = 0; substate < nSubStates; substate++) {
				// weight by the probability of seeing the tag and word
				// together, given the sentence
				double pIS = parent.getIScore(substate); // Parent outside score
				if (pIS == 0) {
					continue;
				}
				double pOS = parent.getOScore(substate); // Parent outside score
				if (pOS == 0) {
					continue;
				}
				double weight = 1;
				weight = (pIS / tree_score) * scalingFactor * pOS;
				if (weight > 1.01) {
					System.out
							.println("Overflow when counting tags? " + weight);
					weight = 0;
				}
				tmpCountsArray[substate] = weight;
			}
			linearizer.increment(probs, child, tag, tmpCountsArray, true); // probs[startIndexWord+substate]
																			// +=
																			// weight;
			// linearizer.increment(probs, child.sigIndex, tag, tmpCountsArray);
			// //probs[startIndexWord+substate] += weight;
			// } else {
			// // int pos = child.from;
			// double[] wordScores = lexicon.scoreWord(child, tag);
			// for (short substate=0; substate<nSubStates; substate++) {
			// //weight by the probability of seeing the tag and word together,
			// given the sentence
			// double pIS = wordScores[substate]; // Parent outside score
			// if (pIS==0) { continue; }
			// double pOS = parent.getOScore(substate); // Parent outside score
			// if (pOS==0) { continue; }
			// double weight = 1;
			// weight = hardCounts ? 1 : (pIS / tree_score) * scalingFactor *
			// pOS;
			// tmpCountsArray[substate] = weight;
			// }
			// linearizer.increment(probs, child.wordIndex, tag,
			// tmpCountsArray); //probs[startIndexWord+substate] += weight;
			//
			// // String sig = lexicon.getSignature(word, pos);
			// double[] sigScores = lexicon.scoreSignature(child, tag);
			// if (sigScores==null)
			// return;
			// for (short substate=0; substate<nSubStates; substate++) {
			// //weight by the probability of seeing the tag and word together,
			// given the sentence
			// double pIS = sigScores[substate]; // Parent outside score
			// if (pIS==0) { continue; }
			// double pOS = parent.getOScore(substate); // Parent outside score
			// if (pOS==0) { continue; }
			// double weight = 1;
			// weight = hardCounts ? 1 : (pIS / tree_score) * scalingFactor *
			// pOS;
			// tmpCountsArray[substate] = weight;
			// }
			// linearizer.increment(probs, child.sigIndex, tag, tmpCountsArray);
			// //probs[startIndexWord+substate] += weight;
			// }
			return;
		}
		List<Tree<StateSet>> children = tree.getChildren();
		StateSet parent = tree.getLabel();
		short parentState = parent.getState();
		int nParentSubStates = grammar.numSubStates[parentState];
		// if (oScore[pStart][pEnd][parentState]==null) break;
		switch (children.size()) {
		case 0:
			// This is a leaf (a preterminal node, if we count the words
			// themselves),
			// nothing to do
			break;
		case 1:
			// first check whether this is a unary chain!
			/*
			 * if (!children.get(0).isPreTerminal() &&
			 * children.get(0).getChildren().size()==1){ // if so, skip the
			 * intermediate node children = children.get(0).getChildren(); }
			 */
			StateSet child = children.get(0).getLabel();
			short childState = child.getState();
			// int thisStartIndex = linearizer.getLinearIndex(new
			// UnaryRule(parentState,
			// childState));//startIndexGrammar[parentState][childState][0];
			int curInd = 0;
			int nChildSubStates = grammar.numSubStates[childState];
			UnaryRule urule = grammar.getUnaryRule(parentState, childState);
			double[][] oldUScores = urule.getScores2();
			double scalingFactor = ScalingTools.calcScaleFactor(parent
					.getOScale() + child.getIScale() - tree_scale);
			// if (scalingFactor==0){
			// System.out.println("p: "+parent.getOScale()+" c: "+child.getIScale()+" t:"+tree_scale);
			// }
			for (short i = 0; i < nChildSubStates; i++) {
				if (oldUScores[i] == null)
					continue;
				double cIS = child.getIScore(i);
				for (short j = 0; j < nParentSubStates; j++) {
					curInd++;
					if (cIS == 0) {
						continue;
					}
					double pOS = parent.getOScore(j); // Parent outside score
					if (pOS == 0) {
						continue;
					}
					double rS = oldUScores[i][j];
					if (rS == 0) {
						continue;
					}
					if (tree_score == 0)
						tree_score = 1;
					double ruleCount = (rS * cIS / tree_score) * scalingFactor
							* pOS;
					if (ruleCount > 1.01) {
						System.out.println("Overflow when counting binaries? "
								+ ruleCount);
						ruleCount = 0;
					}
					if (ruleCount != 0)
						tmpCountsArray[curInd - 1] = ruleCount;
				}
				if (parentState == 0)
					curInd += (nChildSubStates - 1);
			}
			linearizer.increment(probs, urule, tmpCountsArray, true); // probs[thisStartIndex
																		// +
																		// curInd-1]
																		// +=
																		// ruleCount;
			break;
		case 2:
			StateSet leftChild = children.get(0).getLabel();
			short lChildState = leftChild.getState();
			StateSet rightChild = children.get(1).getLabel();
			short rChildState = rightChild.getState();
			int nLeftChildSubStates = grammar.numSubStates[lChildState];
			int nRightChildSubStates = grammar.numSubStates[rChildState];
			// thisStartIndex = linearizer.getLinearIndex(new
			// BinaryRule(parentState, lChildState,
			// rChildState));//startIndexGrammar[parentState][lChildState][rChildState];
			curInd = 0;
			// new double[nLeftChildSubStates][nRightChildSubStates][];
			BinaryRule brule = grammar.getBinaryRule(parentState, lChildState,
					rChildState);
			double[][][] oldBScores = brule.getScores2();

