下面列出了org.apache.commons.lang3.tuple.Pair#getRight ( ) 实例代码，或者点击链接到github查看源代码，也可以在右侧发表评论。
private String getFlowColumnText(IndexFlow f, int col) {
if (f.flow == null)
return null;
Pair<String, String> category = Labels.getCategory(f.flow);
switch (col) {
case 0:
return Labels.name(f);
case 1:
return category.getLeft();
case 2:
return category.getRight();
case 3:
return Numbers.format(getAmount(f));
case 4:
return Labels.refUnit(f);
default:
return null;
}
}
@Test
public void testIncreaseRestrictedCategory() {
List<TicketCategoryModification> categories = Collections.singletonList(
new TicketCategoryModification(null, "default", 10,
new DateTimeModification(LocalDate.now(), LocalTime.now()),
new DateTimeModification(LocalDate.now(), LocalTime.now()),
DESCRIPTION, BigDecimal.TEN, true, "", true, null, null, null, null, null, 0, null, null, AlfioMetadata.empty()));
Pair<Event, String> pair = initEvent(categories, organizationRepository, userManager, eventManager, eventRepository);
Event event = pair.getLeft();
String username = pair.getRight();
TicketCategory category = ticketCategoryRepository.findAllTicketCategories(event.getId()).get(0);
Map<String, String> categoryDescription = ticketCategoryDescriptionRepository.descriptionForTicketCategory(category.getId());
TicketCategoryModification tcm = new TicketCategoryModification(category.getId(), category.getName(), 11,
DateTimeModification.fromZonedDateTime(category.getUtcInception()),
DateTimeModification.fromZonedDateTime(category.getUtcExpiration()),
categoryDescription, category.getPrice(), true, "", true, null, null, null, null, null, 0, null, null, AlfioMetadata.empty());
Result<TicketCategory> result = eventManager.updateCategory(category.getId(), event, tcm, username);
assertTrue(result.isSuccess());
assertEquals(11, ticketRepository.countFreeTickets(event.getId(), category.getId()).intValue());
}
@Test
public void testGCCorrection() {
final int numSamples = 5;
final int numTargets = 10000;
final Pair<ReadCountCollection, double[]> data = GCBiasSimulatedData.simulatedData(numTargets, numSamples);
final ReadCountCollection rcc1 = data.getLeft();
final double[] gcContentByTarget = data.getRight();
final ReadCountCollection correctedCounts1 = GCCorrector.correctCoverage(rcc1, gcContentByTarget);
final double[] correctedNoiseBySample = GATKProtectedMathUtils.columnStdDevs(correctedCounts1.counts());
Arrays.stream(correctedNoiseBySample).forEach(x -> Assert.assertTrue(x < 0.02));
//check that GC correction is approximately idempotent -- if you correct again, very little should happen
final ReadCountCollection correctedCounts2 = GCCorrector.correctCoverage(correctedCounts1, gcContentByTarget);
final double change1 = correctedCounts1.counts().subtract(rcc1.counts()).getFrobeniusNorm();
final double change2 = correctedCounts2.counts().subtract(correctedCounts1.counts()).getFrobeniusNorm();
Assert.assertTrue(change2 < change1 / 10);
}
@Test
public void incrementalMessagesMustBeSentToClientsIfThereAreNoGaps() throws Exception {
int lastMsgSeqNumProcessed = 1000;
sendInitialMBOSnapshot(lastMsgSeqNumProcessed);
final MdpFeedContext incrementContext = new MdpFeedContext(Feed.A, FeedType.I);
final MdpPacket mdpPacketWithIncrement = MdpPacket.instance();
for(int i = lastMsgSeqNumProcessed +1; i < lastMsgSeqNumProcessed + 10; i++) {
ByteBuffer mboSnapshotTestMessage = ModelUtils.getMBOIncrementTestMessage(i);
mdpPacketWithIncrement.wrapFromBuffer(mboSnapshotTestMessage);
gapChannelController.handleIncrementalPacket(incrementContext, mdpPacketWithIncrement);
Pair<MdpFeedContext, MdpPacket> incrementPair = testChannelController.nextIncrementalMessage();
assertNotNull(incrementPair);
MdpPacket mdpPacket = incrementPair.getRight();
assertEquals(i, mdpPacket.getMsgSeqNum());
}
}
public boolean updatePoint(final String lockID) throws Exception {
final Pair<CloseableHttpClient, HttpClientContext> clientAndContext = createClientAndContext();
final CloseableHttpClient httpclient = clientAndContext.getLeft();
final HttpClientContext context = clientAndContext.getRight();
try {
final HttpPost command = createWFSTransaction(httpclient, "1.1.0");
command.setEntity(new StringEntity(update));
final LinkedList<HttpResponse> capturedResponse = new LinkedList<>();
