Example usage for java.util HashSet size

List of usage examples for java.util HashSet size

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Introduction

In this page you can find the example usage for java.util HashSet size.

Prototype

public int size()

Source Link

Document

Returns the number of elements in this set (its cardinality).

Usage

From source file:ch.unil.genescore.pathway.GeneSetLibrary.java

License:asdf

protected double[] getSetChisq(GeneSet set) {

    HashSet<Gene> gSet = set.getGenes();
    double[] ret = new double[gSet.size()];

    // Sum the chi2 stats
    int i = 0;/*from w w  w .  ja v  a 2  s . c  o  m*/
    for (Gene g : gSet) {
        ret[i] = g.getChi2Stat();
        i++;
    }
    return ret;
}

From source file:com.hellblazer.slp.anubis.EndToEndTest.java

public void testSmoke() throws Exception {
    String memberIdKey = "test.member.id";
    ServiceURL url = new ServiceURL("service:http://foo.bar/drink-me");
    List<Listener> listeners = new ArrayList<Listener>();
    for (ApplicationContext context : memberContexts) {
        Listener listener = new Listener(context, memberContexts.size());
        listeners.add(listener);// ww w.  j a  va  2 s.com
        listener.register(getQuery("*"));
    }
    for (ApplicationContext context : memberContexts) {
        HashMap<String, Object> properties = new HashMap<String, Object>();
        properties.put(memberIdKey, context.getBean(Identity.class).id);
        context.getBean(ServiceScope.class).register(url, properties);
    }

    for (Listener listener : listeners) {
        assertTrue(String.format("Listener: %s did not receive all events", listener),
                listener.await(60, TimeUnit.SECONDS));
    }

    for (Listener listener : listeners) {
        assertEquals(listeners.size(), listener.events.size());
        HashSet<Integer> sent = new HashSet<Integer>();
        for (ServiceEvent event : listener.events) {
            assertEquals(EventType.REGISTERED, event.getType());
            assertEquals(url, event.getReference().getUrl());
            sent.add((Integer) event.getReference().getProperties().get(memberIdKey));
            assertEquals(event.getReference().getProperties().get(AnubisScope.MEMBER_IDENTITY),
                    event.getReference().getProperties().get(memberIdKey));
        }
        assertEquals(listeners.size(), sent.size());
    }
}

From source file:com.qwazr.cluster.manager.ClusterManager.java

private ClusterManager(ExecutorService executor, String publicAddress, Set<String> myGroups)
        throws IOException, URISyntaxException {
    myAddress = ClusterNode.toAddress(publicAddress);
    if (logger.isInfoEnabled())
        logger.info("Server: " + myAddress + " Groups: " + ArrayUtils.prettyPrint(myGroups));
    this.myGroups = myGroups;

    this.executor = executor;

    // Load the configuration
    String masters_env = System.getenv("QWAZR_MASTERS");

    // No configuration file ? Okay, we are a simple node
    if (StringUtils.isEmpty(masters_env)) {
        clusterMasterArray = null;//from   w  w  w .  ja  v  a 2  s . c om
        clusterNodeMap = null;
        clusterClient = null;
        checkTimeMap = null;
        lastTimeCheck = null;
        isMaster = false;
        isCluster = false;
        if (logger.isInfoEnabled())
            logger.info("No QWAZR_MASTERS environment variable. This node is not part of a cluster.");
        return;
    }

    // Store the last time a master checked the node
    checkTimeMap = new ConcurrentHashMap<>();
    lastTimeCheck = new AtomicLong();

    // Build the master list and check if I am a master
    boolean isMaster = false;
    HashSet<String> masterSet = new HashSet<>();
    int i = 0;
    String[] masters = StringUtils.split(masters_env, ',');
    for (String master : masters) {
        String masterAddress = ClusterNode.toAddress(master.trim());
        logger.info("Add a master: " + masterAddress);
        masterSet.add(masterAddress);
        if (masterAddress == myAddress) {
            isMaster = true;
            if (logger.isInfoEnabled())
                logger.info("I am a master!");
        }
    }
    isCluster = true;
    clusterMasterArray = masterSet.toArray(new String[masterSet.size()]);
    clusterClient = new ClusterMultiClient(executor, clusterMasterArray, 60000);
    this.isMaster = isMaster;
    if (!isMaster) {
        clusterNodeMap = null;
        return;
    }

