public int doNestedTermConjunctions(
IndexSearcher s, int termsInIndex, int maxOuterClauses, int maxClauses, int iter)
throws IOException {
int ret = 0;
long nMatches = 0;
for (int i = 0; i < iter; i++) {
int oClauses = r.nextInt(maxOuterClauses - 1) + 2;
BooleanQuery oq = new BooleanQuery();
for (int o = 0; o < oClauses; o++) {
int nClauses = r.nextInt(maxClauses - 1) + 2; // min 2 clauses
BooleanQuery bq = new BooleanQuery();
BitSet termflag = new BitSet(termsInIndex);
for (int j = 0; j < nClauses; j++) {
int tnum;
// don't pick same clause twice
tnum = r.nextInt(termsInIndex);
if (termflag.get(tnum)) tnum = termflag.nextClearBit(tnum);
if (tnum < 0 || tnum >= 25) tnum = termflag.nextClearBit(0);
termflag.set(tnum);
Query tq = new TermQuery(terms[tnum]);
bq.add(tq, BooleanClause.Occur.MUST);
} // inner
oq.add(bq, BooleanClause.Occur.MUST);
} // outer
CountingHitCollector hc = new CountingHitCollector();
s.search(oq, hc);
nMatches += hc.getCount();
ret += hc.getSum();
}
System.out.println("Average number of matches=" + (nMatches / iter));
return ret;
}
public void saveToXml(Element ele) {
Document doc = ele.getOwnerDocument();
ele.setAttribute("id", String.valueOf(partNumber));
SaveUtil.appendChildTextElement(ele, "title", String.valueOf(title));
SaveUtil.appendChildTextElement(ele, "instrument", String.valueOf(instrument));
for (int t = 0; t < getTrackCount(); t++) {
if (!isTrackEnabled(t)) continue;
TrackInfo trackInfo = abcSong.getSequenceInfo().getTrackInfo(t);
Element trackEle = (Element) ele.appendChild(doc.createElement("track"));
trackEle.setAttribute("id", String.valueOf(t));
if (trackInfo.hasName()) trackEle.setAttribute("name", trackInfo.getName());
if (trackTranspose[t] != 0)
SaveUtil.appendChildTextElement(trackEle, "transpose", String.valueOf(trackTranspose[t]));
if (trackVolumeAdjust[t] != 0)
SaveUtil.appendChildTextElement(
trackEle, "volumeAdjust", String.valueOf(trackVolumeAdjust[t]));
if (instrument.isPercussion) {
BitSet[] enabledSetByTrack = isCowbellPart() ? cowbellsEnabled : drumsEnabled;
BitSet enabledSet = (enabledSetByTrack == null) ? null : enabledSetByTrack[t];
if (enabledSet != null) {
Element drumsEnabledEle = ele.getOwnerDocument().createElement("drumsEnabled");
trackEle.appendChild(drumsEnabledEle);
if (isCowbellPart()) {
drumsEnabledEle.setAttribute("defaultEnabled", String.valueOf(false));
// Only store the drums that are enabled
for (int i = enabledSet.nextSetBit(0); i >= 0; i = enabledSet.nextSetBit(i + 1)) {
Element drumEle = ele.getOwnerDocument().createElement("note");
drumsEnabledEle.appendChild(drumEle);
drumEle.setAttribute("id", String.valueOf(i));
drumEle.setAttribute("isEnabled", String.valueOf(true));
}
} else {
drumsEnabledEle.setAttribute("defaultEnabled", String.valueOf(true));
// Only store the drums that are disabled
for (int i = enabledSet.nextClearBit(0); i >= 0; i = enabledSet.nextClearBit(i + 1)) {
if (i >= MidiConstants.NOTE_COUNT) break;
Element drumEle = ele.getOwnerDocument().createElement("note");
drumsEnabledEle.appendChild(drumEle);
drumEle.setAttribute("id", String.valueOf(i));
drumEle.setAttribute("isEnabled", String.valueOf(false));
}
}
}
if (!isCowbellPart()) {
if (drumNoteMap[t] != null)
drumNoteMap[t].saveToXml((Element) trackEle.appendChild(doc.createElement("drumMap")));
}
}
}
}
/**
* Splits events of a row if they overlap an island. Islands are areas between the token which are
* included in the result.
