Example usage for java.util BitSet BitSet

List of usage examples for java.util BitSet BitSet

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Introduction

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

Prototype

public BitSet()

Source Link

Document

Creates a new bit set.

Usage

From source file:dendroscope.autumn.hybridnumber.ComputeHybridNumber.java

/**
 * run the algorithm. This can be reentered by rerootings of the same two trees
 *
 * @param tree1/*from w  w  w  . ja  v  a2  s  . c  o  m*/
 * @param tree2
 * @return reduced trees
 */
int run(PhyloTree tree1, PhyloTree tree2, Taxa allTaxa) throws IOException, CanceledException {
    if (!initialized) {
        initialized = true;
        progressListener.setMaximum(20);
        progressListener.setProgress(0);
        startTime = System.currentTimeMillis();
        nextTime = this.startTime + waitTime;
    }

    if (bestScore.get() == LARGE) { // no upper bound given, use cluster network
        System.err.print("Computing upper bound using cluster network: ");
        int upperBound = Utilities.getNumberOfReticulationsInClusterNetwork(tree1, tree2, progressListener);
        System.err.println(upperBound);
        bestScore.set(upperBound);
    }

    Pair<Root, Root> roots = PreProcess.apply(tree1, tree2, allTaxa);
    Root root1 = roots.getFirst();
    Root root2 = roots.getSecond();

    BitSet onlyTree1 = Cluster.setminus(root1.getTaxa(), root2.getTaxa());
    BitSet onlyTree2 = Cluster.setminus(root2.getTaxa(), root1.getTaxa());

    if (root1.getTaxa().cardinality() == onlyTree1.cardinality())
        throw new IOException("None of the taxa in tree2 are contained in tree1");
    if (root2.getTaxa().cardinality() == onlyTree2.cardinality())
        throw new IOException("None of the taxa in tree1 are contained in tree2");

    if (onlyTree1.cardinality() > 0) {
        if (!silent)
            System.err.println("Killing all taxa only present in tree1: " + onlyTree1.cardinality());
        for (int t = onlyTree1.nextSetBit(0); t != -1; t = onlyTree1.nextSetBit(t + 1)) {
            BitSet one = new BitSet();
            one.set(t);
            root1 = CopyWithTaxaRemoved.apply(root1, one);
        }
    }

    if (onlyTree2.cardinality() > 0) {
        if (!silent)
            System.err.println("Killing all taxa only present in tree2: " + onlyTree2.cardinality());
        for (int t = onlyTree2.nextSetBit(0); t != -1; t = onlyTree2.nextSetBit(t + 1)) {
            BitSet one = new BitSet();
            one.set(t);
            root2 = CopyWithTaxaRemoved.apply(root2, one);
        }
    }

    if (!root1.getTaxa().equals(root2.getTaxa()))
        throw new IOException("Trees have unequal taxon sets (even after killing)");

    // run the refine algorithm
    if (!silent)
        System.err.println("Computing common refinement of both trees");
    Refine.apply(root1, root2);

    if (true) {
        System.err.println(root1.toStringTree());
        System.err.println(root2.toStringTree());
    }

    if (tree1.getRoot() == null || tree2.getRoot() == null) {
        throw new IOException("Can't compute hybrid number, at least one of the trees is empty or unrooted");
    }

    // we maintain both trees in lexicographic order for ease of comparison
    root1.reorderSubTree();
    root2.reorderSubTree();

    if (!silent)
        System.err.println("Computing hybridization number using Autumn algorithm...");
    if (!silent)
        System.err.println("(Number of worker threads: " + (additionalThreads + 1) + ")");

    int result = computeHybridNumberRec(root1, root2, false, null, null, true, 0, new ValuesList());
    if (!silent)
        System.err.println("(Result: " + result + ")");
    if (!silent)
        System.err.println("Hybridization number: " + bestScore.get());
    if (bestScore.get() > result)
        throw new IOException("bestScore > result: " + bestScore.get() + " " + result);

