code stringlengths 73 34.1k | label stringclasses 1
value |
|---|---|
private void validate() {
if ((this.segments.length < 0) && (!this.snapshot)) {
throw new IllegalArgumentException("segments.length:" + Integer.valueOf(this.segments.length));
}
for (int i = 0; i < this.segments.length; i++) {
if (this.segments[i] < 0) {
throw new IllegalArgumentExcepti... | java |
public static Integer computeGrammarSize(GrammarRules rules, Integer paaSize) {
// The final grammar's size in BYTES
//
int res = 0;
// The final size is the sum of the sizes of all rules
//
for (GrammarRuleRecord r : rules) {
String ruleStr = r.getRuleString();
String[] tokens = r... | java |
public static GrammarRules performPruning(double[] ts, GrammarRules grammarRules) {
RulePruningAlgorithm pruner = new RulePruningAlgorithm(grammarRules, ts.length);
pruner.pruneRules();
return pruner.regularizePrunedRules();
} | java |
public static double computeCover(boolean[] cover) {
int covered = 0;
for (boolean i : cover) {
if (i) {
covered++;
}
}
return (double) covered / (double) cover.length;
} | java |
private boolean compatible(int i, int j, Set<Integer> T[][]) {
if(s2comp[i] != s2comp[j]) return false;
for(int k = 0; k < nbLabels; k++) {
if(! T[i][k].equals(T[j][k])) return false;
}
return true;
} | java |
public boolean register(E e, String name) {
if (resolve.containsKey(name)) {
return false;
}
resolve.put(name, e);
rev.put(e, name);
return true;
} | java |
@Override
public boolean substituteVM(VM curId, VM nextId) {
if (VM.TYPE.equals(elemId)) {
if (rev.containsKey(nextId)) {
//the new id already exists. It is a failure scenario.
return false;
}
String fqn = rev.remove(curId);
if... | java |
@SuppressWarnings("unchecked")
public static NamingService<VM> getVMNames(Model mo) {
return (NamingService<VM>) mo.getView(ID + VM.TYPE);
} | java |
@SuppressWarnings("unchecked")
public static NamingService<Node> getNodeNames(Model mo) {
return (NamingService<Node>) mo.getView(ID + Node.TYPE);
} | java |
public boolean applyEvents(Hook k, Model i) {
for (Event n : getEvents(k)) {
if (!n.apply(i)) {
return false;
}
}
return true;
} | java |
public boolean addEvent(Hook k, Event n) {
Set<Event> l = events.get(k);
if (l == null) {
l = new HashSet<>();
events.put(k, l);
}
return l.add(n);
} | java |
public Set<Event> getEvents(Hook k) {
Set<Event> l = events.get(k);
return l == null ? Collections.emptySet() : l;
} | java |
@Override
public void addDim(int c, int[] cUse, IntVar[] dUse, int[] alias) {
capacities.add(c);
cUsages.add(cUse);
dUsages.add(dUse);
aliases.add(alias);
} | java |
@Override
public boolean beforeSolve(ReconfigurationProblem r) {
super.beforeSolve(r);
for (int i = 0; i < aliases.size(); i++) {
int capa = capacities.get(i);
int[] alias = aliases.get(i);
int[] cUse = cUsages.get(i);
int[] dUses = new int[dUsages.get... | java |
public static List<ChocoView> resolveDependencies(Model mo, List<ChocoView> views, Collection<String> base) throws SchedulerException {
Set<String> done = new HashSet<>(base);
List<ChocoView> remaining = new ArrayList<>(views);
List<ChocoView> solved = new ArrayList<>();
while (!remainin... | java |
public static List<RuleInterval> getZeroIntervals(int[] coverageArray) {
ArrayList<RuleInterval> res = new ArrayList<RuleInterval>();
int start = -1;
boolean inInterval = false;
int intervalsCounter = -1;
// slide over the array from left to the right
//
for (int i = 0; i < coverageArray.... | java |