*
* @param row
* @param graph
* @param text
* @param startTokenIndex token index of the first token in the match
* @param endTokenIndex token index of the last token in the match
*/
private static void splitRowsOnIslands(
Row row,
final SDocumentGraph graph,
STextualDS text,
long startTokenIndex,
long endTokenIndex) {
BitSet tokenCoverage = new BitSet();
// get the sorted token
List<SToken> sortedTokenList = graph.getSortedTokenByText();
// add all token belonging to the right text to the bit set
ListIterator<SToken> itToken = sortedTokenList.listIterator();
while (itToken.hasNext()) {
SToken t = itToken.next();
if (text == null || text == CommonHelper.getTextualDSForNode(t, graph)) {
RelannisNodeFeature feat =
(RelannisNodeFeature) t.getFeature(ANNIS_NS, FEAT_RELANNIS_NODE).getValue();
long tokenIndexRaw = feat.getTokenIndex();
tokenIndexRaw = clip(tokenIndexRaw, startTokenIndex, endTokenIndex);
int tokenIndex = (int) (tokenIndexRaw - startTokenIndex);
tokenCoverage.set(tokenIndex);
}
}
ListIterator<GridEvent> itEvents = row.getEvents().listIterator();
while (itEvents.hasNext()) {
GridEvent event = itEvents.next();
BitSet eventBitSet = new BitSet();
eventBitSet.set(event.getLeft(), event.getRight() + 1);
// restrict event bitset on the locations where token are present
eventBitSet.and(tokenCoverage);
// if there is is any 0 bit before the right border there is a break in the event
// and we need to split it
if (eventBitSet.nextClearBit(event.getLeft()) <= event.getRight()) {
// remove the original event
row.removeEvent(itEvents);
// The event bitset now marks all the locations which the event should
// cover.
// Make a list of new events for each connected range in the bitset
int subElement = 0;
int offset = eventBitSet.nextSetBit(0);
while (offset >= 0) {
int end = eventBitSet.nextClearBit(offset) - 1;
if (offset < end) {
GridEvent newEvent = new GridEvent(event);
newEvent.setId(event.getId() + "_islandsplit_" + subElement++);
newEvent.setLeft(offset);
newEvent.setRight(end);
row.addEvent(itEvents, newEvent);
}
offset = eventBitSet.nextSetBit(end + 1);
}
} // end if we need to split
}
}
/**
* Remove the occurrence of a given value in a copied slice of array defined by the array part
* from [begin, begin+length).
*
* @param values the input array
* @param begin start index of the array to include
* @param length number of elements to include from begin
* @param removedValue the value to be removed from the sliced array
* @return the copy of the sliced array after removing the removedValue
*/
private static double[] removeAndSlice(
final double[] values, final int begin, final int length, final double removedValue) {
MathArrays.verifyValues(values, begin, length);
final double[] temp;
// BitSet(length) to indicate where the removedValue is located
final BitSet bits = new BitSet(length);
for (int i = begin; i < begin + length; i++) {
if (Precision.equalsIncludingNaN(removedValue, values[i])) {
bits.set(i - begin);
}
}
// Check if empty then create a new copy
if (bits.isEmpty()) {
temp = copyOf(values, begin, length); // Nothing removed, just copy
} else if (bits.cardinality() == length) {
temp = new double[0]; // All removed, just empty
} else { // Some removable, so new
temp = new double[length - bits.cardinality()];
int start = begin; // start index from source array (i.e values)
int dest = 0; // dest index in destination array(i.e temp)
int nextOne = -1; // nextOne is the index of bit set of next one
int bitSetPtr = 0; // bitSetPtr is start index pointer of bitset
while ((nextOne = bits.nextSetBit(bitSetPtr)) != -1) {
final int lengthToCopy = nextOne - bitSetPtr;
System.arraycopy(values, start, temp, dest, lengthToCopy);
dest += lengthToCopy;
start = begin + (bitSetPtr = bits.nextClearBit(nextOne));
}
// Copy any residue past start index till begin+length
if (start < begin + length) {
System.arraycopy(values, start, temp, dest, begin + length - start);
}
}
return temp;
}
@Test
public void testBitSetNextClearBit() throws Exception {
BitSet bit = new BitSet();
bit.set(0);
int position = bit.nextClearBit(0);
assertThat(position, is(1));
