private static Node readNode(TrieReader reader, int depth, int maxDepth) throws IOException {
if (depth > maxDepth) {
skipNode(reader);
return null;
}
long count = reader.readCount();
int depthPlus1 = depth + 1;
long sym1 = reader.readSymbol();
// 0+ daughters
if (sym1 == -1L) return NodeFactory.createNode(count);
// 1+ daughters
Node node1 = readNode(reader, depthPlus1, maxDepth);
long sym2 = reader.readSymbol();
if (sym2 == -1L) return NodeFactory.createNodeFold((char) sym1, node1, count);
Node node2 = readNode(reader, depthPlus1, maxDepth);
long sym3 = reader.readSymbol();
if (sym3 == -1L) return NodeFactory.createNode((char) sym1, node1, (char) sym2, node2, count);
Node node3 = readNode(reader, depthPlus1, maxDepth);
long sym4 = reader.readSymbol();
if (sym4 == -1L)
return NodeFactory.createNode(
(char) sym1, node1, (char) sym2, node2, (char) sym3, node3, count);
Node node4 = readNode(reader, depthPlus1, maxDepth);
// 4+ daughters
StringBuilder cBuf = new StringBuilder();
cBuf.append((char) sym1);
cBuf.append((char) sym2);
cBuf.append((char) sym3);
cBuf.append((char) sym4);
List<Node> nodeList = new ArrayList<Node>();
nodeList.add(node1);
nodeList.add(node2);
nodeList.add(node3);
nodeList.add(node4);
long sym;
while ((sym = reader.readSymbol()) != -1L) {
cBuf.append((char) sym);
nodeList.add(readNode(reader, depthPlus1, maxDepth));
}
Node[] nodes = nodeList.toArray(EMPTY_NODE_ARRAY);
char[] cs = Strings.toCharArray(cBuf);
return NodeFactory.createNode(cs, nodes, count); // > 3 daughters
}
/**
* Removes strings with counts below the specified minimum. Counts for remaining strings are not
* affected. Pruning may be interleaved with updating counts in any order.
*
* @param minCount Minimum count required to retain a substring count.
* @throws IllegalArgumentException If the count is less than <code>1</code>.
*/
public void prune(int minCount) {
if (minCount < 1) {
String msg = "Prune minimum count must be more than 1." + " Found minCount=" + minCount;
throw new IllegalArgumentException(msg);
}
mRootNode = mRootNode.prune(minCount);
if (mRootNode == null) mRootNode = NodeFactory.createNode(0);
}
static <E extends ValueNode> E createNode(NodeFactory<E> factory, Object... constants) {
ArgumentNode[] argumentNodes = arguments(factory.getExecutionSignature().size());
List<Object> argumentList = new ArrayList<>();
argumentList.addAll(Arrays.asList(constants));
if (ChildrenNode.class.isAssignableFrom(factory.getNodeClass())
|| BuiltinNode.class.isAssignableFrom(factory.getNodeClass())) {
argumentList.add(argumentNodes);
} else {
argumentList.addAll(Arrays.asList(argumentNodes));
}
return factory.createNode(argumentList.toArray(new Object[argumentList.size()]));
}
private Node instantiateNodeForRecipe(
RecipeTraceInfo recipeTrace,
final ReteNodeRecipe recipe,
Collection<ReteNodeRecipe> sameClassRecipes) {
if (recipe instanceof IndexerRecipe) {
// INSTANTIATE AND HOOK UP
// (cannot delay hooking up, because parent determines indexer implementation)
ensureParents(recipeTrace);
final ReteNodeRecipe parentRecipe =
recipeTrace.getParentRecipeTraces().iterator().next().getRecipe();
final Indexer result =
nodeFactory.createIndexer(
reteContainer,
(IndexerRecipe) recipe,
asSupplier(
(Address<? extends Supplier>)
reteContainer.network.getExistingNodeByRecipe(parentRecipe)),
recipeTrace);
// REMEMBER
if (Options.nodeSharingOption != Options.NodeSharingOption.NEVER) {
getNodesByRecipe().put(recipe, reteContainer.makeAddress(result));
sameClassRecipes.add(recipe);