public static double getCoverAsFraction(int seriesLength, GrammarRules rules) {
boolean[] coverageArray = new boolean[seriesLength];
for (GrammarRuleRecord rule : rules) {
if (0 == rule.ruleNumber()) {
continue;
}
ArrayList<RuleInterval> arrPos = rule.getRuleIntervals();
for (R... | java |
public static double getMeanRuleCoverage(int length, GrammarRules rules) {
// get the coverage array
//
int[] coverageArray = new int[length];
for (GrammarRuleRecord rule : rules) {
if (0 == rule.ruleNumber()) {
continue;
}
ArrayList<RuleInterval> arrPos = rule.getRuleIntervals... | java |
public void removeLayerFromCache(LayerImpl layer) {
if (layer.getId() != layerId) {
throw new IllegalStateException();
}
LayerCacheImpl layerCache = layerCacheRef.get();
if (layerCache != null) {
layerCache.remove(layer.getKey(), layer);
}
} | java |
public final V put(K key, V value) {
BinTreeNode<K,V> prev = null;
BinTreeNode<K,V> node = root;
int key_hash_code = key.hashCode();
while(node != null) {
prev = node;
if(key_hash_code < node.keyHashCode) {
node = node.left;
}
else {
if((key_hash_code > node.keyHashCode) || !node.key.equals... | java |
private final V remove_semi_leaf(BinTreeNode<K,V> node, BinTreeNode<K,V> prev,
int son, BinTreeNode<K,V> m) {
if(prev == null) {
root = m;
}
else {
if(son == 0)
prev.left = m;
else
prev.right = m;
}
return node.value;
} | java |
private final V finish_removal(BinTreeNode<K,V> node, BinTreeNode<K,V> prev,
int son, BinTreeNode<K,V> m) {
if(m != null) { // set up the links for m
m.left = node.left;
m.right = node.right;
}
if(prev == null)
root = m;
else {
if(son == 0)
prev.left = m;
else
prev.right = m;
}... | java |
private final BinTreeNode<K,V> extract_next(BinTreeNode<K,V> node) {
BinTreeNode<K,V> prev = node.right;
BinTreeNode<K,V> curr = prev.left;
if(curr == null) {
node.right = node.right.right;
return prev;
}
while(curr.left != null) {
prev = curr;
curr = curr.left;
}
prev.left = curr.right;
... | java |
public final Collection<V> values() {
return new AbstractCollection<V>() {
public Iterator<V> iterator() {
final Iterator<Map.Entry<K,V>> ite = entryIterator();
return new Iterator<V>() {
public boolean hasNext() { return ite.hasNext(); }
public void remove() { ite.remove(); }
public V ... | java |
public final Set<Map.Entry<K,V>> entrySet() {
return new AbstractSet<Map.Entry<K,V>>() {
public Iterator<Map.Entry<K,V>> iterator() {
return entryIterator();
}
public int size() {
return size;
}
};
} | java |
public final Set<K> keySet() {
return new AbstractSet<K>() {
public Iterator<K> iterator() {
final Iterator<Map.Entry<K,V>> ite = entryIterator();
return new Iterator<K>() {
public boolean hasNext() { return ite.hasNext(); }
public void remove() { ite.remove(); }
public K next() ... | java |
public void processChildren(Node node) {
for (Node cursor = node.getFirstChild(); cursor != null; cursor = cursor.getNext()) {
if (cursor.getType() == Token.CALL) {
// The node is a function or method call
Node name = cursor.getFirstChild();
if (name != null && name.getType() == Token.NAME && // n... | java |
public List<IntVar> getIncoming(Node n) {
List<IntVar> l = incoming.get(n);
if (l == null) {
l = Collections.emptyList();
}
return l;
} | java |
public List<IntVar> getOutgoing(Node n) {
List<IntVar> l = outgoings.get(n);
if (l == null) {
l = Collections.emptyList();
}
return l;
} | java |
private void checkModel(Model mo, boolean start) throws SatConstraintViolationException {
for (SatConstraintChecker<?> c : checkers) {