}
private int registerItem(Item item, String name, int idHint) {
if (item
instanceof
ItemBlock) // ItemBlock, adjust id and clear the slot already occupied by the corresponding
// block
{
Block block = ((ItemBlock) item).field_150939_a;
int id = iBlockRegistry.getId(block);
if (id == -1) // ItemBlock before its Block
{
if (idHint < 0
|| availabilityMap.get(idHint)
|| idHint
> MAX_BLOCK_ID) // non-suitable id, allocate one in the block id range, add would
// use the item id range otherwise
{
id =
availabilityMap.nextClearBit(
MIN_BLOCK_ID); // find suitable id here, iItemRegistry would search from
// MIN_ITEM_ID
if (id > MAX_BLOCK_ID)
throw new RuntimeException(
String.format("Invalid id %d - maximum id range exceeded.", id));
FMLLog.fine(
"Allocated id %d for ItemBlock %s in the block id range, original id requested: %d.",
id, name, idHint);
} else // idHint is suitable without changes
{
id = idHint;
}
} else // ItemBlock after its Block
{
FMLLog.fine(
"Found matching Block %s for ItemBlock %s at id %d, original id requested: %d",
block, item, id, idHint);
freeSlot(
id, item); // temporarily free the slot occupied by the Block for the item registration
}
idHint = id;
}
int itemId = iItemRegistry.add(idHint, name, item, availabilityMap);
if (item instanceof ItemBlock) // verify
{
if (itemId != idHint)
throw new IllegalStateException(
String.format("ItemBlock at block id %d insertion failed, got id %d.", idHint, itemId));
verifyItemBlockName((ItemBlock) item);
}
// block the Block Registry slot with the same id
useSlot(itemId);
return itemId;
}
/**
* Return the next free dimension ID. Note: you are not guaranteed a contiguous block of free ids.
* Always call for each individual ID you wish to get.
*
* @return the next free dimension ID
*/
public static int getNextFreeDimId() {
int next = 0;
while (true) {
next = dimensionMap.nextClearBit(next);
if (dimensions.containsKey(next)) {
dimensionMap.set(next);
} else {
return next;
}
}
}
@Override
public int nextId() {
try {
lock.lock();
int id;
if (nextMinId == Integer.MIN_VALUE) {
id = Integer.MIN_VALUE;
} else {
id = idList.nextClearBit(nextMinId);
}
if (id == Integer.MIN_VALUE) {
throw new IllegalStateException("All id's are used");
}
idList.set(id);
nextMinId = id + 1;
return id;
} finally {
lock.unlock();
}
}
/**
* Allocate a block of memory that will be tracked in the MemoryManager's page table; this is
* intended for allocating large blocks of memory that will be shared between operators.
*/
public MemoryBlock allocatePage(long size) {
if (size > MAXIMUM_PAGE_SIZE_BYTES) {
throw new IllegalArgumentException(
"Cannot allocate a page with more than " + MAXIMUM_PAGE_SIZE_BYTES + " bytes");
}
final int pageNumber;
synchronized (this) {
pageNumber = allocatedPages.nextClearBit(0);
if (pageNumber >= PAGE_TABLE_SIZE) {
throw new IllegalStateException(
"Have already allocated a maximum of " + PAGE_TABLE_SIZE + " pages");
}
allocatedPages.set(pageNumber);
}
final MemoryBlock page = executorMemoryManager.allocate(size);
page.pageNumber = pageNumber;
pageTable[pageNumber] = page;
if (logger.isTraceEnabled()) {
logger.trace("Allocate page number {} ({} bytes)", pageNumber, size);
}
return page;
}
@Nullable
private Range calcContinousRange(final BitSet mask) {
int lowestByte = mask.nextSetBit(0);
int highestByte;
if (lowestByte >= 0) {
highestByte = mask.nextClearBit(lowestByte);
if (highestByte > 0) {
int nextChunk = mask.nextSetBit(highestByte);
if (nextChunk < 0) {
myContinuousRange.start = lowestByte;
myContinuousRange.end = highestByte;
return myContinuousRange;
} else {
return null;
}
} else {
myContinuousRange.start = lowestByte;
myContinuousRange.end = PAGE_SIZE;
return myContinuousRange;
}
} else {
return null;
}
}
@Override
Val apply(Env env, Env.StackHelp stk, AST asts[]) {
Frame fr = stk.track(asts[1].exec(env)).getFrame();
Frame returningFrame;
long nrows = fr.numRows();
if (asts[2] instanceof ASTNumList) {
final ASTNumList nums = (ASTNumList) asts[2];
long[] rows = nums._isList ? nums.expand8Sort() : null;
if (rows != null) {
if (rows.length == 0) { // Empty inclusion list?