    return bestScore.get();
}

From source file:hivemall.ftvec.ranking.ItemPairsSamplingUDTF.java

@Override
public void process(Object[] args) throws HiveException {
    final int numPosItems;
    final BitSet bits;
    if (bitsetInput) {
        if (_rand == null) {
            this._rand = new Random(43);
        }/*  w  w w . ja v  a2  s.  com*/
        long[] longs = HiveUtils.asLongArray(args[0], listOI, listElemOI);
        bits = BitSet.valueOf(longs);
        numPosItems = bits.cardinality();
    } else {
        if (_bitset == null) {
            bits = new BitSet();
            this._bitset = bits;
            this._rand = new Random(43);
        } else {
            bits = _bitset;
            bits.clear();
        }
        numPosItems = HiveUtils.setBits(args[0], listOI, listElemOI, bits);
    }

    if (numPosItems == 0) {
        return;
    }
    final int numNegItems = maxItemId + 1 - numPosItems;
    if (numNegItems == 0) {
        return;
    } else if (numNegItems < 0) {
        throw new UDFArgumentException(
                "maxItemId + 1 - numPosItems = " + maxItemId + " + 1 - " + numPosItems + " = " + numNegItems);
    }

    if (withReplacement) {
        sampleWithReplacement(numPosItems, numNegItems, bits);
    } else {
        sampleWithoutReplacement(numPosItems, numNegItems, bits);
    }
}

From source file:org.apache.tez.runtime.library.output.UnorderedKVOutput.java

@Override
public synchronized List<Event> close() throws Exception {
    boolean outputGenerated = this.kvWriter.close();

    DataMovementEventPayloadProto.Builder payloadBuilder = DataMovementEventPayloadProto.newBuilder();

    LOG.info("Closing KVOutput: RawLength: " + this.kvWriter.getRawLength() + ", CompressedLength: "
            + this.kvWriter.getCompressedLength());

    if (dataViaEventsEnabled && outputGenerated
            && this.kvWriter.getCompressedLength() <= dataViaEventsMaxSize) {
        LOG.info("Serialzing actual data into DataMovementEvent, dataSize: "
                + this.kvWriter.getCompressedLength());
        byte[] data = this.kvWriter.getData();
        DataProto.Builder dataProtoBuilder = DataProto.newBuilder();
        dataProtoBuilder.setData(ByteString.copyFrom(data));
        dataProtoBuilder.setRawLength((int) this.kvWriter.getRawLength());
        dataProtoBuilder.setCompressedLength((int) this.kvWriter.getCompressedLength());
        payloadBuilder.setData(dataProtoBuilder.build());
    }//from   w ww  .  j  av  a 2s . c om

    // Set the list of empty partitions - single partition on this case.
    if (!outputGenerated) {
        LOG.info("No output was generated");
        BitSet emptyPartitions = new BitSet();
        emptyPartitions.set(0);
        ByteString emptyPartitionsBytesString = TezCommonUtils
                .compressByteArrayToByteString(TezUtilsInternal.toByteArray(emptyPartitions));
        payloadBuilder.setEmptyPartitions(emptyPartitionsBytesString);
    }
    if (outputGenerated) {
        String host = getHost();
        ByteBuffer shuffleMetadata = getContext()
                .getServiceProviderMetaData(ShuffleUtils.SHUFFLE_HANDLER_SERVICE_ID);
        int shufflePort = ShuffleUtils.deserializeShuffleProviderMetaData(shuffleMetadata);
        payloadBuilder.setHost(host);
        payloadBuilder.setPort(shufflePort);
        payloadBuilder.setPathComponent(getContext().getUniqueIdentifier());
    }
    DataMovementEventPayloadProto payloadProto = payloadBuilder.build();

    DataMovementEvent dmEvent = DataMovementEvent.create(0, payloadProto.toByteString().asReadOnlyByteBuffer());
    List<Event> events = Lists.newArrayListWithCapacity(1);
    events.add(dmEvent);
    return events;
}

From source file:mastodon.algorithms.SALinearAlgorithm.java

protected void tryPruning() {
    //choose the number of species in list to perturb based on a Poisson distributions with rate equal to variable "mean" above
    int numberToSet = 0;
    int numberToClear = 0;

    while (numberToSet < 1 || numberToSet > currPrunedSpeciesCount) {
        numberToSet = pd.sample() + 1;/*from w ww  . j a va 2  s .  co m*/
    }

    if (numberToSet > (bts.getTaxaCount() - currPrunedSpeciesCount)) {
        numberToSet = bts.getTaxaCount() - currPrunedSpeciesCount;
    }

    //if we are pruning by one more species now, clear one species less from the pruning list this time
    if (currPruning.cardinality() < currPrunedSpeciesCount) {
        numberToClear = numberToSet - 1;
    } else {
        numberToClear = numberToSet;
    }