    // We load the cluster node map
    clusterNodeMap = new ClusterNodeMap();
}

From source file:ch.unil.genescore.pathway.GeneSetLibrary.java

License:asdf

protected void computeHypGeomPvalue(GeneSet set) {
    ArrayList<Double> quantiles = Pascal.set.hypGeomQuantiles_;
    double[] pvals = new double[quantiles.size()];
    if (set.getGenes().size() == 0) {
        for (int i = 0; i < quantiles.size(); i++) {
            pvals[i] = 1;/*w  ww .  j  ava2  s.c  o m*/
        }
        set.setHypGeomPvalues(pvals);
        return;
    }

    for (int j = 0; j < quantiles.size(); j++) {
        double[] valAr = new double[genesForSimulation_.size()];
        for (int i = 0; i < genesForSimulation_.size(); i++) {
            valAr[i] = genesForSimulation_.get(i).getChi2Stat();
        }
        Arrays.sort(valAr);
        int n = (int) Math.floor(valAr.length * quantiles.get(j));
        double cutoffVal = valAr[n];
        int setSize = valAr.length - n - 1;
        HashSet<Gene> pathwayGenes = set.getGenes();
        if (pathwayGenes.size() == 0)
            return;

        int q = 0;
        for (Gene g : pathwayGenes) {
            if (g.getChi2Stat() > cutoffVal)
                q += 1;
        }

        HypergeometricDistribution myHypgeom = new HypergeometricDistribution(valAr.length, setSize,
                pathwayGenes.size());
        double pval = 1 - myHypgeom.cumulativeProbability((q - 1));
        pvals[j] = pval;
    }
    set.setHypGeomPvalues(pvals);
}

From source file:ch.unil.genescore.pathway.GeneSetLibrary.java

License:asdf

public void computeApproxPathwayCorrelationLowerBound() {

    DenseMatrix corMat = new DenseMatrix(geneSets_.size(), geneSets_.size());
    for (int i = 0; i < geneSets_.size(); i++) {
        HashSet<Gene> leftSet = geneSets_.get(i).genes_;
        double leftSize = leftSet.size();
        for (int j = 0; j < geneSets_.size(); j++) {
            HashSet<Gene> rightSet = geneSets_.get(j).genes_;
            double rightSize = rightSet.size();
            HashSet<Gene> copyLeftSet = new HashSet<Gene>(leftSet);
            copyLeftSet.retainAll(rightSet);
            double count = copyLeftSet.size();
            double corr = count / Math.sqrt(leftSize * rightSize);
            //double corr = count;

            corMat.set(i, j, corr);//from w w w  .j a va2 s  . com
        }
    }
    pathwayCorMat_ = corMat;
}

From source file:maui.main.MauiTopicExtractor.java

/**
 * Builds the model from the files/*from  w  ww. j  av  a2  s. c  o m*/
 */
public void extractKeyphrases(HashSet<String> fileNames) throws Exception {

    // Check whether there is actually any data
    if (fileNames.size() == 0) {
        throw new Exception("Couldn't find any data in " + inputDirectoryName);
    }

    mauiFilter.setVocabularyName(vocabularyName);
    mauiFilter.setVocabularyFormat(vocabularyFormat);
    mauiFilter.setDocumentLanguage(documentLanguage);
    mauiFilter.setStemmer(stemmer);
    mauiFilter.setStopwords(stopwords);
    if (wikipedia != null) {
        mauiFilter.setWikipedia(wikipedia);
    } else if (wikipediaServer.equals("localhost") && wikipediaDatabase.equals("database")) {
        mauiFilter.setWikipedia(wikipedia);
    } else {
        mauiFilter.setWikipedia(wikipediaServer, wikipediaDatabase, cacheWikipediaData, wikipediaDataDirectory);
    }
    if (!vocabularyName.equals("none") && !vocabularyName.equals("wikipedia")) {
        loadThesaurus(stemmer, stopwords, vocabularyDirectory);
        mauiFilter.setVocabulary(vocabulary);
    }