} else if (rows[0] >= 0) { // Positive (inclusion) list
if (rows[rows.length - 1] > nrows)
throw new IllegalArgumentException("Row must be an integer from 0 to " + (nrows - 1));
} else { // Negative (exclusion) list
// Invert the list to make a positive list, ignoring out-of-bounds values
BitSet bs = new BitSet((int) nrows);
for (int i = 0; i < rows.length; i++) {
int idx = (int) (-rows[i] - 1); // The positive index
if (idx >= 0 && idx < nrows) bs.set(idx); // Set column to EXCLUDE
}
rows = new long[(int) nrows - bs.cardinality()];
for (int i = bs.nextClearBit(0), j = 0; i < nrows; i = bs.nextClearBit(i + 1))
rows[j++] = i;
}
}
final long[] ls = rows;
returningFrame =
new MRTask() {
@Override
public void map(Chunk[] cs, NewChunk[] ncs) {
if (nums.cnt() == 0) return;
long start = cs[0].start();
long end = start + cs[0]._len;
long min = ls == null ? (long) nums.min() : ls[0],
max =
ls == null
? (long) nums.max() - 1
: ls[ls.length - 1]; // exclusive max to inclusive max when stride == 1
// [ start, ..., end ] the chunk
// 1 [] nums out left: nums.max() < start
// 2 [] nums out rite: nums.min() > end
// 3 [ nums ] nums run left: nums.min() < start && nums.max() <=
// end
// 4 [ nums ] nums run in : start <= nums.min() && nums.max() <=
// end
// 5 [ nums ] nums run rite: start <= nums.min() && end <
// nums.max()
if (!(max < start || min > end)) { // not situation 1 or 2 above
long startOffset = (min > start ? min : start); // situation 4 and 5 => min > start;
for (int i = (int) (startOffset - start); i < cs[0]._len; ++i) {
if ((ls == null && nums.has(start + i))
|| (ls != null && Arrays.binarySearch(ls, start + i) >= 0)) {
for (int c = 0; c < cs.length; ++c) {
if (cs[c] instanceof CStrChunk) ncs[c].addStr(cs[c], i);
else if (cs[c] instanceof C16Chunk) ncs[c].addUUID(cs[c], i);
else if (cs[c].isNA(i)) ncs[c].addNA();
else ncs[c].addNum(cs[c].atd(i));
}
}
}
}
}
}.doAll(fr.types(), fr).outputFrame(fr.names(), fr.domains());
} else if ((asts[2] instanceof ASTNum)) {
long[] rows = new long[] {(long) (((ASTNum) asts[2])._v.getNum())};
returningFrame = fr.deepSlice(rows, null);
} else if ((asts[2] instanceof ASTExec) || (asts[2] instanceof ASTId)) {
Frame predVec = stk.track(asts[2].exec(env)).getFrame();
if (predVec.numCols() != 1)
throw new IllegalArgumentException(
"Conditional Row Slicing Expression evaluated to "
+ predVec.numCols()
+ " columns. Must be a boolean Vec.");
returningFrame = fr.deepSlice(predVec, null);
} else
throw new IllegalArgumentException(
"Row slicing requires a number-list as the last argument, but found a "
+ asts[2].getClass());
return new ValFrame(returningFrame);
}
public static void removeEmptySpace(
LinkedHashMap<String, ArrayList<Row>> rowsByAnnotation, Row tokenRow) {
List<Range<Integer>> gaps = new LinkedList<>();
BitSet totalOccupancyGrid = new BitSet();
for (Map.Entry<String, ArrayList<Row>> layer : rowsByAnnotation.entrySet()) {
for (Row r : layer.getValue()) {
totalOccupancyGrid.or(r.getOccupancyGridCopy());
}
}
// We always include the token row in the occupancy grid since it is not
// a gap. Otherwise empty token would trigger gaps if the token list
// is included in the visualizer output.
