@Test
public void testUnsignedTreeSetSerializable() {
NavigableSet<Integer> set =
new TreeSet<>(
(Comparator<Integer> & Serializable) ((x, y) -> Integer.compareUnsigned(x, y)));
set.addAll(Arrays.asList(-100, 0, 100));
assertEquals(0, set.first().intValue());
assertEquals(-100, set.last().intValue());
byte[] serializedSet = writeSetToBytes(set, true);
NavigableSet<Integer> set1 = readSetFromBytes(serializedSet);
assertEquals(0, set1.first().intValue());
assertEquals(-100, set1.last().intValue());
assertEquals(set, set1);
}
public void testKeyPutRandomUniform() throws Exception {
final NavigableSet<Integer> keys = new TreeSet<Integer>();
long seed = System.currentTimeMillis();
System.out.println("testKeyPutRandomUniform seed : " + seed);
final MersenneTwisterFast random = new MersenneTwisterFast(seed);
while (keys.size() < KEYS_COUNT) {
int key = random.nextInt(Integer.MAX_VALUE);
sbTree.put(key, createValue(key, OSBTreeValuePage.MAX_BINARY_VALUE_SIZE + 4));
keys.add(key);
doReset();
}
Assert.assertEquals(sbTree.firstKey(), keys.first());
doReset();
Assert.assertEquals(sbTree.lastKey(), keys.last());
doReset();
for (int key : keys) {
Assert.assertEquals(
sbTree.get(key), createValue(key, OSBTreeValuePage.MAX_BINARY_VALUE_SIZE + 4));
doReset();
}
}
@Test
public void WriteDBInt_lastKey_set_middle() {
int numberOfRecords = 1000;
/* Creates connections to MapDB */
DB db1 = DBMaker.memoryDB().transactionDisable().make();
/* Creates maps */
NavigableSet<Integer> map1 = db1.treeSet("column1");
/* Inserts initial values in maps */
for (int i = 0; i < numberOfRecords; i++) {
map1.add(i);
}
assertEquals((Object) (numberOfRecords - 1), map1.last());
map1.clear();
/* Inserts some values in maps */
for (int i = 100; i < 110; i++) {
map1.add(i);
}
assertEquals(10, map1.size());
assertFalse(map1.isEmpty());
assertEquals((Object) 109, map1.last());
assertEquals((Object) 100, map1.first());
}
@Test
public void testUnsignedTreeSetMRef() {
NavigableSet<Integer> set = new TreeSet<>(Integer::compareUnsigned);
set.addAll(Arrays.asList(-100, 0, 100));
assertEquals(0, set.first().intValue());
assertEquals(-100, set.last().intValue());
}
/**
* Finds range of server deltas needed to transform against, then transforms all client ops
* against the server ops.
*/
private VersionedWaveletDelta transformSubmittedDelta(
WaveletDelta submittedDelta, HashedVersion appliedVersion)
throws OperationException, InvalidHashException {
NavigableSet<VersionedWaveletDelta> serverDeltas =
deserializedTransformedDeltas.tailSet(
deserializedTransformedDeltas.floor(
emptyDeserializedDeltaAtVersion(appliedVersion.getVersion())),
true);
if (serverDeltas.size() == 0) {
LOG.warning("Got empty server set, but not sumbitting to head! " + submittedDelta);
// Not strictly an invalid hash, but it's a related issue
throw new InvalidHashException("Cannot submit to head");
}
// Confirm that the target version/hash of this delta is valid.
if (!serverDeltas.first().version.equals(appliedVersion)) {
LOG.warning(
"Mismatched hashes: expected: "
+ serverDeltas.first().version
+ " got: "
+ appliedVersion);
// Don't leak the hash to the client in the error message.
throw new InvalidHashException("Mismatched hashes at version " + appliedVersion.getVersion());
}
ParticipantId clientAuthor = submittedDelta.getAuthor();
List<WaveletOperation> clientOps = submittedDelta.getOperations();
for (VersionedWaveletDelta d : serverDeltas) {
// If the client delta transforms to nothing before we've traversed all the server
// deltas, return the version at which the delta was obliterated (rather than the
// current version) to ensure that delta submission is idempotent.