run(new Runnable() {
@Override
public void run() {
try {
capturedResponse.add(httpclient.execute(command, context));
} catch (final Exception e) {
throw new RuntimeException("update point client failed", e);
}
}
}, 500000);
final HttpResponse r = capturedResponse.getFirst();
return r.getStatusLine().getStatusCode() == Status.OK.getStatusCode();
} finally {
httpclient.close();
}
}
private void assertEqualVariantFiles(final File outputFile, final String eColiExpectedOut) {
// Get the actual data:
final Pair<VCFHeader, List<VariantContext>> actualVcfInfo = VariantContextTestUtils.readEntireVCFIntoMemory(outputFile.getAbsolutePath());
final List<VariantContext> actualVariantContexts = actualVcfInfo.getRight();
final VCFHeader actualVcfHeader = actualVcfInfo.getLeft();
final VCFInfoHeaderLine actualFuncotationHeaderLine = actualVcfHeader.getInfoHeaderLine(VcfOutputRenderer.FUNCOTATOR_VCF_FIELD_NAME);
// Get the expected data:
final Pair<VCFHeader, List<VariantContext>> expectedVcfInfo = VariantContextTestUtils.readEntireVCFIntoMemory(new File(eColiExpectedOut).getAbsolutePath());
final List<VariantContext> expectedVariantContexts = expectedVcfInfo.getRight();
final VCFHeader expectedVcfHeader = expectedVcfInfo.getLeft();
final VCFInfoHeaderLine expectedFuncotationHeaderLine = expectedVcfHeader.getInfoHeaderLine(VcfOutputRenderer.FUNCOTATOR_VCF_FIELD_NAME);
// Check that they're equal:
Assert.assertEquals(actualFuncotationHeaderLine, expectedFuncotationHeaderLine);
VariantContextTestUtils.assertEqualVariants(actualVariantContexts, expectedVariantContexts);
}
/**
*
* @param readCountsFile A simulated read counts file with GC bias effects
* @param targetsFile A simulated targets file with GC content annotation
*/
public static void makeGCBiasInputFiles(final Pair<ReadCountCollection, double[]> data,
final File readCountsFile, final File targetsFile) throws IOException {
final ReadCountCollection inputCounts = data.getLeft();
final double[] gcContentByTarget = data.getRight();
ReadCountCollectionUtils.write(readCountsFile, inputCounts);
final TargetWriter writer = new TargetWriter(targetsFile, Collections.singleton(TargetAnnotation.GC_CONTENT));
for (int i = 0; i < gcContentByTarget.length; i++) {
final Target unannotatedTarget = inputCounts.records().get(i).getTarget();
final TargetAnnotationCollection annotations = new TargetAnnotationCollection();
annotations.put(TargetAnnotation.GC_CONTENT, Double.toString(gcContentByTarget[i]));
final Target target = new Target(unannotatedTarget.getName(), unannotatedTarget.getInterval(), annotations);
writer.writeRecord(target);
}
writer.close();
}
/**
* Mocks the addition and removal of range highlighters for the given ranges to the given editor
* and file with the given text attributes.
*
* <p>When using this call, it is also advised to call {@link PowerMock#verify(Object...)} on
* <code>AbstractEditorAnnotation.class</code> to ensure that the {@link
* IExpectationSetters#atLeastOnce()} restriction is met.
*
* <p>{@link #prepareMockAddRemoveRangeHighlighters()} must be called before the first call to
* this methods and {@link #replayMockAddRemoveRangeHighlighters()} must be called after the last
* call to this method to replay the added mocking logic.
*
* @param ranges the ranges whose highlighter addition and removal to mock
* @param file the file of the annotation
* @param editor the editor of the annotation
* @param textAttributes the text attributes of the annotation
* @throws Exception see {@link PowerMock#expectPrivate(Object, Method, Object...)}
*/
private void mockAddRemoveRangeHighlighters(
List<Pair<Integer, Integer>> ranges, IFile file, Editor editor, TextAttributes textAttributes)
throws Exception {
for (Pair<Integer, Integer> range : ranges) {
int rangeStart = range.getLeft();
int rangeEnd = range.getRight();
RangeHighlighter rangeHighlighter = mockRangeHighlighter(rangeStart, rangeEnd);
PowerMock.expectPrivate(
AbstractEditorAnnotation.class,
"addRangeHighlighter",
rangeStart,
rangeEnd,
editor,
textAttributes,
file)
.andStubReturn(rangeHighlighter);
PowerMock.expectPrivate(
AbstractEditorAnnotation.class, "removeRangeHighlighter", editor, rangeHighlighter)
.atLeastOnce()
.asStub();
}
}
/**
* Tell if a template should be ignored for ISSN.