// See https://github.com/korpling/ANNIS/issues/281 for the corresponding
// bug report.
if (tokenRow != null) {
totalOccupancyGrid.or(tokenRow.getOccupancyGridCopy());
}
// The Range class can give us the next bit that is not set. Use this
// to detect gaps. A gap starts from the next non-set bit and goes to
// the next set bit.
Range<Integer> gap = Range.closed(-1, totalOccupancyGrid.nextSetBit(0));
while (true) {
int gapStart = totalOccupancyGrid.nextClearBit(gap.upperEndpoint() + 1);
int gapEnd = totalOccupancyGrid.nextSetBit(gapStart);
if (gapEnd <= 0) {
break;
}
gap = Range.closed(gapStart, gapEnd - 1);
gaps.add(gap);
}
int gapID = 0;
int totalOffset = 0;
for (Range<Integer> gRaw : gaps) {
// adjust the space range itself
Range<Integer> g =
Range.closed(gRaw.lowerEndpoint() - totalOffset, gRaw.upperEndpoint() - totalOffset);
int offset = g.upperEndpoint() - g.lowerEndpoint();
totalOffset += offset;
for (Entry<String, ArrayList<Row>> rowEntry : rowsByAnnotation.entrySet()) {
ArrayList<Row> rows = rowEntry.getValue();
for (Row r : rows) {
List<GridEvent> eventsCopy = new LinkedList<>(r.getEvents());
for (GridEvent e : eventsCopy) {
if (e.getLeft() >= g.upperEndpoint()) {
r.removeEvent(e);
e.setLeft(e.getLeft() - offset);
e.setRight(e.getRight() - offset);
r.addEvent(e);
}
}
// add a special space event
String spaceCaption = "";
if ("tok".equalsIgnoreCase(rowEntry.getKey())) {
spaceCaption = "(...)";
}
GridEvent spaceEvent =
new GridEvent("gap-" + gapID, g.lowerEndpoint(), g.lowerEndpoint(), spaceCaption);
spaceEvent.setSpace(true);
r.addEvent(spaceEvent);
gapID++;
}
}
}
}
synchronized void put(long hash, K key, V value, boolean ifPresent, boolean ifAbsent) {
// search for the previous entry
int h = smallMap.startSearch(hash);
boolean foundSmall = false, foundLarge = false;
while (true) {
int pos = smallMap.nextPos();
if (pos < 0) {
K key2 = key instanceof CharSequence ? (K) key.toString() : key;
final DirectStore store = map.get(key2);
if (store == null) {
if (ifPresent && !ifAbsent) return;
break;
}
if (ifAbsent) return;
bytes.storePositionAndSize(store, 0, store.size());
foundLarge = true;
break;
} else {
bytes.storePositionAndSize(store, pos * smallEntrySize, smallEntrySize);
K key2 = getKey();
if (equals(key, key2)) {
if (ifAbsent && !ifPresent) return;
foundSmall = true;
break;
}
}
}
tmpBytes.clear();
if (csKey)
//noinspection ConstantConditions
tmpBytes.writeUTFΔ((CharSequence) key);
else tmpBytes.writeObject(key);
long startOfValuePos = tmpBytes.position();
if (bytesMarshallable) ((BytesMarshallable) value).writeMarshallable(tmpBytes);
else tmpBytes.writeObject(value);
long size = tmpBytes.position();
if (size <= smallEntrySize) {
if (foundSmall) {
bytes.position(0);
bytes.write(tmpBytes, 0, size);
return;
} else if (foundLarge) {
remove(hash, key);
}
// look for a free spot.
int position = h & (entriesPerSegment - 1);
int free = usedSet.nextClearBit(position);
if (free >= entriesPerSegment) free = usedSet.nextClearBit(0);
if (free < entriesPerSegment) {
bytes.storePositionAndSize(store, free * smallEntrySize, smallEntrySize);
bytes.write(tmpBytes, 0, size);
smallMap.put(h, free);
usedSet.set(free);
this.size++;
return;
}
}
if (foundSmall) {
remove(hash, key);
} else if (foundLarge) {
// can it be reused.