if (clientOps.isEmpty()) {
return new VersionedWaveletDelta(new WaveletDelta(clientAuthor, clientOps), d.version);
}
ParticipantId serverAuthor = d.delta.getAuthor();
List<WaveletOperation> serverOps = d.delta.getOperations();
if (clientAuthor.equals(serverAuthor) && clientOps.equals(serverOps)) {
return d;
}
clientOps = transformOps(clientOps, clientAuthor, serverOps, serverAuthor);
}
return new VersionedWaveletDelta(new WaveletDelta(clientAuthor, clientOps), currentVersion);
}
@Test
public void testUnsignedTreeSetNotSerializable() {
NavigableSet<Integer> set = new TreeSet<>((x, y) -> Integer.compareUnsigned(x, y));
set.addAll(Arrays.asList(-100, 0, 100));
assertEquals(0, set.first().intValue());
assertEquals(-100, set.last().intValue());
byte[] serializedSet = writeSetToBytes(set, false);
assertEquals(null, serializedSet);
}
public void testKeyDeleteRandomGaussian() throws Exception {
NavigableSet<Integer> keys = new TreeSet<Integer>();
long seed = System.currentTimeMillis();
System.out.println("testKeyDeleteRandomGaussian seed : " + seed);
MersenneTwisterFast random = new MersenneTwisterFast(seed);
while (keys.size() < KEYS_COUNT) {
int key = (int) (random.nextGaussian() * Integer.MAX_VALUE / 2 + Integer.MAX_VALUE);
if (key < 0) continue;
sbTree.put(key, createValue(key, OSBTreeValuePage.MAX_BINARY_VALUE_SIZE + 4));
keys.add(key);
Assert.assertEquals(
sbTree.get(key), createValue(key, OSBTreeValuePage.MAX_BINARY_VALUE_SIZE + 4));
doReset();
}
Iterator<Integer> keysIterator = keys.iterator();
while (keysIterator.hasNext()) {
int key = keysIterator.next();
if (key % 3 == 0) {
sbTree.remove(key);
keysIterator.remove();
}
doReset();
}
Assert.assertEquals(sbTree.firstKey(), keys.first());
doReset();
Assert.assertEquals(sbTree.lastKey(), keys.last());
doReset();
for (int key : keys) {
if (key % 3 == 0) {
Assert.assertNull(sbTree.get(key));
} else {
Assert.assertEquals(
sbTree.get(key), createValue(key, OSBTreeValuePage.MAX_BINARY_VALUE_SIZE + 4));
}
doReset();
}
}
protected boolean useLogarithmicProblemScale(List<XYSeries> seriesList) {
NavigableSet<Double> xValueSet = new TreeSet<Double>();
int xValueListSize = 0;
for (XYSeries series : seriesList) {
for (XYDataItem dataItem : (List<XYDataItem>) series.getItems()) {
xValueSet.add(dataItem.getXValue());
xValueListSize++;
}
}
if (xValueListSize < LOG_SCALE_MIN_DATASETS_COUNT) {
return false;
}
// If 60% of the points are in 20% of the value space, use a logarithmic scale
double threshold = 0.2 * (xValueSet.last() - xValueSet.first());
int belowThresholdCount = xValueSet.headSet(threshold).size();
return belowThresholdCount >= (0.6 * xValueSet.size());
}
public static void routing(Number160 key, Peer[] peers, int start) {
System.out.println("routing: searching for key " + key);
NavigableSet<PeerAddress> pa1 = new TreeSet<PeerAddress>(PeerMap.createComparator(key));
NavigableSet<PeerAddress> queried = new TreeSet<PeerAddress>(PeerMap.createComparator(key));
Number160 result = Number160.ZERO;
Number160 resultPeer = new Number160("0xd75d1a3d57841fbc9e2a3d175d6a35dc2e15b9f");
int round = 0;
while (!resultPeer.equals(result)) {
System.out.println("round " + round);
round++;
pa1.addAll(peers[start].getPeerBean().peerMap().getAll());
queried.add(peers[start].getPeerAddress());
System.out.println("closest so far: " + queried.first());
PeerAddress next = pa1.pollFirst();
while (queried.contains(next)) {
next = pa1.pollFirst();
}
result = next.getPeerId();
start = findNr(next.getPeerId().toString(), peers);
}
}
/** headSet returns set with keys in requested range */
public void testDescendingHeadSetContents() {
NavigableSet set = dset5();
SortedSet sm = set.headSet(m4);
assertTrue(sm.contains(m1));
assertTrue(sm.contains(m2));
assertTrue(sm.contains(m3));
assertFalse(sm.contains(m4));
assertFalse(sm.contains(m5));
Iterator i = sm.iterator();
Object k;
k = (Integer) (i.next());