if (start && !c.startsWith(mo)) {
SatConstraint cs = c.getConstraint();
if (cs != null) {
throw new DiscreteViola... | java |
private static JSONObject toJSON(Mapping c) {
JSONObject o = new JSONObject();
o.put("offlineNodes", nodesToJSON(c.getOfflineNodes()));
o.put("readyVMs", vmsToJSON(c.getReadyVMs()));
JSONObject ons = new JSONObject();
for (Node n : c.getOnlineNodes()) {
JSONObject w ... | java |
public void fillMapping(Model mo, JSONObject o) throws JSONConverterException {
Mapping c = mo.getMapping();
for (Node u : newNodes(mo, o, "offlineNodes")) {
c.addOfflineNode(u);
}
for (VM u : newVMs(mo, o, "readyVMs")) {
c.addReadyVM(u);
}
JSONObj... | java |
private static Set<Node> newNodes(Model mo, JSONObject o, String key) throws JSONConverterException {
checkKeys(o, key);
Object x = o.get(key);
if (!(x instanceof JSONArray)) {
throw new JSONConverterException("array expected at key '" + key + "'");
}
Set<Node> s = ne... | java |
private static Set<VM> newVMs(Model mo, JSONObject o, String key) throws JSONConverterException {
checkKeys(o, key);
Object x = o.get(key);
if (!(x instanceof JSONArray)) {
throw new JSONConverterException("array expected at key '" + key + "'");
}
Set<VM> s = new Has... | java |
public boolean add(String key, ModuleDepInfo info) {
if (info == null) {
throw new NullPointerException();
}
boolean modified = false;
ModuleDepInfo existing = get(key);
if (!containsKey(key) || existing != info) {
if (existing != null) {
modified = existing.add(info);
} else {
supe... | java |
public boolean addAll(ModuleDeps other) {
boolean modified = false;
for (Map.Entry<String, ModuleDepInfo> entry : other.entrySet()) {
modified |= add(entry.getKey(), new ModuleDepInfo(entry.getValue()));
}
return modified;
} | java |
public int minVMAllocation(int vmIdx, int v) {
int vv = Math.max(v, vmAllocation.get(vmIdx));
vmAllocation.set(vmIdx, vv);
return vv;
} | java |
public double capOverbookRatio(int nIdx, double d) {
if (d < 1) {
return ratios.get(nIdx);
}
double v = Math.min(ratios.get(nIdx), d);
ratios.set(nIdx, v);
return v;
} | java |
@Override
public boolean beforeSolve(ReconfigurationProblem p) throws SchedulerException {
for (VM vm : source.getMapping().getAllVMs()) {
int vmId = p.getVM(vm);
int v = getVMAllocation(vmId);
if (v < 0) {
int prevUsage = rc.getConsumption(vm);
... | java |
private boolean capHosting(int nIdx, int min, int nbZeroes) {
Node n = rp.getNode(nIdx);
double capa = getSourceResource().getCapacity(n) * getOverbookRatio(nIdx)/*.getLB()*/;
int card = (int) (capa / min) + nbZeroes + 1;
if (card < source.getMapping().getRunningVMs(n).size()) {
// T... | java |
private void checkInitialSatisfaction() {
//Seems to me we don't support ratio change
for (Node n : rp.getSourceModel().getMapping().getOnlineNodes()) {
int nIdx = rp.getNode(n);
double ratio = getOverbookRatio(nIdx)/*.getLB()*/;
double capa = getSourceResource().getC... | java |
public static TObjectIntMap<VM> getWeights(ReconfigurationProblem rp, List<CShareableResource> rcs) {
Model mo = rp.getSourceModel();
int[] capa = new int[rcs.size()];
int[] cons = new int[rcs.size()];
TObjectIntMap<VM> cost = new TObjectIntHashMap<>();
for (Node n : mo.getMappi... | java |
private boolean distinctVMStates() {
boolean ok = vms.size() == running.size() + sleeping.size() + ready.size() + killed.size();
//It is sure there is no solution as a VM cannot have multiple destination state
Map<VM, VMState> states = new HashMap<>();