    FastVector atts = new FastVector(3);
    atts.addElement(new Attribute("filename", (FastVector) null));
    atts.addElement(new Attribute("doc", (FastVector) null));
    atts.addElement(new Attribute("keyphrases", (FastVector) null));
    Instances data = new Instances("keyphrase_training_data", atts, 0);

    System.err.println("-- Extracting keyphrases... ");

    Vector<Double> correctStatistics = new Vector<Double>();
    Vector<Double> precisionStatistics = new Vector<Double>();
    Vector<Double> recallStatistics = new Vector<Double>();

    for (String fileName : fileNames) {

        double[] newInst = new double[3];

        newInst[0] = (double) data.attribute(0).addStringValue(fileName);
        ;

        File documentTextFile = new File(inputDirectoryName + "/" + fileName + ".txt");
        File documentTopicsFile = new File(inputDirectoryName + "/" + fileName + ".key");

        try {

            String documentText;
            if (!documentEncoding.equals("default")) {
                documentText = FileUtils.readFileToString(documentTextFile, documentEncoding);
            } else {
                documentText = FileUtils.readFileToString(documentTextFile);
            }

            // Adding the text of the document to the instance
            newInst[1] = (double) data.attribute(1).addStringValue(documentText);

        } catch (Exception e) {
            System.err.println("Problem with reading " + documentTextFile);
            e.printStackTrace();
            newInst[1] = Instance.missingValue();
        }

        try {

            String documentTopics;
            if (!documentEncoding.equals("default")) {
                documentTopics = FileUtils.readFileToString(documentTopicsFile, documentEncoding);
            } else {
                documentTopics = FileUtils.readFileToString(documentTopicsFile);
            }

            // Adding the topics to the file
            newInst[2] = (double) data.attribute(2).addStringValue(documentTopics);

        } catch (Exception e) {
            if (debugMode) {
                System.err.println("No existing topics for " + documentTextFile);
            }
            newInst[2] = Instance.missingValue();
        }

        data.add(new Instance(1.0, newInst));

        mauiFilter.input(data.instance(0));

        data = data.stringFreeStructure();
        if (debugMode) {
            System.err.println("-- Processing document: " + fileName);
        }
        Instance[] topRankedInstances = new Instance[topicsPerDocument];
        Instance inst;

        // Iterating over all extracted keyphrases (inst)
        while ((inst = mauiFilter.output()) != null) {

            int index = (int) inst.value(mauiFilter.getRankIndex()) - 1;

            if (index < topicsPerDocument) {
                topRankedInstances[index] = inst;
            }
        }

        if (debugMode) {
            System.err.println("-- Keyphrases and feature values:");
        }
        FileOutputStream out = null;
        PrintWriter printer = null;

        if (!documentTopicsFile.exists()) {
            out = new FileOutputStream(documentTopicsFile);
            if (!documentEncoding.equals("default")) {
                printer = new PrintWriter(new OutputStreamWriter(out, documentEncoding));
            } else {
                printer = new PrintWriter(out);
            }
        }

        double numExtracted = 0, numCorrect = 0;
        wikipedia = mauiFilter.getWikipedia();