}
return result;
} else {
// INSTANTIATE
Node result = nodeFactory.createNode(reteContainer, recipe, recipeTrace);
// REMEMBER
if (Options.nodeSharingOption == Options.NodeSharingOption.ALL) {
getNodesByRecipe().put(recipe, reteContainer.makeAddress(result));
sameClassRecipes.add(recipe);
}
// HOOK UP
// (recursion-tolerant due to this delayed order of initialization)
ensureParents(recipeTrace);
if (recipe instanceof InputRecipe) inputConnector.connectInput((InputRecipe) recipe, result);
else connectionFactory.connectToParents(recipeTrace, result);
return result;
}
}
/**
* A <code>TrieCharSeqCounter</code> stores counts for substrings of strings. When the counter is
* constructed, a maximum length is specified, and counts are only stored for strings up to that
* length. For instance, an n-gram language model needs only counts for strings up to length n.
*
* <p>Strings may be added to the counter using {@link #incrementSubstrings(char[],int,int)}, which
* increments the counts for all substrings of the specified character slice up to the specified
* maximum length substring. The method {@link #incrementPrefixes(char[],int,int)} increments only
* the prefixes of the specified string. All substrings are incremented by incrementing prefixes for
* each suffix. A substring counter may be pruned using {@link #prune(int)}, which removes all
* substrings with count below the specified threshold.
*
* <p>There are a wide range of reporting methods for trie-based counters.
*
* <p><i>Implementation Note:</i> The trie counters are a heavily unfolded implementation of a
* character-based Patricia (PAT) trie.
*
* @author Bob Carpenter
* @version 3.8
* @since LingPipe2.0
*/
public class TrieCharSeqCounter implements CharSeqCounter {
Node mRootNode = NodeFactory.createNode(0);
final int mMaxLength;
/**
* Construct a substring counter that stores substrings up to the specified maximum length.
*
* @param maxLength Maximum length of substrings stored by this counter.
* @throws IllegalArgumentException If the maximum length is negative.
*/
public TrieCharSeqCounter(int maxLength) {
if (maxLength < 0) {
String msg = "Max length must be >= 0." + " Found length=" + maxLength;
throw new IllegalArgumentException(msg);
}
mMaxLength = maxLength;
}
// following is CharSeqCounter interface w. inherited comments
public long count(char[] cs, int start, int end) {
Strings.checkArgsStartEnd(cs, start, end);
return mRootNode.count(cs, start, end);
}
public long extensionCount(char[] cs, int start, int end) {
Strings.checkArgsStartEnd(cs, start, end);
return mRootNode.contextCount(cs, start, end);
}
public char[] observedCharacters() {
return com.aliasi.util.Arrays.copy(mRootNode.outcomes(new char[] {}, 0, 0));
}
public char[] charactersFollowing(char[] cs, int start, int end) {
Strings.checkArgsStartEnd(cs, start, end);
return com.aliasi.util.Arrays.copy(mRootNode.outcomes(cs, start, end));
}
public int numCharactersFollowing(char[] cs, int start, int end) {
Strings.checkArgsStartEnd(cs, start, end);
return mRootNode.numOutcomes(cs, start, end);
}
/**
* Returns the sum of counts for all non-empty character sequences.
*
* @return The sum of counts for all non-empty character sequences.
*/
public long totalSequenceCount() {
long sum = 0l;
long[][] uniqueTotals = uniqueTotalNGramCount();
for (int i = 0; i < uniqueTotals.length; ++i) sum += uniqueTotals[i][1];
return sum;
}
/**
* Returns the sum of the counts of all character sequences of the specified length.