*
* @param template Template to be checked.
* @return True if the template should be ignored.
*/
public boolean shouldIgnoreTemplate(PageElementTemplate template) {
// Check parameters
if (template == null) {
return false;
}
// Check if the template should be ignored
Map<String, List<Pair<String, String>>> ignoreTemplates = version.getIgnoreTemplates();
String templateName = Page.normalizeTitle(template.getTemplateName());
List<Pair<String, String>> listParams = ignoreTemplates.get(templateName);
if (listParams == null) {
return false;
}
for (Pair<String, String> param : listParams) {
if (param.getLeft() != null) {
String paramValue = template.getParameterValue(param.getLeft());
if (param.getRight() != null) {
if ((paramValue != null) &&
(paramValue.trim().equals(param.getRight()))) {
return true; // Ignore all templates with this name and parameter set to a given value
}
} else {
if (paramValue != null) {
return true; // Ignore all templates with this name and parameter present
}
}
} else {
return true; // Ignore all templates with this name
}
}
return false;
}
public static String buildTaxonString(Pair<String, String> taxonRelPair) {
if (taxonRelPair != null) {
String taxId = "taxon:"+removePrefix(taxonRelPair.getLeft(), ':');
String rel = taxonRelPair.getRight();
if (rel != null) {
return rel+"("+taxId+")";
}
return taxId;
}
return null;
}
private void expandDeferredFinalStates(Deque<DetElement> finalQueue) {
HashBiMap<Integer, GallicWeight> outputStateIdToFinalSuffix = HashBiMap.create();
while (!finalQueue.isEmpty()) {
DetElement element = finalQueue.removeFirst();
for (GallicWeight gallicWeight : element.residual.getWeights()) {
// factorization is like a simple version of the divisor/divide calculation earlier
Pair<GallicWeight, GallicWeight> factorized = gallicSemiring.factorize(gallicWeight);
GallicWeight prefix = factorized.getLeft();
GallicWeight suffix = factorized.getRight();
if (!outputStateIdToFinalSuffix.inverse().containsKey(suffix)) {
// we don't have a synthetic state for this suffix yet
MutableState newOutputState = outputFst.newState();
outputStateIdToFinalSuffix.put(newOutputState.getId(), suffix);
if (suffix.getLabels().isEmpty()) {
// this suffix is a real final state, and there's no more work to do
newOutputState.setFinalWeight(suffix.getWeight());
} else {
// this suffix still has more labels to emit, so leave final weight as zero and enqueue for expansion
finalQueue.addLast(new DetElement(newOutputState.getId(), suffix));
}
}
Integer outputStateId = outputStateIdToFinalSuffix.inverse().get(suffix);
MutableState nextState = checkNotNull(outputFst.getState(outputStateId), "state should exist", outputStateId);
MutableState thisState = checkNotNull(outputFst.getState(element.inputStateId));
Preconditions.checkArgument(prefix.getLabels().size() == 1, "prefix size should be 1", prefix);
int oLabel = prefix.getLabels().get(0);
// note that openfst has an 'increment subsequent epsilons' feature so that these paths can still be
// guarenteed to be deterministic (with just multiple definitions of <EPS>; this feature would go here
// if we decide to implement it in the future
outputFst.addArc(thisState, this.outputEps, oLabel, nextState, prefix.getWeight());
}
}
}
public Pair<Experiment, Experiment> crossover(Experiment parentA, Experiment parentB) {
StringFeatureFactory featureFactory = (StringFeatureFactory)featureFactories.get(SEARCH_SERVER_URLS);
Pair<URL, URL> urls = featureFactory.crossover(
new URL(parentA.getSearchServerUrl()),
new URL(parentB.getSearchServerUrl()));
Pair<CustomHandler, CustomHandler> customHandlers = Pair.of(null, null);
if (featureFactories.get(CustomHandlerFactory.NAME) != null) {
customHandlers = featureFactories.get(CustomHandlerFactory.NAME)
.crossover(parentA.getCustomHandler(), parentB.getCustomHandler());
}
QueryFactory queryFactory = (QueryFactory)featureFactories.get(
QueryFactory.NAME);
Pair<Query, Query> queries = queryFactory.crossover(parentA.getQuery(), parentB.getQuery());
URL urlA = (MathUtil.RANDOM.nextFloat() <= 0.5) ? urls.getLeft()
: urls.getRight();
CustomHandler customHandlerA = (MathUtil.RANDOM.nextFloat() <= 0.5) ?