        HashMap<Article, Integer> topics = null;

        if (printGraph) {
            topics = new HashMap<Article, Integer>();
        }

        int p = 0;
        String root = "";
        for (int i = 0; i < topicsPerDocument; i++) {
            if (topRankedInstances[i] != null) {
                if (!topRankedInstances[i].isMissing(topRankedInstances[i].numAttributes() - 1)) {
                    numExtracted += 1.0;
                }
                if ((int) topRankedInstances[i].value(topRankedInstances[i].numAttributes() - 1) == 1) {
                    numCorrect += 1.0;
                }
                if (printer != null) {
                    String topic = topRankedInstances[i].stringValue(mauiFilter.getOutputFormIndex());
                    printer.print(topic);

                    if (printGraph) {

                        Article article = wikipedia.getArticleByTitle(topic);
                        if (article == null) {
                            article = wikipedia.getMostLikelyArticle(topic, new CaseFolder());
                        }
                        if (article != null) {
                            if (root == "") {
                                root = article.getTitle();
                            }
                            topics.put(article, new Integer(p));
                        } else {
                            if (debugMode) {
                                System.err.println(
                                        "Couldn't find article for " + topic + " in " + documentTopicsFile);
                            }
                        }
                        p++;
                    }
                    if (additionalInfo) {
                        printer.print("\t");
                        printer.print(topRankedInstances[i].stringValue(mauiFilter.getNormalizedFormIndex()));
                        printer.print("\t");
                        printer.print(Utils.doubleToString(
                                topRankedInstances[i].value(mauiFilter.getProbabilityIndex()), 4));
                    }
                    printer.println();
                }
                if (debugMode) {
                    System.err.println(topRankedInstances[i]);
                }
            }
        }

        if (printGraph) {
            String graphFile = documentTopicsFile.getAbsolutePath().replace(".key", ".gv");
            computeGraph(topics, root, graphFile);
        }
        if (numExtracted > 0) {
            if (debugMode) {
                System.err.println("-- " + numCorrect + " correct");
            }
            double totalCorrect = mauiFilter.getTotalCorrect();
            correctStatistics.addElement(new Double(numCorrect));
            precisionStatistics.addElement(new Double(numCorrect / numExtracted));
            recallStatistics.addElement(new Double(numCorrect / totalCorrect));

        }
        if (printer != null) {
            printer.flush();
            printer.close();
            out.close();
        }
    }

    if (correctStatistics.size() != 0) {

        double[] st = new double[correctStatistics.size()];
        for (int i = 0; i < correctStatistics.size(); i++) {
            st[i] = correctStatistics.elementAt(i).doubleValue();
        }
        double avg = Utils.mean(st);
        double stdDev = Math.sqrt(Utils.variance(st));

        if (correctStatistics.size() == 1) {
            System.err.println("\n-- Evaluation results based on 1 document:");

        } else {
            System.err.println("\n-- Evaluation results based on " + correctStatistics.size() + " documents:");
        }
        System.err.println("Avg. number of correct keyphrases per document: " + Utils.doubleToString(avg, 2)
                + " +/- " + Utils.doubleToString(stdDev, 2));

        st = new double[precisionStatistics.size()];
        for (int i = 0; i < precisionStatistics.size(); i++) {
            st[i] = precisionStatistics.elementAt(i).doubleValue();
        }
        double avgPrecision = Utils.mean(st);
        double stdDevPrecision = Math.sqrt(Utils.variance(st));

        System.err.println("Precision: " + Utils.doubleToString(avgPrecision * 100, 2) + " +/- "
                + Utils.doubleToString(stdDevPrecision * 100, 2));

        st = new double[recallStatistics.size()];
        for (int i = 0; i < recallStatistics.size(); i++) {
            st[i] = recallStatistics.elementAt(i).doubleValue();
        }
        double avgRecall = Utils.mean(st);
        double stdDevRecall = Math.sqrt(Utils.variance(st));

        System.err.println("Recall: " + Utils.doubleToString(avgRecall * 100, 2) + " +/- "
                + Utils.doubleToString(stdDevRecall * 100, 2));

        double fMeasure = 2 * avgRecall * avgPrecision / (avgRecall + avgPrecision);
        System.err.println("F-Measure: " + Utils.doubleToString(fMeasure * 100, 2));

        System.err.println("");
    }
    mauiFilter.batchFinished();
}

From source file:io.pravega.service.server.containers.StreamSegmentMapperTests.java