*
* @return The sum of the counts of all character sequences of the specified length.
*/
public long totalSequenceCount(int length) {
return mRootNode.totalNGramCount(length);
}
/**
* Returns the number of character sequences with non-zero counts, including the empty (zero
* length) character sequence.
*
* @return Number of character sequences with non-zero counts.
*/
public long uniqueSequenceCount() {
return mRootNode.size();
}
/**
* Returns the number of character sequences of the specified length with non-zero counts.
*
* @return The number of character sequences of the specified length with non-zero counts.
*/
public long uniqueSequenceCount(int nGramOrder) {
return mRootNode.uniqueNGramCount(nGramOrder);
}
/**
* Removes strings with counts below the specified minimum. Counts for remaining strings are not
* affected. Pruning may be interleaved with updating counts in any order.
*
* @param minCount Minimum count required to retain a substring count.
* @throws IllegalArgumentException If the count is less than <code>1</code>.
*/
public void prune(int minCount) {
if (minCount < 1) {
String msg = "Prune minimum count must be more than 1." + " Found minCount=" + minCount;
throw new IllegalArgumentException(msg);
}
mRootNode = mRootNode.prune(minCount);
if (mRootNode == null) mRootNode = NodeFactory.createNode(0);
}
/**
* Returns an array of frequency counts for n-grams of the specified n-gram order sorted in
* descending frequency order. This form of result is sometimes called a Zipf plot because of the
* sorting.
*
* @param nGramOrder Order of n-gram counted.
* @return Array of frequency counts, sorted in decreasing order of rank.
*/
public int[] nGramFrequencies(int nGramOrder) {
List<Long> counts = countsList(nGramOrder);
int[] result = new int[counts.size()];
for (int i = 0; i < result.length; ++i) result[i] = counts.get(i).intValue();
java.util.Arrays.sort(result);
for (int i = result.length / 2; i >= 0; --i) {
int iOpp = result.length - i - 1;
int tmp = result[i];
result[i] = result[iOpp];
result[iOpp] = tmp;
}
return result;
}
/**
* Returns the array of unique and total n-gram counts for each n-gram length. The return array is
* indexed in the first position by n-gram length, and in the second position by <code>0</code>
* for unique counts and <code>1</code> for total counts. Thus for <code>0<=n<=maxLength()
* </code>:
*
* <blockquote>
*
* <code>
* uniqueTotalNGramCount()[n][0] == uniqueNGramCount(n)
* </code>
*
* </blockquote>
*
* and
*
* <blockquote>
*
* <code>
* uniqueTotalNGramCount()[n][1] == totalNGramCount(n)
* </code>
*
* </blockquote>
*
* If unique and total counts are required for several n-gram depths, this method is much more
* efficient than calling all of the individual methods separately.
*
* @return The array of unique and total n-gram counts for each n-gram length.
*/
public long[][] uniqueTotalNGramCount() {
long[][] result = new long[mMaxLength + 1][2];
mRootNode.addNGramCounts(result, 0);
return result;
}
/**
* Returns a counter of occurrences of the highest frequency n-grams of a specified n-gram order.
* The actual n-grams are represented as strings in the result; recall that strings are instances
* of {@link CharSequence}.
*
* <p>The maximum number of results returned must be specified, because the entire set of n-grams
* is usually too large to return as a counter.
*
* @param nGramOrder Order of n-gram to count.
* @param maxReturn Maximum number of objects returned.
*/
public ObjectToCounterMap<String> topNGrams(int nGramOrder, int maxReturn) {
NBestCounter counter = new NBestCounter(maxReturn, true);
mRootNode.topNGrams(counter, new char[nGramOrder], 0, nGramOrder);
return counter.toObjectToCounter();
}
/**
* Returns the count in the training corpus for the specified sequence of characters. The count
* returned may have been reduced from the raw counts in training cases by pruning.
*
* @param cSeq Character sequence.