for (VM v : running) {
... | java |
@Override
@SuppressWarnings("squid:S3346")
public ReconfigurationPlan buildReconfigurationPlan(Solution s, Model src) throws SchedulerException {
ReconfigurationPlan plan = new DefaultReconfigurationPlan(src);
for (NodeTransition action : nodeActions) {
action.insertActions(s, plan);... | java |
private void defaultHeuristic() {
IntStrategy intStrat = Search.intVarSearch(new FirstFail(csp), new IntDomainMin(), csp.retrieveIntVars(true));
SetStrategy setStrat = new SetStrategy(csp.retrieveSetVars(), new InputOrder<>(csp), new SetDomainMin(), true);
RealStrategy realStrat = new RealStrate... | java |
private void makeCardinalityVariables() {
vmsCountOnNodes = new ArrayList<>(nodes.size());
int nbVMs = vms.size();
for (Node n : nodes) {
vmsCountOnNodes.add(csp.intVar(makeVarLabel("nbVMsOn('", n, "')"), 0, nbVMs, true));
}
vmsCountOnNodes = Collections.unmodifiableL... | java |
@Override
public Iterator<Action> iterator() {
Set<Action> sorted = new TreeSet<>(startFirstComparator);
sorted.addAll(actions);
return sorted.iterator();
} | java |
private void addDirectionalEdge(Edge e) {
if (edgeAccess.getCapacity() < getEdgeIndex(edgePos) + EDGE_SIZE)
edgeAccess.ensureCapacity(edgeAccess.getCapacity() + INITIAL_EDGE_FILE_SIZE);
long fromId = nodIdMapping.get(e.getFromNodeId());
long toId = nodIdMapping.get(e.getToNodeId());
long fromIndex... | java |
public static DefaultConstraintsCatalog newBundle() {
DefaultConstraintsCatalog c = new DefaultConstraintsCatalog();
c.add(new AmongBuilder());
c.add(new BanBuilder());
c.add(new ResourceCapacityBuilder());
c.add(new RunningCapacityBuilder());
c.add(new FenceBuilder());
... | java |
public boolean add(SatConstraintBuilder c) {
if (this.builders.containsKey(c.getIdentifier())) {
return false;
}
this.builders.put(c.getIdentifier(), c);
return true;
} | java |
public int compare(T o1, T o2) {
if(o1 == o2) return 0;
String str1 = (o1 == null) ? "null" : o1.toString();
String str2 = (o2 == null) ? "null" : o2.toString();
return str1.compareTo(str2);
} | java |
public static CaseSyntax of(Character separator, CaseConversion allCharCase) {
return of(separator, allCharCase, allCharCase, allCharCase);
} | java |
protected void registerDefaultDatatypes() {
registerStandardDatatype(String.class);
registerStandardDatatype(Boolean.class);
registerStandardDatatype(Character.class);
registerStandardDatatype(Currency.class);
registerCustomDatatype(Datatype.class); // internal trick...
registerNumberDatatypes(... | java |
public void setExtraDatatypes(List<String> datatypeList) {
getInitializationState().requireNotInitilized();
for (String fqn : datatypeList) {
registerCustomDatatype(fqn);
}
} | java |
public static CompressionCodec getGzipCodec(Configuration conf) {
try {
return (CompressionCodec) ReflectionUtils.newInstance(
conf.getClassByName("org.apache.hadoop.io.compress.GzipCodec").asSubclass(CompressionCodec.class),
conf);
} catch (ClassNotFoundExcep... | java |
public static boolean isNearMultipleBorders(@Nonnull final Point point, @Nonnull final Territory territory) {
checkDefined("point", point);
if (territory != Territory.AAA) {
final int territoryNumber = territory.getNumber();
if (territory.getParentTerritory() != null) {
... | java |
public void enqueue(RepairDigramRecord digramRecord) {
// System.out.println("before == " + this.toString());
// if the same key element is in the queue - something went wrong with tracking...