/**
 * Tests the ability of the StreamSegmentMapper to generate/return the Id of an existing StreamSegment, as well as
 * retrieving existing attributes.//w  ww  . j a v a  2  s. co  m
 */
@Test
public void testGetOrAssignStreamSegmentId() {
    final int segmentCount = 10;
    final int transactionsPerSegment = 5;

    @Cleanup
    TestContext context = new TestContext();

    HashSet<String> storageSegments = new HashSet<>();
    for (int i = 0; i < segmentCount; i++) {
        String segmentName = getName(i);
        storageSegments.add(segmentName);
        setAttributes(segmentName, storageSegments.size() % ATTRIBUTE_COUNT, context);

        for (int j = 0; j < transactionsPerSegment; j++) {
            // There is a small chance of a name conflict here, but we don't care. As long as we get at least one
            // Transaction per segment, we should be fine.
            String transactionName = StreamSegmentNameUtils.getTransactionNameFromId(segmentName,
                    UUID.randomUUID());
            storageSegments.add(transactionName);
            setAttributes(transactionName, storageSegments.size() % ATTRIBUTE_COUNT, context);
        }
    }

    // We setup all necessary handlers, except the one for create. We do not need to create new Segments here.
    setupOperationLog(context);
    Predicate<String> isSealed = segmentName -> segmentName.hashCode() % 2 == 0;
    Function<String, Long> getInitialLength = segmentName -> (long) Math.abs(segmentName.hashCode());
    setupStorageGetHandler(context, storageSegments, segmentName -> new StreamSegmentInformation(segmentName,
            getInitialLength.apply(segmentName), isSealed.test(segmentName), false, new ImmutableDate()));

    // First, map all the parents (stand-alone segments).
    for (String name : storageSegments) {
        if (StreamSegmentNameUtils.getParentStreamSegmentName(name) == null) {
            long id = context.mapper.getOrAssignStreamSegmentId(name, TIMEOUT).join();
            Assert.assertNotEquals("No id was assigned for StreamSegment " + name,
                    ContainerMetadata.NO_STREAM_SEGMENT_ID, id);
            SegmentMetadata sm = context.metadata.getStreamSegmentMetadata(id);
            Assert.assertNotNull("No metadata was created for StreamSegment " + name, sm);
            long expectedLength = getInitialLength.apply(name);
            boolean expectedSeal = isSealed.test(name);
            Assert.assertEquals("Metadata does not have the expected length for StreamSegment " + name,
                    expectedLength, sm.getDurableLogLength());
            Assert.assertEquals(
                    "Metadata does not have the expected value for isSealed for StreamSegment " + name,
                    expectedSeal, sm.isSealed());

            val segmentState = context.stateStore.get(name, TIMEOUT).join();
            Map<UUID, Long> expectedAttributes = segmentState == null ? null : segmentState.getAttributes();
            SegmentMetadataComparer.assertSameAttributes(
                    "Unexpected attributes in metadata for StreamSegment " + name, expectedAttributes, sm);
        }
    }

    // Now, map all the Transactions.
    for (String name : storageSegments) {
        String parentName = StreamSegmentNameUtils.getParentStreamSegmentName(name);
        if (parentName != null) {
            long id = context.mapper.getOrAssignStreamSegmentId(name, TIMEOUT).join();
            Assert.assertNotEquals("No id was assigned for Transaction " + name,
                    ContainerMetadata.NO_STREAM_SEGMENT_ID, id);
            SegmentMetadata sm = context.metadata.getStreamSegmentMetadata(id);
            Assert.assertNotNull("No metadata was created for Transaction " + name, sm);
            long expectedLength = getInitialLength.apply(name);
            boolean expectedSeal = isSealed.test(name);
            Assert.assertEquals("Metadata does not have the expected length for Transaction " + name,
                    expectedLength, sm.getDurableLogLength());
            Assert.assertEquals(
                    "Metadata does not have the expected value for isSealed for Transaction " + name,
                    expectedSeal, sm.isSealed());

            val segmentState = context.stateStore.get(name, TIMEOUT).join();
            Map<UUID, Long> expectedAttributes = segmentState == null ? null : segmentState.getAttributes();
            SegmentMetadataComparer.assertSameAttributes(
                    "Unexpected attributes in metadata for Transaction " + name, expectedAttributes, sm);