customHandlers.getLeft() : customHandlers.getRight();
Query queryA = (MathUtil.RANDOM.nextFloat() <= 0.5) ?
queries.getLeft() : queries.getRight();
Experiment childA = new Experiment("childA", urlA.toString(),
customHandlerA, queryA);
URL urlB = (MathUtil.RANDOM.nextFloat() <= 0.5) ? urls.getLeft() : urls.getRight();
CustomHandler customHandlerB = (MathUtil.RANDOM.nextFloat() <= 0.5) ?
customHandlers.getLeft() : customHandlers.getRight();
Query queryB = (MathUtil.RANDOM.nextFloat() <= 0.5) ?
queries.getLeft() : queries.getRight();
Experiment childB = new Experiment("childB", urlB.toString(),
customHandlerB, queryB);
addFilterQueries(childA);
addFilterQueries(childB);
return Pair.of(childA, childB);
}
@Override
public InternalDataStatistics<T, NumericHistogram, PartitionStatisticsQueryBuilder<NumericHistogram>> duplicate() {
final Pair<String, byte[]> pair =
PartitionStatisticsQueryBuilder.decomposeIndexAndPartitionFromId(extendedId);
return new RowRangeHistogramStatistics<>(
adapterId,
pair.getLeft(), // indexName
pair.getRight());
}
/**
* Generates a complete category GraphQL query with a selection of the given category identifier.
*
* @param identifier Category identifier, usually the category id
* @return GraphQL query as string
*/
public String generateQuery(String identifier) {
Pair<QueryQuery.CategoryArgumentsDefinition, CategoryTreeQueryDefinition> args = generateQueryArgs(identifier);
QueryQuery.CategoryArgumentsDefinition searchArgs = args.getLeft();
CategoryTreeQueryDefinition queryArgs = args.getRight();
return Operations.query(query -> query
.category(searchArgs, queryArgs)).toString();
}
private String toBase10String(final Quantity quantity) {
final BigDecimal amount = quantity.getNumber();
final long value = amount.unscaledValue().longValue();
final int exponent = -amount.scale();
final Pair<Long, Integer> resultAndTimes = removeFactorsForBase(value, 10);
final int postFactoringExponent = exponent + resultAndTimes.getRight();
final Pair<Long, Integer> valueAndExponent = ensureExponentIsMultipleOf3(resultAndTimes.getLeft(), postFactoringExponent);
return valueAndExponent.getLeft() + new SuffixFormatter().format(quantity.getFormat(), valueAndExponent.getRight());
}
public static Optional<Byte> getReadBaseQualityAtReferenceCoordinate(final GATKRead read, final int refCoord) {
if (refCoord < read.getStart() || read.getEnd() < refCoord) {
return Optional.empty();
}
final Pair<Integer, CigarOperator> offsetAndOperator = getReadIndexForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refCoord);
return (offsetAndOperator.getRight() != null && offsetAndOperator.getRight().consumesReadBases()) ?
Optional.of(read.getBaseQuality(offsetAndOperator.getLeft())) : Optional.empty();
}
public static Range fromPair(Pair<Double, Double> pair) {
return new Range(pair.getLeft(), pair.getRight());
}
@Nullable
private static Boolean entriesContainAllWithin(@Nonnull List<IndexEntry> entries, int maxDistance) {
if (entries.isEmpty()) {
return null;
}
List<List<Integer>> positionLists = getPositionsLists(entries);
if (positionLists.stream().anyMatch(List::isEmpty)) {
// Remove any empty lists. They indicate that the token is so prevalent
// that the position list information is not retained.
positionLists = positionLists.stream().filter(list -> !list.isEmpty()).collect(Collectors.toList());
if (positionLists.isEmpty()) {
// If they are all empty, then we assume that they were all close.
return Boolean.TRUE;
}
}
PriorityQueue<Pair<Integer, Iterator<Integer>>> minQueue = new PriorityQueue<>(positionLists.size(), Comparator.comparingInt(Pair::getLeft));
int max = Integer.MIN_VALUE;
for (List<Integer> positionList : positionLists) {
Iterator<Integer> positionIterator = positionList.iterator();
int value = positionIterator.next();
max = Math.max(max, value);
minQueue.add(Pair.of(value, positionIterator));
}
while (true) {
// Pop the smallest position off of the queue and check to see
// if it is within maxDistance of the current largest value.