if (elements.containsKey(digramRecord.str)) {
throw new IllegalArgumentException(
"Element wit... | java |
public RepairDigramRecord get(String key) {
RepairQueueNode el = this.elements.get(key);
if (null != el) {
return el.payload;
}
return null;
} | java |
private void removeNodeFromList(RepairQueueNode el) {
// the head case
//
if (null == el.prev) {
if (null != el.next) {
this.head = el.next;
this.head.prev = null;
el=null;
}
else {
// can't happen? yep. if there is only one element exists...
this.he... | java |
public int evaluate(Model mo, Class<? extends Action> a, Element e) throws SchedulerException {
ActionDurationEvaluator<Element> ev = durations.get(a);
if (ev == null) {
throw new SchedulerModelingException(null, "Unable to estimate the duration of action '" + a.getSimpleName() + "' related ... | java |
protected void parseParameter(String parameter, CliParserState parserState, CliParameterConsumer parameterConsumer) {
if (parserState.isOptionsComplete()) {
// no more options (e.g. --foo), only arguments from here
List<CliArgumentContainer> argumentList = this.cliState.getArguments(parserState.require... | java |
private int printHelpOptions(CliOutputSettings settings, Map<CliOption, CliOptionHelpInfo> option2HelpMap, StringBuilder parameters,
Collection<CliOptionContainer> modeOptions) {
int maxOptionColumnWidth = 0;
for (CliOptionContainer option : modeOptions) {
CliOption cliOption = option.getOption();
... | java |
public boolean contains(Object o) {
for(T e : elemArray) {
if((o == e) || ((o != null) && o.equals(e))) {
return true;
}
}
return false;
} | java |
public Set<Action> getDependencies(Action a) {
if (!demandingNodes.containsKey(a)) {
return Collections.emptySet();
}
Node n = demandingNodes.get(a);
Set<Action> allActions = getFreeings(n);
Set<Action> pre = new HashSet<>();
for (Action action : allActions) {... | java |
public static boolean isExplodeRequires(HttpServletRequest request) {
if (isIncludeRequireDeps(request)) {
// don't expand require deps if we're including them in the response.
return false;
}
boolean result = false;
IAggregator aggr = (IAggregator)request.getAttribute(IAggregator.AGGREGATOR_REQATTR... | java |
public static boolean isHasFiltering(HttpServletRequest request) {
IAggregator aggr = (IAggregator)request.getAttribute(IAggregator.AGGREGATOR_REQATTRNAME);
IOptions options = aggr.getOptions();
return (options != null) ? !options.isDisableHasFiltering() : true;
} | java |
@Nonnull
static Boundary createBoundaryForTerritoryRecord(final int territoryRecord) {
return new Boundary(
DATA_MODEL.getLatMicroDegMin(territoryRecord), DATA_MODEL.getLonMicroDegMin(territoryRecord),
DATA_MODEL.getLatMicroDegMax(territoryRecord), DATA_MODEL.getLonMicroDegMa... | java |
boolean containsPoint(@Nonnull final Point p) {
if (!p.isDefined()) {
return false;
}
final int latMicroDeg = p.getLatMicroDeg();
if ((latMicroDegMin > latMicroDeg) || (latMicroDeg >= latMicroDegMax)) {
return false;
}
final int lonMicroDeg = p.get... | java |
public static List<Precedence> newPrecedence(VM vmBefore, Collection<VM> vmsAfter) {
return newPrecedence(Collections.singleton(vmBefore), vmsAfter);
} | java |
public static List<Precedence> newPrecedence(Collection<VM> vmsBefore, VM vmAfter) {
return newPrecedence(vmsBefore, Collections.singleton(vmAfter));