* @return Count of character sequence in model.
*/
public long count(CharSequence cSeq) {
return count(com.aliasi.util.Arrays.toArray(cSeq), 0, cSeq.length());
}
/**
* Returns the sum of the counts of all character sequences one character longer than the
* specified character sequence.
*
* @param cSeq Character sequence.
* @return The sum of the counts of all character sequences one character longer than the
* specified character sequence.
*/
public long extensionCount(CharSequence cSeq) {
return mRootNode.contextCount(com.aliasi.util.Arrays.toArray(cSeq), 0, cSeq.length());
}
/**
* Increments the count of all substrings of the specified character array slice up to the maximum
* length specified in the constructor.
*
* @param cs Underlying character array.
* @param start Index of first character in slice.
* @param end Index of one past last character in slice.
* @throws IndexOutOfBoundsException If the specified start and one plus end point are not in the
* bounds of character sequence.
*/
public void incrementSubstrings(char[] cs, int start, int end) {
incrementSubstrings(cs, start, end, 1);
}
/**
* Increments by the specified count all substrings of the specified character array slice up to
* the maximum length specified in the constructor.
*
* @param cs Underlying character array.
* @param start Index of first character in slice.
* @param end Index of one past last character in slice.
* @param count Amount to increment.
* @throws IndexOutOfBoundsException If the specified start and one plus end point are not in the
* bounds of character sequence.
*/
public void incrementSubstrings(char[] cs, int start, int end, int count) {
Strings.checkArgsStartEnd(cs, start, end);
// increment maximal strings and prefixes
for (int i = start; i + mMaxLength <= end; ++i) incrementPrefixes(cs, i, i + mMaxLength, count);
// increment short final strings and prefixes
for (int i = Math.max(start, end - mMaxLength + 1); i < end; ++i)
incrementPrefixes(cs, i, end, count);
}
/**
* Increments the count of all substrings of the specified character sequence up to the maximum
* length specified in the constructor.
*
* @param cSeq Character sequence.
*/
public void incrementSubstrings(CharSequence cSeq) {
incrementSubstrings(cSeq, 1);
}
/**
* Increments by the specified count all substrings of the specified character sequence up to the
* maximum length specified in the constructor.
*
* @param cSeq Character sequence.
* @param count Amount to increment.
*/
public void incrementSubstrings(CharSequence cSeq, int count) {
incrementSubstrings(com.aliasi.util.Arrays.toArray(cSeq), 0, cSeq.length(), count);
}
/**
* Increments the count of all prefixes of the specified character sequence up to the maximum
* length specified in the constructor.
*
* @param cs Underlying character array.
* @param start Index of first character in slice.
* @param end Index of one past last character in slice.
* @throws IndexOutOfBoundsException If the specified start and one plus end point are not in the
* bounds of character sequence.
*/
public void incrementPrefixes(char[] cs, int start, int end) {
incrementPrefixes(cs, start, end, 1);
}
/**
* Increments the count of all prefixes of the specified character sequence up to the maximum
* length specified in the constructor.
*
* @param cs Underlying character array.
* @param start Index of first character in slice.
* @param end Index of one past last character in slice.
* @param count Amount to increment.
* @throws IndexOutOfBoundsException If the specified start and one plus end point are not in the
* bounds of character sequence.