Pair<Integer, Iterator<Integer>> minElem = minQueue.poll();
int min = minElem.getLeft();
if (max - min <= maxDistance) {
// Current span is within maximum allowed. Return true.
return Boolean.TRUE;
}
Iterator<Integer> minIterator = minElem.getRight();
if (minIterator.hasNext()) {
// Advance this iterator and place it back in the queue with the
// new associated value.
int nextValue = minIterator.next();
max = Math.max(max, nextValue);
minQueue.add(Pair.of(nextValue, minIterator));
} else {
// Exhausted one of the position lists. We didn't find a span that
// was less than or equal to the maximum allowed span.
break;
}
}
return Boolean.FALSE;
}
@Override
public void restoreState(Pair<Long, Long> state) {
currentCount.set(state.getLeft());
processed = state.getRight();
}
@Test
public void testInbreedingCoeffForMultiallelicVC() {
//make sure that compound hets (with no ref) don't add to het count
VariantContext test1 = makeVC("1", Arrays.asList(Aref, T, C),
makeG("s1",Aref,T,2530,0,7099,366,3056,14931),
makeG("s2",T,T,7099,2530,0,7099,366,3056,14931),
makeG("s3",T,C,7099,2530,7099,3056,0,14931),
makeG("s4",Aref,T,2530,0,7099,366,3056,14931),
makeG("s5",T,T,7099,2530,0,7099,366,3056,14931),
makeG("s6",Aref,T,2530,0,7099,366,3056,14931),
makeG("s7",T,T,7099,2530,0,7099,366,3056,14931),
makeG("s8",Aref,T,2530,0,7099,366,3056,14931),
makeG("s9",T,T,7099,2530,0,7099,366,3056,14931),
makeG("s10",Aref,T,2530,0,7099,366,3056,14931));
final Pair<Integer, Double> pair1 = InbreedingCoeff.calculateIC(test1, test1.getGenotypes());
final int count1 = pair1.getLeft();
final double ICresult1 = pair1.getRight();
Assert.assertEquals(count1, 10, "count1");
Assert.assertEquals(ICresult1, -0.3333333, DELTA_PRECISION, "Pass");
//make sure that hets with different alternate alleles all get counted
VariantContext test2 = makeVC("2", Arrays.asList(Aref, T, C),
makeG("s1",Aref,C,4878,1623,11297,0,7970,8847),
makeG("s2",Aref,T,2530,0,7099,366,3056,14931),
makeG("s3",Aref,T,3382,0,6364,1817,5867,12246),
makeG("s4",Aref,T,2488,0,9110,3131,9374,12505),
makeG("s5",Aref,C,4530,2006,18875,0,6847,23949),
makeG("s6",Aref,T,5325,0,18692,389,16014,24570),
makeG("s7",Aref,T,2936,0,29743,499,21979,38630),
makeG("s8",Aref,T,6902,0,8976,45,5844,9061),
makeG("s9",Aref,T,5732,0,10876,6394,11408,17802),
makeG("s10",Aref,T,2780,0,25045,824,23330,30939));
final Pair<Integer, Double> pair2 = InbreedingCoeff.calculateIC(test2, test2.getGenotypes());
final int count2 = pair2.getLeft();
final double ICresult2 = pair2.getRight();
Assert.assertEquals(ICresult2, -1.0, DELTA_PRECISION, "Pass");
Assert.assertEquals(count2, 10, "count2");
//test the annotate method
final Map<String, Object> annots = new InbreedingCoeff().annotate(null, test2, null);
Assert.assertEquals(annots.keySet(), Collections.singleton(GATKVCFConstants.INBREEDING_COEFFICIENT_KEY), "annots");
Assert.assertEquals(annots.values().size(), 1, "size");
Assert.assertEquals(Double.parseDouble((String)annots.values().iterator().next()), -1.0, DELTA_PRECISION, "ic");
final Map<String, Object> annots3 = new InbreedingCoeff(Collections.singleton("s1")).annotate(null, test2, null);
Assert.assertTrue(annots3.isEmpty());//not enough samples
final Map<String, Object> annots4 = new InbreedingCoeff(new LinkedHashSet<>(Arrays.asList("s1", "s2", "s3", "s4", "s5", "s6", "s7", "s8", "s9"))).annotate(null, test2, null);
Assert.assertTrue(annots4.isEmpty());//not enough samples
}