            // Check parenthood.
            Assert.assertNotEquals("No parent defined in metadata for Transaction " + name,
                    ContainerMetadata.NO_STREAM_SEGMENT_ID, sm.getParentId());
            long parentId = context.metadata.getStreamSegmentId(parentName, false);
            Assert.assertEquals("Unexpected parent defined in metadata for Transaction " + name, parentId,
                    sm.getParentId());
        }
    }
}

From source file:org.hyperic.hq.authz.server.session.ResourceGroupManagerImpl.java

/**
 * Get the resource groups with the specified ids
 * @param ids the resource group ids/* ww w .  j  a  v a 2 s.c  o m*/
 * @param pc Paging information for the request
 * 
 */
@Transactional(readOnly = true)
public PageList<ResourceGroupValue> getResourceGroupsById(AuthzSubject whoami, Integer[] ids, PageControl pc)
        throws PermissionException {
    if (ids.length == 0) {
        return new PageList<ResourceGroupValue>();
    }

    PageControl allPc = new PageControl();
    // get all roles, sorted but not paged
    allPc.setSortattribute(pc.getSortattribute());
    allPc.setSortorder(pc.getSortorder());
    Collection<ResourceGroup> all = getAllResourceGroups(whoami, false);

    // build an index of ids
    HashSet<Integer> index = new HashSet<Integer>();
    index.addAll(Arrays.asList(ids));
    int numToFind = index.size();

    // find the requested roles
    List<ResourceGroup> groups = new ArrayList<ResourceGroup>(numToFind);
    Iterator<ResourceGroup> i = all.iterator();
    while (i.hasNext() && (groups.size() < numToFind)) {
        ResourceGroup g = i.next();
        if (index.contains(g.getId())) {
            groups.add(g);
        }
    }

    // TODO: G
    PageList<ResourceGroupValue> plist = _groupPager.seek(groups, pc.getPagenum(), pc.getPagesize());
    plist.setTotalSize(groups.size());

    return plist;
}

From source file:org.apache.sysml.hops.codegen.opt.ReachabilityGraph.java

private ArrayList<Pair<CutSet, Double>> evaluateCutSets(ArrayList<ArrayList<NodeLink>> candCS,
        ArrayList<ArrayList<NodeLink>> remain) {
    ArrayList<Pair<CutSet, Double>> cutSets = new ArrayList<>();

    for (ArrayList<NodeLink> cand : candCS) {
        HashSet<NodeLink> probe = new HashSet<>(cand);

        //determine subproblems for cutset candidates
        HashSet<NodeLink> part1 = new HashSet<>();
        rCollectInputs(_root, probe, part1);
        HashSet<NodeLink> part2 = new HashSet<>();
        for (NodeLink rNode : cand)
            rCollectInputs(rNode, probe, part2);

        //select, score and create cutsets
        if (!CollectionUtils.containsAny(part1, part2) && !part1.isEmpty() && !part2.isEmpty()) {
            //score cutsets (smaller is better)
            double base = UtilFunctions.pow(2, _matPoints.size());
            double numComb = UtilFunctions.pow(2, cand.size());
            double score = (numComb - 1) / numComb * base + 1 / numComb * UtilFunctions.pow(2, part1.size())
                    + 1 / numComb * UtilFunctions.pow(2, part2.size());

            //construct cutset
            cutSets.add(Pair.of(new CutSet(cand.stream().map(p -> p._p).toArray(InterestingPoint[]::new),
                    part1.stream().map(p -> p._p).toArray(InterestingPoint[]::new),
                    part2.stream().map(p -> p._p).toArray(InterestingPoint[]::new)), score));
        } else {//from w  ww.j  a  va2s.  c om
            remain.add(cand);
        }
    }

    return cutSets;
}