assertEquals(m1, k);
k = (Integer) (i.next());
assertEquals(m2, k);
k = (Integer) (i.next());
assertEquals(m3, k);
assertFalse(i.hasNext());
sm.clear();
assertTrue(sm.isEmpty());
assertEquals(2, set.size());
assertEquals(m4, set.first());
}
/** headSet returns set with keys in requested range */
public void testHeadSetContents() {
NavigableSet set = set5();
SortedSet sm = set.headSet(four);
assertTrue(sm.contains(one));
assertTrue(sm.contains(two));
assertTrue(sm.contains(three));
assertFalse(sm.contains(four));
assertFalse(sm.contains(five));
Iterator i = sm.iterator();
Object k;
k = (Integer) (i.next());
assertEquals(one, k);
k = (Integer) (i.next());
assertEquals(two, k);
k = (Integer) (i.next());
assertEquals(three, k);
assertFalse(i.hasNext());
sm.clear();
assertTrue(sm.isEmpty());
assertEquals(2, set.size());
assertEquals(four, set.first());
}
public void testKeyDeleteRandomUniform() throws Exception {
NavigableSet<Integer> keys = new TreeSet<Integer>();
for (int i = 0; i < KEYS_COUNT; i++) {
sbTree.put(i, createValue(i, OSBTreeValuePage.MAX_BINARY_VALUE_SIZE + 4));
keys.add(i);
doReset();
}
Iterator<Integer> keysIterator = keys.iterator();
while (keysIterator.hasNext()) {
int key = keysIterator.next();
if (key % 3 == 0) {
sbTree.remove(key);
keysIterator.remove();
}
doReset();
}
Assert.assertEquals(sbTree.firstKey(), keys.first());
doReset();
Assert.assertEquals(sbTree.lastKey(), keys.last());
doReset();
for (int key : keys) {
if (key % 3 == 0) {
Assert.assertNull(sbTree.get(key));
} else {
Assert.assertEquals(
sbTree.get(key), createValue(key, OSBTreeValuePage.MAX_BINARY_VALUE_SIZE + 4));
}
doReset();
}
}
RandomSelection select(boolean narrow, boolean mixInNotPresentItems, boolean permitReversal) {
ThreadLocalRandom random = ThreadLocalRandom.current();
NavigableSet<Integer> canonicalSet = this.canonical;
BTreeSet<Integer> testAsSet = this.test;
List<Integer> canonicalList = new ArrayList<>(canonicalSet);
BTreeSet<Integer> testAsList = this.test;
Assert.assertEquals(canonicalSet.size(), testAsSet.size());
Assert.assertEquals(canonicalList.size(), testAsList.size());
// sometimes select keys first, so we cover full range
List<Integer> allKeys = randomKeys(canonical, mixInNotPresentItems);
List<Integer> keys = allKeys;
int narrowCount = random.nextInt(3);
while (narrow && canonicalList.size() > 10 && keys.size() > 10 && narrowCount-- > 0) {
boolean useLb = random.nextBoolean();
boolean useUb = random.nextBoolean();
if (!(useLb | useUb)) continue;
// select a range smaller than the total span when we have more narrowing iterations left
int indexRange = keys.size() / (narrowCount + 1);
boolean lbInclusive = true;
Integer lbKey = canonicalList.get(0);
int lbKeyIndex = 0, lbIndex = 0;
boolean ubInclusive = true;
Integer ubKey = canonicalList.get(canonicalList.size() - 1);
int ubKeyIndex = keys.size(), ubIndex = canonicalList.size();
if (useLb) {
lbKeyIndex = random.nextInt(0, indexRange - 1);
Integer candidate = keys.get(lbKeyIndex);
if (useLb = (candidate > lbKey && candidate <= ubKey)) {
lbInclusive = random.nextBoolean();
lbKey = keys.get(lbKeyIndex);
lbIndex = Collections.binarySearch(canonicalList, lbKey);
if (lbIndex >= 0 && !lbInclusive) lbIndex++;
else if (lbIndex < 0) lbIndex = -1 - lbIndex;
}
}
if (useUb) {
ubKeyIndex =
random.nextInt(Math.max(lbKeyIndex, keys.size() - indexRange), keys.size() - 1);
Integer candidate = keys.get(ubKeyIndex);
if (useUb = (candidate < ubKey && candidate >= lbKey)) {
ubInclusive = random.nextBoolean();
ubKey = keys.get(ubKeyIndex);
ubIndex = Collections.binarySearch(canonicalList, ubKey);
if (ubIndex >= 0 && ubInclusive) {
ubIndex++;
} else if (ubIndex < 0) ubIndex = -1 - ubIndex;
}
}
if (ubIndex < lbIndex) {
ubIndex = lbIndex;
ubKey = lbKey;
ubInclusive = false;
}
canonicalSet =
!useLb
? canonicalSet.headSet(ubKey, ubInclusive)
: !useUb
? canonicalSet.tailSet(lbKey, lbInclusive)