    BitSet bitsToSet = new BitSet();
    BitSet bitsToClear = new BitSet();

    for (int e = 0; e < numberToSet; e++) {
        int choice = 0;
        while (true) {
            choice = (int) (Random.nextDouble() * bts.getTaxaCount());
            if (!currPruning.get(choice) && !bitsToSet.get(choice)) {
                break;
            }
        }
        bitsToSet.set(choice);
    }

    for (int e = 0; e < numberToClear; e++) {
        int choice = 0;
        while (true) {
            choice = (int) (Random.nextDouble() * bts.getTaxaCount());
            if (currPruning.get(choice) && !bitsToClear.get(choice)) {
                break;
            }
        }
        bitsToClear.set(choice);
    }

    currPruning.or(bitsToSet);
    currPruning.xor(bitsToClear);

    currScore = bts.pruneFast(currPruning);
    bts.unPrune();
}

From source file:org.apache.tez.dag.utils.TaskSpecificLaunchCmdOption.java

/**
 * Get the set of tasks that need additional launch command options within a vertex
 *
 * @param tasksInVertex/*from w  w w.  j a v a2s  .c o m*/
 * @return Set<Integer> containing the task indexes to be profiled
 */
private BitSet parseTasks(String tasksInVertex) {
    BitSet taskSet = new BitSet();
    if (Strings.isNullOrEmpty(tasksInVertex)) {
        return taskSet;
    }
    Iterable<String> tasks = Splitter.on(",").omitEmptyStrings().trimResults().split(tasksInVertex);
    for (String task : tasks) {
        /**
         * TODO: this is horrible way to check the ranges.
         * Should use RangeSet when guava is upgraded.  Also, need to support partial
         * ranges like "1:", ":50".  With current implementation partial ranges are not
         * allowed.
         */
        if (task.endsWith(":") || task.startsWith(":")) {
            //invalid range. e.g :20, 6: are not supported.
            LOG.warn("Partial range is considered as an invalid option");
            return null;
        }
        Matcher taskMatcher = RANGE_REGEX.matcher(task);
        if (taskMatcher.find()) {
            int start = Integer.parseInt((taskMatcher.group(1).trim()));
            int end = Integer.parseInt((taskMatcher.group(2).trim()));
            for (int i = Math.min(start, end); i <= Math.max(start, end); i++) {
                taskSet.set(i);
            }
        } else {
            taskSet.set(Integer.parseInt(task.trim()));
        }
    }
    return taskSet;
}

From source file:mastodon.algorithms.MHLinearAlgorithm.java

protected void tryPruning() {
    //choose the number of species in list to perturb based on a Poisson distributions with rate equal to variable "mean" above
    int numberToSet = 0;
    int numberToClear = 0;

    while (numberToSet < 1 || numberToSet > currPrunedSpeciesCount) {
        numberToSet = pd.sample() + 1;/* w  w w .j ava2s . c o m*/
    }

    if (numberToSet > (bts.getTaxaCount() - currPrunedSpeciesCount)) {
        numberToSet = bts.getTaxaCount() - currPrunedSpeciesCount;
    }

    //if we are pruning by one more species now, clear one species less from the pruning list this time
    if (currPruning.cardinality() < currPrunedSpeciesCount) {
        numberToClear = numberToSet - 1;
    } else {
        numberToClear = numberToSet;
    }

    BitSet bitsToSet = new BitSet();
    BitSet bitsToClear = new BitSet();

    for (int e = 0; e < numberToSet; e++) {
        int choice = 0;
        while (true) {
            choice = (int) (Random.nextDouble() * bts.getTaxaCount());
            if (!currPruning.get(choice) && !bitsToSet.get(choice)) {
                break;
            }
        }
        bitsToSet.set(choice);
    }

    for (int e = 0; e < numberToClear; e++) {
        int choice = 0;
        while (true) {
            choice = (int) (Random.nextDouble() * bts.getTaxaCount());
            if (currPruning.get(choice) && !bitsToClear.get(choice)) {
                break;
            }
        }
        bitsToClear.set(choice);
    }

    currPruning.or(bitsToSet);
    currPruning.xor(bitsToClear);

    currScore = bts.pruneFast(currPruning);
    bts.unPrune();