} | java |
public static List<Precedence> newPrecedence(Collection<VM> vmsBefore, Collection<VM> vmsAfter) {
List<Precedence> l = new ArrayList<>(vmsBefore.size() * vmsAfter.size());
for (VM vmb : vmsBefore) {
for (VM vma : vmsAfter) {
l.add(new Precedence(vmb, vma));
}
... | java |
private ESat isConsistent() {
int[][] l = new int[nbDims][nbBins];
for (int i = 0; i < bins.length; i++) {
if (bins[i].isInstantiated()) {
for (int d = 0; d < nbDims; d++) {
int v = bins[i].getValue();
l[d][v] += iSizes[d][i];
... | java |
@Override
public int getPropagationConditions(int idx) {
return idx < bins.length ? IntEventType.all() : IntEventType.BOUND.getMask() + IntEventType.INSTANTIATE.getMask();
} | java |
private void computeSumItemSizes() {
for (int d = 0; d < nbDims; d++) {
long sum = 0;
for (int i = 0; i < iSizes[d].length; i++) {
sum += iSizes[d][i];
}
this.sumISizes[d] = sum;
}
} | java |
@Override
public void clearCached(ICacheManager mgr) {
Map<String, CacheEntry> moduleBuilds;
synchronized (this) {
moduleBuilds = _moduleBuilds;
_moduleBuilds = null;
}
if (moduleBuilds != null) {
for (Map.Entry<String, CacheEntry> entry : moduleBuilds.entrySet()) {
entry.getValue().delet... | java |
public static SplittableElementSet<VM> newVMIndex(Collection<VM> c, TIntIntHashMap idx) {
return new SplittableElementSet<>(c, idx);
} | java |
public static SplittableElementSet<Node> newNodeIndex(Collection<Node> c, TIntIntHashMap idx) {
return new SplittableElementSet<>(c, idx);
} | java |
public boolean forEachPartition(IterateProcedure<E> p) {
int curIdx = index.get(values.get(0).id());
int from;
int to;
for (from = 0, to = 0; to < values.size(); to++) {
int cIdx = index.get(values.get(to).id());
if (curIdx != cIdx) {
if (!p.extrac... | java |
public Set<E> getSubSet(int k) {
int from = -1;
//TODO: very bad. Bounds should be memorized
for (int x = 0; x < values.size(); x++) {
int cIdx = index.get(values.get(x).id());
if (cIdx == k && from == -1) {
from = x;
}
if (from >= ... | java |
public List<ElementSubSet<E>> getPartitions() {
final List<ElementSubSet<E>> partitions = new ArrayList<>();
forEachPartition((idx, key, from, to) -> {
partitions.add(new ElementSubSet<>(SplittableElementSet.this, key, from, to));
return true;
});
return partition... | java |
public ICacheKeyGenerator combine(ICacheKeyGenerator otherKeyGen) {
if (this.equals(otherKeyGen)) {
return this;
}
@SuppressWarnings("unchecked")
AbstractCollectionCacheKeyGenerator<T> other = (AbstractCollectionCacheKeyGenerator<T>)otherKeyGen;
if (isProvisional() && other.isProvisional()) {
// ... | java |
public static final void setReader(String format, TreeReader reader) {
String key = format.toLowerCase();
readers.put(key, reader);
if (JSON.equals(key)) {
cachedJsonReader = reader;
}
} | java |
protected int resolveInclude() throws XMLStreamException {
// we are no more in fallback mode
this.fallback = false;
this.depth++;
int eventType = -1;
// read attributes...
String href = getAttributeValue(null, "href");
LOGGER.trace("Resolving xi:include to href {}", href);
String xpoin... | java |
protected void closeInitialInclude() throws XMLStreamException {
LOGGER.trace("Closing xi:include");
int eventType = -1;
// we ascend the XML until the initial include is closed.