*/
public void incrementPrefixes(char[] cs, int start, int end, int count) {
Strings.checkArgsStartEnd(cs, start, end);
mRootNode = mRootNode.increment(cs, start, end, count);
}
/**
* Decrements all of the substrings of the specified character slice by one. This method may be
* used in conjunction with {@link #incrementSubstrings(char[],int,int)} to implement counts for
* conditional probability estimates without affecting underlying estimates. For example, the
* following code:
*
* <blockquote>
*
* <pre>
* char[] cs = "abcdefghi".toCharArray();
* counter.incrementSubstrings(cs,3,7);
* counter.decrementSubstrings(cs,3,5);
* </pre>
*
* </blockquote>
*
* will increment the substrings of <code>"defg"</code> and then decrement the
* substrings of <code>"de"</code>, causing the net effect of incrementing the counts of
* substrings <code>"defg"</code>, <code>"efg"</code>, <code>"fg"
* </code>, <code>"g"</code>, <code>"def"</code>, <code>"ef"</code>,
* and <code>"f"</code>. This has the effect of increasing the estimate of <code>g
* </code> given <code>def</code>, without increasing the estimate of <code>d</code> in an empty
* context.
*
* @param cs Underlying array of characters in slice.
* @param start Index of first character in slice.
* @param end Index of one past last character in slice.
* @throws IllegalArgumentException If the array slice is valid.
*/
public void decrementSubstrings(char[] cs, int start, int end) {
Strings.checkArgsStartEnd(cs, start, end);
for (int i = start; i < end; ++i)
for (int j = i; j <= end; ++j) mRootNode = mRootNode.decrement(cs, i, j);
}
/**
* Returns a string representation of the trie structure of counts underlying this counter.
*
* <p><b>Warning:</b> The resulting string will be very large if the number of substrings is
* large. To avoid blowing out memory, do not call this method for large counters.
*
* @return String representation of this counter.
*/
@Override
public String toString() {
return mRootNode.toString();
}
void toStringBuilder(StringBuilder sb) {
mRootNode.toString(sb, 0);
}
/**
* Decrements the unigram count for the specified character. This method is useful for training
* conditional probabilities, even though it is not powerful enough to do it in full generality.
*
* @param c Decrement the unigram count for the specified character.
*/
public void decrementUnigram(char c) {
decrementUnigram(c, 1);
}
/**
* Decrements the unigram count by the specified amount for the specified character. This method
* is useful for training conditional probabilities, even though it is not powerful enough to do
* it in full generality.
*
* @param c Decrement the unigram count for the specified character.
* @param count Amount to decrement.
*/
public void decrementUnigram(char c, int count) {
mRootNode = mRootNode.decrement(new char[] {c}, 0, 1, count);
}
private List<Long> countsList(int nGramOrder) {
List<Long> accum = new ArrayList<Long>();
mRootNode.addCounts(accum, nGramOrder);
return accum;
}
/**
* Writes an encoding of this counter to the specified output stream. It may be read back in using
* {@link #readFrom(InputStream)}.
*
* <p>The output is produced using a {@link BitTrieWriter} wrapped around a {@link BitOutput}
* wrapped around the specified underlying output stream. First, the bit output is used to
* delta-code the maximum n-gram plus 1. Then, the trie is encoded as described in {@link
* BitTrieWriter}. Finally, the bit output is flushed. The underlying output stream is neither
* flushed nor closed, allowing them to be used for other pruposes after this counter is written.
*
* <p>If necessary for efficiency, streams should be buffered before being passed to this method.
*
* @param out Underlying output stream for writing.
* @throws IOException If there is an underlying I/O error.
*/
public void writeTo(OutputStream out) throws IOException {
BitOutput bitOut = new BitOutput(out);
bitOut.writeDelta(mMaxLength + 1L);
TrieWriter writer = new BitTrieWriter(bitOut);
writeCounter(this, writer, mMaxLength);
bitOut.flush();
}
/**
* Writes the specified sequence counter to the specified trie writer, restricting output to
* n-grams not longer than the specified maximum.
*
* @param counter Counter to write.
* @param writer Trie writer to which counter is written.
* @param maxNGram Maximum length n-gram written.
* @throws IOException If there is an underlying I/O error.
*/
public static void writeCounter(CharSeqCounter counter, TrieWriter writer, int maxNGram)
throws IOException {
writeCounter(new char[maxNGram], 0, counter, writer);
}
/**
* Reads a trie character sequence counter from the specified input stream.