}

From source file:com.joliciel.jochre.graphics.VectorizerImplTest.java

@Test
public void testArrayListize(@NonStrict final Shape shape, @NonStrict final JochreImage image) {
    final int threshold = 100;
    final int whiteGapFillFactor = 5;

    new NonStrictExpectations() {
        {//from ww w  . j ava 2s. c o m
            shape.getHeight();
            returns(8);
            shape.getWidth();
            returns(8);
            shape.getJochreImage();
            returns(image);
            image.getBlackThreshold();
            returns(threshold);

            int[] pixels = { 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1,
                    0, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1,
                    1, 1, 0, 0, 0 };

            for (int x = -1; x <= 8; x++)
                for (int y = -1; y <= 8; y++) {
                    shape.isPixelBlack(x, y, threshold, whiteGapFillFactor);
                    if (x >= 0 && x < 8 && y >= 0 && y < 8)
                        returns(pixels[y * 8 + x] == 1);
                    else
                        returns(false);
                }

            int[] outlinePixels = { 0, 1, 1, 0, 0, 1, 1, 1, // row 0
                    0, 1, 0, 1, 0, 1, 0, 1, // row 1
                    0, 0, 1, 1, 0, 0, 1, 1, // row 2
                    0, 0, 1, 1, 0, 1, 1, 0, // row 3
                    0, 0, 0, 1, 1, 0, 1, 0, // row 4
                    0, 0, 0, 1, 0, 1, 0, 0, // row 5
                    0, 0, 1, 0, 1, 0, 0, 0, // row 6
                    1, 1, 1, 1, 1, 0, 0, 0, // row 7
            };

            BitSet outline = new BitSet();
            for (int i = 0; i < 8 * 8; i++)
                outline.set(i, outlinePixels[i] == 1);

            shape.getOutline(threshold);
            returns(outline);

        }
    };

    VectorizerImpl vectorizer = new VectorizerImpl();
    GraphicsServiceInternal graphicsService = new GraphicsServiceImpl();
    vectorizer.setGraphicsService(graphicsService);
    vectorizer.setWhiteGapFillFactor(whiteGapFillFactor);
    List<LineSegment> lines = vectorizer.vectorize(shape);
    int i = 0;
    for (LineSegment lineSegment : lines) {
        double slope = (double) (lineSegment.getEndY() - lineSegment.getStartY())
                / (double) (lineSegment.getEndX() - lineSegment.getStartX());
        LOG.debug("Line " + i++ + "(" + lineSegment.getStartX() + "," + lineSegment.getStartY() + ") " + "("
                + lineSegment.getEndX() + "," + lineSegment.getEndY() + "). Length = " + lineSegment.getLength()
                + ", Slope = " + slope);
    }

}

From source file:org.rdfhdt.hdt.impl.BufferedCompressedStreaming.java

public BufferedCompressedStreaming(OutputStream out, CSSpecification spec, PrefixDictionary prefixes,
        Map<String, Boolean> predicateDiscrete) {

    // Import prefixes
    this.prefixes = prefixes;

    if (this.prefixes.size() > 0)
        usePrefixes = true;/*from   w w  w .j  a v a2 s  . co m*/

    // Import predicateDiscrete
    this.predicateDiscrete = predicateDiscrete;

    // load max size dictionary
    String specMaxSizeDictionary = spec.get(CSVocabulary.SPEC_MAX_SIZE_DICTIONARY);
    max_size_dictionary = CSVocabulary.DEFAULT_MAX_SIZE_DICTIONARY;
    if (specMaxSizeDictionary != null && !"".equals(specMaxSizeDictionary)) {
        try {
            max_size_dictionary = Integer.parseInt(specMaxSizeDictionary);
        } catch (NumberFormatException e) {
            max_size_dictionary = CSVocabulary.DEFAULT_MAX_SIZE_DICTIONARY;
        }
    }
    // load block size if present
    String specBlockSize = spec.get(CSVocabulary.SPEC_BLOCK_SIZE);
    block_size = CSVocabulary.DEFAULT_BLOCK_SIZE;
    if (specBlockSize != null && !"".equals(specBlockSize)) {
        try {
            block_size = Integer.parseInt(specBlockSize);
        } catch (NumberFormatException e) {
            block_size = CSVocabulary.DEFAULT_BLOCK_SIZE;
        }
    }