			scalingFactor = ScalingTools.calcScaleFactor(parent.getOScale()
					+ leftChild.getIScale() + rightChild.getIScale()
					- tree_scale);
			// if (scalingFactor==0){
			// System.out.println("p: "+parent.getOScale()+" l: "+leftChild.getIScale()+" r:"+rightChild.getIScale()+" t:"+tree_scale);
			// }
			int nRuleStates = oldBScores[0][0].length;
			int divisor = nParentSubStates / nRuleStates;
			if (divisor == 0)
				System.out.println("not possible");
			for (short i = 0; i < nLeftChildSubStates; i++) {
				double lcIS = leftChild.getIScore(i);
				for (short j = 0; j < nRightChildSubStates; j++) {
					// if (oldBScores[i][j]==null) continue;
					if (nRuleStates == nParentSubStates) {
						for (short k = 0; k < nParentSubStates; k++) {
							curInd++;
							if (lcIS == 0) {
								continue;
							}
							double rcIS = rightChild.getIScore(j);
							if (rcIS == 0) {
								continue;
							}
							double pOS = parent.getOScore(k); // Parent outside
																// score
							if (pOS == 0) {
								continue;
							}
							double rS = oldBScores[i][j][k];
							if (rS == 0) {
								continue;
							}
							if (tree_score == 0)
								tree_score = 1;
							double ruleCount = (rS * lcIS / tree_score) * rcIS
									* scalingFactor * pOS;
							if (ruleCount > 1.01) {
								System.out
										.println("Overflow when counting unaries? "
												+ ruleCount);
								ruleCount = 0;
							}
							if (ruleCount > 0)
								tmpCountsArray[curInd - 1] = ruleCount;// probs[thisStartIndex
																		// +
																		// curInd-1]
																		// +=
																		// ruleCount;
						}
					} else {
						for (short k = 0; k < nParentSubStates; k++) {
							curInd++;
							if (lcIS == 0) {
								continue;
							}
							double rcIS = rightChild.getIScore(j);
							if (rcIS == 0) {
								continue;
							}
							double pOS = parent.getOScore(k); // Parent outside
																// score
							if (pOS == 0) {
								continue;
							}
							double rS = oldBScores[i / divisor][j / divisor][k
									/ divisor];
							if (rS == 0) {
								continue;
							}
							if (tree_score == 0)
								tree_score = 1;
							double ruleCount = (rS * lcIS / tree_score) * rcIS
									* scalingFactor * pOS;
							if (ruleCount > 1.01) {
								System.out
										.println("Overflow when counting unaries? "
												+ ruleCount);
								ruleCount = 0;
							}
							if (ruleCount > 0)
								tmpCountsArray[curInd - 1] = ruleCount;// probs[thisStartIndex
																		// +
																		// curInd-1]
																		// +=
																		// ruleCount;
						}

					}
				}
			}
			linearizer.increment(probs, brule, tmpCountsArray, true); // probs[thisStartIndex
																		// +
																		// curInd-1]
																		// +=
																		// ruleCount;

			break;
		default:
			throw new Error("Malformed tree: more than two children");
		}

		for (Tree<StateSet> child : children) {
			incrementExpectedGoldCounts(linearizer, probs, child, tree_score,
					tree_scale);
		}
	}

	public void countPosteriors(double[][] cumulativePosteriors,
			Tree<StateSet> tree, double tree_score, int tree_scale) {

		if (tree.isLeaf())
			return;

		StateSet node = tree.getLabel();
		short state = node.getState();

		final int nSubStates = grammar.numSubStates[state];
		double scalingFactor = ScalingTools.calcScaleFactor(node.getOScale()
				+ node.getIScale() - tree_scale);

		for (short substate = 0; substate < nSubStates; substate++) {
			double pIS = node.getIScore(substate); // Parent outside score
			if (pIS == 0) {
				continue;
			}
			double pOS = node.getOScore(substate); // Parent outside score
			if (pOS == 0) {
				continue;
			}
			double weight = 1;
			weight = (pIS / tree_score) * scalingFactor * pOS;
			if (weight > 1.01) {
				System.out.println("Overflow when counting tags? " + weight);
				weight = 0;
			}
			cumulativePosteriors[state][substate] += weight;
		}

		for (Tree<StateSet> child : tree.getChildren()) {
			countPosteriors(cumulativePosteriors, child, tree_score, tree_scale);
		}
	}

}