*
* <p>The expected encoding is described in {@link #writeTo(OutputStream)}.
*
* <p>If necessary for efficiency, streams should be buffered before being passed to this method.
*
* @param in Underlying input stream for reading.
* @throws IOException If there is an underlying I/O error.
*/
public static TrieCharSeqCounter readFrom(InputStream in) throws IOException {
BitInput bitIn = new BitInput(in);
int maxNGram = (int) (bitIn.readDelta() - 1L);
BitTrieReader reader = new BitTrieReader(bitIn);
return readCounter(reader, maxNGram);
}
/**
* Reads a trie character sequence counter from the specified trie reader, restricting the result
* to the specified maximum n-gram.
*
* @param reader Reader from which to read the trie.
* @param maxNGram Maximum length n-gram to read.
* @return The counter read from the reader.
* @throws IOException If there is an underlying I/O error.
*/
public static TrieCharSeqCounter readCounter(TrieReader reader, int maxNGram) throws IOException {
TrieCharSeqCounter counter = new TrieCharSeqCounter(maxNGram);
counter.mRootNode = readNode(reader, 0, maxNGram);
return counter;
}
static void writeCounter(char[] cs, int pos, CharSeqCounter counter, TrieWriter writer)
throws IOException {
long count = counter.count(cs, 0, pos);
writer.writeCount(count);
if (pos < cs.length) { // daughters within n-gram bound
char[] csNext = counter.charactersFollowing(cs, 0, pos);
for (int i = 0; i < csNext.length; ++i) {
writer.writeSymbol(csNext[i]);
cs[pos] = csNext[i];
writeCounter(cs, pos + 1, counter, writer);
}
}
writer.writeSymbol(-1L); // end of daughters
}
private static void skipNode(TrieReader reader) throws IOException {
reader.readCount();
while (reader.readSymbol() != -1) skipNode(reader);
}
private static Node readNode(TrieReader reader, int depth, int maxDepth) throws IOException {
if (depth > maxDepth) {
skipNode(reader);
return null;
}
long count = reader.readCount();
int depthPlus1 = depth + 1;
long sym1 = reader.readSymbol();
// 0+ daughters
if (sym1 == -1L) return NodeFactory.createNode(count);
// 1+ daughters
Node node1 = readNode(reader, depthPlus1, maxDepth);
long sym2 = reader.readSymbol();
if (sym2 == -1L) return NodeFactory.createNodeFold((char) sym1, node1, count);
Node node2 = readNode(reader, depthPlus1, maxDepth);
long sym3 = reader.readSymbol();
if (sym3 == -1L) return NodeFactory.createNode((char) sym1, node1, (char) sym2, node2, count);
Node node3 = readNode(reader, depthPlus1, maxDepth);
long sym4 = reader.readSymbol();
if (sym4 == -1L)
return NodeFactory.createNode(
(char) sym1, node1, (char) sym2, node2, (char) sym3, node3, count);
Node node4 = readNode(reader, depthPlus1, maxDepth);
// 4+ daughters
StringBuilder cBuf = new StringBuilder();
cBuf.append((char) sym1);
cBuf.append((char) sym2);
cBuf.append((char) sym3);
cBuf.append((char) sym4);
List<Node> nodeList = new ArrayList<Node>();
nodeList.add(node1);
nodeList.add(node2);
nodeList.add(node3);
nodeList.add(node4);
long sym;
while ((sym = reader.readSymbol()) != -1L) {
cBuf.append((char) sym);
nodeList.add(readNode(reader, depthPlus1, maxDepth));
}
Node[] nodes = nodeList.toArray(EMPTY_NODE_ARRAY);
char[] cs = Strings.toCharArray(cBuf);
return NodeFactory.createNode(cs, nodes, count); // > 3 daughters
}
static final Node[] EMPTY_NODE_ARRAY = new Node[0];
}