    // load if the dictionary of subject must be stored
    String specStoreSubjectDictionary = spec.get(CSVocabulary.STORE_SUBJ_DICTIONARY);

    store_subj_dictionary = CSVocabulary.DEFAULT_STORE_SUBJ_DICTIONARY;
    if (specStoreSubjectDictionary != null && !"".equals(specStoreSubjectDictionary)) {

        store_subj_dictionary = Boolean.parseBoolean(specStoreSubjectDictionary);

    }

    // load if the predicates are not related with the same types and/or tags
    String specDisableLiteralTags = spec.get(CSVocabulary.DISABLE_CONSISTENT_PREDICATES);

    disable_consistent_predicates = CSVocabulary.DEFAULT_CONSISTENT_PREDICATES;
    if (specDisableLiteralTags != null && !"".equals(specDisableLiteralTags)) {

        disable_consistent_predicates = Boolean.parseBoolean(specDisableLiteralTags);

    }

    offset_tag = 1; // auxiliary offset by default for the last quote "
    if (disable_consistent_predicates)
        offset_tag = 0;

    if (store_subj_dictionary)
        subjects = new LRUDictionary<String, Integer>(max_size_dictionary);

    predicates = new HashMap<String, Integer>();
    // Consider ConcurrentHashMap<String, Integer>(); for parallel creation
    literalTagsByPredicate = new ArrayList<String>();
    sizeofTags = new ArrayList<Integer>();
    predicateLiterals = new BitSet();
    objects = new ArrayList<LRUDictionary<String, Integer>>(max_size_dictionary);
    structures = new LRUDictionary<String, Integer>(max_size_dictionary);

    currentBlock = new Block(store_subj_dictionary);

    subjectsToProcess = new ConcurrentHashMap<String, ArrayList<TripleString>>();

    this.out = out;
}

From source file:org.lockss.servlet.AddContentTab.java

/**
 * Handle a request/*from   www.java2s.  co m*/
 *
 * @throws java.io.IOException
 */
public void lockssHandleRequest() throws IOException {
    if (!StringUtil.isNullString(req.getParameter("isDaemonReady"))) {
        if (pluginMgr.areAusStarted()) {
            resp.setStatus(200);
            PrintWriter wrtr = resp.getWriter();
            resp.setContentType("text/plain");
            wrtr.println("true");
        } else {
            PrintWriter wrtr = resp.getWriter();
            resp.setContentType("text/plain");
            wrtr.println("false");
            resp.sendError(202, "Not ready");
        }
        return;
    }

    if (StringUtil.isNullString(action)) {
        try {
            getMultiPartRequest();
            if (multiReq != null) {
                action = multiReq.getString(ACTION_TAG);
            }
        } catch (FormDataTooLongException e) {
            errMsg = "Uploaded file too large: " + e.getMessage();
            // leave action null, will call displayAuSummary() below
        }
    }

    outputFmt = OUTPUT_HTML; // default output is html

    String outputParam = req.getParameter("output");
    if (!StringUtil.isNullString(outputParam)) {
        if ("html".equalsIgnoreCase(outputParam)) {
            outputFmt = OUTPUT_HTML;
        } else {
            log.warning("Unknown output format: " + outputParam);
        }
    }
    String optionsParam = req.getParameter("options");

    tableOptions = new BitSet();

    if (isDebugUser()) {
        log.debug2("Debug user.  Setting OPTION_DEBUG_USER");
        tableOptions.set(StatusTable.OPTION_DEBUG_USER);
    }

    for (String s : StringUtil.breakAt(optionsParam, ',')) {
        if ("norows".equalsIgnoreCase(s)) {
            tableOptions.set(StatusTable.OPTION_NO_ROWS);
        }
    }

    tableName = req.getParameter("table");
    tableKey = req.getParameter("key");
    if (StringUtil.isNullString(tableName)) {
        tableName = "AuOverview";
    }
    if (StringUtil.isNullString(tableKey)) {
        tableKey = null;
    }
    sortKey = req.getParameter("sort");
    if (StringUtil.isNullString(sortKey)) {
        sortKey = null;
    }
    groupKey = req.getParameter("group");
    if (StringUtil.isNullString(groupKey)) {
        groupKey = "publisher";
    }
    type = req.getParameter("type");
    if (StringUtil.isNullString(type)) {
        type = "";
    }
    typeKey = req.getParameter("type");
    String auStartString = req.getParameter("start");
    if (auStartString == null) {
        auStart = 'a';
    } else {
        auStart = auStartString.charAt(0);
    }
    String auEndString = req.getParameter("end");
    if (auEndString == null) {
        auEnd = 'a';
    } else {
        auEnd = auEndString.charAt(0);
    }
    filterKey = req.getParameter("filter");
    if (StringUtil.isNullString(filterKey)) {
        filterKey = "";
    }
    timeKey = req.getParameter("timeKey");
    if (StringUtil.isNullString(timeKey)) {
        timeKey = "";
    }
    switch (outputFmt) {
    case OUTPUT_HTML:
        doHtmlStatusTable();
        break;
    }
}