if (bytes.capacity() <= size || bytes.capacity() - size < (size >> 3)) {
bytes.write(tmpBytes, startOfValuePos, size);
return;
}
remove(hash, key);
}
size = size - startOfValuePos;
DirectStore store = new DirectStore(bmf, size);
bytes.storePositionAndSize(store, 0, size);
bytes.write(tmpBytes, startOfValuePos, size);
K key2 = key instanceof CharSequence ? (K) key.toString() : key;
map.put(key2, store);
offHeapUsed += size;
this.size++;
}
private BitSetCover calculateCoverRecursively(
int indexNextCandidate, BitSet visited, double accumulatedWeight) {
// Check memoization table
if (memo.containsKey(visited)) {
return memo.get(visited).copy(); // Cache hit
}
// Find the next unvisited vertex WITH neighbors (if a vertex has no neighbors, then we don't
// need to select it
// because it doesn't cover any edges)
int indexNextVertex = -1;
Set<V> neighbors = Collections.emptySet();
for (int index = visited.nextClearBit(indexNextCandidate);
index >= 0 && index < N;
index = visited.nextClearBit(index + 1)) {
neighbors = new LinkedHashSet<>(neighborIndex.neighborsOf(vertices.get(index)));
for (Iterator<V> it = neighbors.iterator(); it.hasNext(); ) // Exclude all visited vertices
if (visited.get(vertexIDDictionary.get(it.next()))) it.remove();
if (!neighbors.isEmpty()) {
indexNextVertex = index;
break;
}
}
// Base case 1: all vertices have been visited
if (indexNextVertex == -1) { // We've visited all vertices, return the base case
BitSetCover vertexCover = new BitSetCover(N, 0);
if (accumulatedWeight
<= upperBoundOnVertexCoverWeight) { // Found new a solution that matches our bound.
// Tighten the bound.
upperBoundOnVertexCoverWeight = accumulatedWeight - 1;
}
return vertexCover;
// Base case 2 (pruning): this vertex cover can never be better than the best cover we already
// have. Return a cover with a large weight, such that the other branch will be preferred over
// this branch.
} else if (accumulatedWeight >= upperBoundOnVertexCoverWeight) {
return new BitSetCover(N, N);
}
// Recursion
// TODO JK: Can we use a lower bound or estimation which of these 2 branches produces a better
// solution? If one of them is more likely to produce a better solution,
// then that branch should be explored first! Futhermore, if the lower bound+accumulated cost >
// upperBoundOnVertexCoverWeight, then we may prune.
// Create 2 branches (N(v) denotes the set of neighbors of v. G_{v} indicates the graph obtained
// by removing vertex v and all vertices incident to it.):
// Right branch (N(v) are added to the cover, and we solve for G_{N(v) \cup v }.):
BitSet visitedRightBranch = (BitSet) visited.clone();
visitedRightBranch.set(indexNextVertex);
for (V v : neighbors) visitedRightBranch.set(vertexIDDictionary.get(v));
double weight = this.getWeight(neighbors);
BitSetCover rightCover =
calculateCoverRecursively(
indexNextVertex + 1, visitedRightBranch, accumulatedWeight + weight);
rightCover.addAllVertices(
neighbors.stream().mapToInt(vertexIDDictionary::get).boxed().collect(Collectors.toList()),
weight);
// Left branch (vertex v is added to the cover, and we solve for G_{v}):
BitSet visitedLeftBranch = (BitSet) visited.clone();
visitedLeftBranch.set(indexNextVertex);
weight = vertexWeightMap.get(vertices.get(indexNextVertex));
BitSetCover leftCover =
calculateCoverRecursively(
indexNextVertex + 1, visitedLeftBranch, accumulatedWeight + weight);
leftCover.addVertex(indexNextVertex, weight); // Delayed update of the left cover
// Return the best branch
if (leftCover.weight <= rightCover.weight) {
memo.put(visited, leftCover.copy());
return leftCover;
} else {
memo.put(visited, rightCover.copy());
return rightCover;
}
}
int firstZero(BitSet t) {
return t.nextClearBit(0);
}