while (this.depth > 0) {
eventType = this.mainReader.next();
if (eventType == XMLStreamConstants.START_ELEMENT) ... | java |
public boolean read()
{
if (state == State.READING_FRAME_SIZE)
{
// try to read the frame size completely
if (!internalRead(frameSizeBuffer))
return false;
// if the frame size has been read completely, then prepare to read the
// actu... | java |
public boolean write()
{
assert state == State.WRITING;
boolean writeFailed = false;
try
{
if (response.streamTo(transport) < 0)
{
writeFailed = true;
return false;
}
else if (!response.isFullyStreamed(... | java |
public void changeSelectInterests()
{
switch (state)
{
case READY_TO_WRITE: // set the OP_WRITE interest
state = State.WRITING;
break;
case READY_TO_READ_FRAME_SIZE:
state = State.READING_FRAME_SIZE;
break;
... | java |
public void invoke()
{
assert state == State.READ_FRAME_COMPLETE : "Invoke called in invalid state: " + state;
TTransport inTrans = getInputTransport();
TProtocol inProt = thriftFactories.inputProtocolFactory.getProtocol(inTrans);
TProtocol outProt = thriftFactories.outputProtocolFa... | java |
private boolean internalRead(Buffer buffer)
{
try
{
return !(buffer.readFrom(transport) < 0);
}
catch (IOException e)
{
logger.warn("Got an IOException in internalRead!", e);
return false;
}
} | java |
public void close()
{
freeDataBuffer();
frameSizeBuffer.free();
transport.close();
if (response != null)
response.close();
} | java |
public ArrayList<SameLengthMotifs> classifyMotifs(double lengthThreshold,
GrammarRules grammarRules) {
// reset vars
ArrayList<SameLengthMotifs> allClassifiedMotifs = new ArrayList<SameLengthMotifs>();
// down to business
ArrayList<SAXMotif> allMotifs = getAllMotifs(grammarRules);
... | java |
protected ArrayList<SAXMotif> getAllMotifs(GrammarRules grammarRules) {
// result
ArrayList<SAXMotif> allMotifs = new ArrayList<SAXMotif>();
int ruleNumber = grammarRules.size();
// iterate over all rules
for (int i = 0; i < ruleNumber; i++) {
// iterate over all segments/motifs/... | java |
protected ArrayList<SameLengthMotifs> removeOverlappingInSimiliar(
ArrayList<SameLengthMotifs> allClassifiedMotifs, GrammarRules grammarRules, double[] ts,
double thresouldCom) {
ArrayList<SAXMotif> motifsBeDeleted = new ArrayList<SAXMotif>();
SAXPointsNumber[] pointsNumberRemoveStrategy = c... | java |
protected boolean decideRemove(SAXMotif motif1, SAXMotif motif2,
SAXPointsNumber[] pointsNumberRemoveStrategy) {
// motif1 details
int motif1Start = motif1.getPos().getStart();
int motif1End = motif1.getPos().getEnd() - 1;
int length1 = motif1End - motif1Start;
// motif2 details
... | java |
protected ArrayList<SameLengthMotifs> refinePatternsByClustering(GrammarRules grammarRules,
double[] ts, ArrayList<SameLengthMotifs> allClassifiedMotifs, double fractionTopDist) {
DistanceComputation dc = new DistanceComputation();
double[] origTS = ts;
ArrayList<SameLengthMotifs> newAllClassified... | java |
private ArrayList<String[]> findCluster(Cluster cluster, double cutDist, int minPatternPerCls) {
ArrayList<String[]> clusterTSIdx = new ArrayList<String[]>();
if (cluster.getDistance() != null) {
// if (cluster.getDistance() > cutDist) {
if (cluster.getDistanceValue() > cutDist) {
i... | java |
private ArrayList<String> getNameInCluster(Cluster cluster) {
ArrayList<String> itemsInCluster = new ArrayList<String>();
String nodeName;
if (cluster.isLeaf()) {
nodeName = cluster.getName();
itemsInCluster.add(nodeName);
}
else {
// String[] clusterName = cluster.getNam... | java |
private ArrayList<SameLengthMotifs> SeparateMotifsByClustering(ArrayList<String[]> clusterTSIdx,
SameLengthMotifs sameLenMotifs) {
ArrayList<SameLengthMotifs> newResult = new ArrayList<SameLengthMotifs>();
if (clusterTSIdx.size() > 1) {
ArrayList<SAXMotif> subsequences = sameLenMotifs.getSameLen... | java |
@Override
public BtrpOperand go(BtrPlaceTree parent) {
String cname = getText();
if (catalog == null) {
return ignoreError("No constraints available");
}
SatConstraintBuilder b = catalog.getConstraint(cname);
if (b == null) {
ignoreError("Unknown cons... | java |
public static Process runProcess(String... cmdParts) throws IOException {
return new ProcessBuilder(buildCommandline(cmdParts))
.inheritIO()
.start();
} | java |
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