From source file:org.rdfhdt.hdt.impl.BufferedCompressedStreamingNoDictionary.java

public BufferedCompressedStreamingNoDictionary(OutputStream out, CSSpecification spec,
        PrefixDictionary prefixes, Map<String, Boolean> predicateDiscrete) {

    /* TEST *//*from  w  ww  .j a  v  a 2s . c  om*/
    // predicateNoDictObjects.put("http://www.w3.org/2000/01/rdf-schema#label",true);

    // Import prefixes
    this.prefixes = prefixes;

    if (this.prefixes.size() > 0)
        usePrefixes = true;

    // Import predicateDiscrete
    this.predicateDiscrete = predicateDiscrete;

    // Import predicateUniq
    // this.predicateUniq = predicateUniq;

    // load max size dictionary
    String specMaxSizeDictionary = spec.get(CSVocabulary.SPEC_MAX_SIZE_DICTIONARY);
    max_size_dictionary = CSVocabulary.DEFAULT_MAX_SIZE_DICTIONARY;
    if (specMaxSizeDictionary != null && !"".equals(specMaxSizeDictionary)) {
        try {
            max_size_dictionary = Integer.parseInt(specMaxSizeDictionary);
        } catch (NumberFormatException e) {
            max_size_dictionary = CSVocabulary.DEFAULT_MAX_SIZE_DICTIONARY;
        }
    }
    // load block size if present
    String specBlockSize = spec.get(CSVocabulary.SPEC_BLOCK_SIZE);
    block_size = CSVocabulary.DEFAULT_BLOCK_SIZE;
    if (specBlockSize != null && !"".equals(specBlockSize)) {
        try {
            block_size = Integer.parseInt(specBlockSize);
        } catch (NumberFormatException e) {
            block_size = CSVocabulary.DEFAULT_BLOCK_SIZE;
        }
    }

    // load if the dictionary of subjects must be stored
    String specStoreDictionary = spec.get(CSVocabulary.STORE_SUBJ_DICTIONARY);

    store_subj_dictionary = CSVocabulary.DEFAULT_STORE_SUBJ_DICTIONARY;
    if (specStoreDictionary != null && !"".equals(specStoreDictionary)) {

        store_subj_dictionary = Boolean.parseBoolean(specStoreDictionary);

    }

    // load if the dictionary of objects must be stored
    specStoreDictionary = spec.get(CSVocabulary.STORE_OBJ_DICTIONARY);

    store_obj_dictionary = false;

    // load if the predicates are not related with the same types and/or tags
    String specDisableLiteralTags = spec.get(CSVocabulary.DISABLE_CONSISTENT_PREDICATES);

    disable_consistent_predicates = CSVocabulary.DEFAULT_CONSISTENT_PREDICATES;
    if (specDisableLiteralTags != null && !"".equals(specDisableLiteralTags)) {

        disable_consistent_predicates = Boolean.parseBoolean(specDisableLiteralTags);

    }

    offset_tag = 1; // auxiliary offset by default for the last quote "
    if (disable_consistent_predicates)
        offset_tag = 0;

    if (store_subj_dictionary)
        subjects = new LRUDictionary<String, Integer>(max_size_dictionary);

    predicates = new HashMap<String, Integer>();
    // Consider ConcurrentHashMap<String, Integer>(); for parallel creation
    literalTagsByPredicate = new ArrayList<String>();
    sizeofTags = new ArrayList<Integer>();
    predicateLiterals = new BitSet();

    structures = new LRUDictionary<String, Integer>(max_size_dictionary);

    currentBlock = new BlockNoDictionary(store_subj_dictionary);

    subjectsToProcess = new ConcurrentHashMap<String, ArrayList<TripleString>>();

    this.out = out;
}