: canonicalSet.subSet(lbKey, lbInclusive, ubKey, ubInclusive);
testAsSet =
!useLb
? testAsSet.headSet(ubKey, ubInclusive)
: !useUb
? testAsSet.tailSet(lbKey, lbInclusive)
: testAsSet.subSet(lbKey, lbInclusive, ubKey, ubInclusive);
keys = keys.subList(lbKeyIndex, ubKeyIndex);
canonicalList = canonicalList.subList(lbIndex, ubIndex);
testAsList = testAsList.subList(lbIndex, ubIndex);
Assert.assertEquals(canonicalSet.size(), testAsSet.size());
Assert.assertEquals(canonicalList.size(), testAsList.size());
}
// possibly restore full set of keys, to test case where we are provided existing keys that
// are out of bounds
if (keys != allKeys && random.nextBoolean()) keys = allKeys;
Comparator<Integer> comparator = naturalOrder();
if (permitReversal && random.nextBoolean()) {
if (allKeys != keys) keys = new ArrayList<>(keys);
if (canonicalSet != canonical) canonicalList = new ArrayList<>(canonicalList);
Collections.reverse(keys);
Collections.reverse(canonicalList);
testAsList = testAsList.descendingSet();
canonicalSet = canonicalSet.descendingSet();
testAsSet = testAsSet.descendingSet();
comparator = reverseOrder();
}
Assert.assertEquals(canonicalSet.size(), testAsSet.size());
Assert.assertEquals(canonicalList.size(), testAsList.size());
if (!canonicalSet.isEmpty()) {
Assert.assertEquals(canonicalSet.first(), canonicalList.get(0));
Assert.assertEquals(canonicalSet.last(), canonicalList.get(canonicalList.size() - 1));
Assert.assertEquals(canonicalSet.first(), testAsSet.first());
Assert.assertEquals(canonicalSet.last(), testAsSet.last());
Assert.assertEquals(canonicalSet.first(), testAsList.get(0));
Assert.assertEquals(canonicalSet.last(), testAsList.get(testAsList.size() - 1));
}
return new RandomSelection(
keys, canonicalSet, testAsSet, canonicalList, testAsList, comparator);
}
/**
* Attempts to find an EC number for every domain in {@code census}, skipping those which are
* already listed in this ECFinder. Prints to {@code output} periodically.
*/
public void buildFromCensus(CensusResultList census, File output) {
ScopDatabase scop = ScopFactory.getSCOP();
CensusSignificance sig = CensusSignificanceFactory.forCeSymmOrd();
int i = 0;
for (CensusResult result : census.getEntries()) {
try {
String scopId = result.getId();
if (this.ecsByAsymmDomain.containsKey(scopId)
|| this.ecsBySymmDomain.containsKey(scopId)
|| ecsByUnknownDomain.contains(scopId)) {
continue;
}
ScopDomain domain = scop.getDomainByScopID(scopId);
if (domain == null) {
logger.error(result.getId() + " is null");
continue;
}
// got a result; what's its EC?
// we need to find the correct polymers corresponding to the domain
// note that this still isn't perfect, since we don't know what part of the polymer actually
// does the function
List<RCSBPolymer> polymers = new ArrayList<RCSBPolymer>();
Set<String> chains = domain.getChains();
RCSBDescription desc = RCSBDescriptionFactory.get(domain.getPdbId());
for (RCSBPolymer polymer : desc.getPolymers()) {
for (Character chain : polymer.getChains()) {
if (chains.contains(String.valueOf(chain))) {
polymers.add(polymer);
break;
}
}
}
// get the EC numbers
// use a set because we don't want > 1 just because we have duplicates
NavigableSet<String> ecs = new TreeSet<String>();
for (RCSBPolymer polymer : polymers) {
String ec = polymer.getEnzClass();
if (ec != null) ecs.add(ec);
}
if (ecs.size() == 1) {
String ec = ecs.first();
if (sig.isSignificant(result)) {
ecsBySymmDomain.put(scopId, ec);
} else {
ecsByAsymmDomain.put(scopId, ec);
}
} else if (ecs.size() > 1) {
logger.info(
"Found different EC numbers for "
+ domain.getScopId()); // technically, this doesn't mean anything's wrong
} else {
// logger.debug("Didn't find EC for " + scopId);
ecsByUnknownDomain.add(scopId);
}
if (i > 0 && i % 100 == 0) {
print(output);
logger.debug("Working on #" + i);
}
} catch (RuntimeException e) {
e.printStackTrace();
logger.error(e);
} finally {
i++;
}
}
}