Example usage for java.util BitSet set

List of usage examples for java.util BitSet set

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Introduction

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

Prototype

public void set(int fromIndex, int toIndex)

Source Link

Document

Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to true .

Usage

From source file:org.caleydo.core.util.impute.KNNImpute.java

/**
 * split the neighbor hood in two groups based on 2 k-means
 *
 * @param neighborhood/*from  ww  w . j  ava2  s  . c o  m*/
 * @return
 */
private Pair<List<Gene>, List<Gene>> twoMeanClusterSplit(List<Gene> neighborhood) {
    final int n = neighborhood.size();

    final int maxit = desc.getMaxit();
    final double eps = desc.getEps();

    int a_start = r.nextInt(n);
    int b_start = r.nextInt(n);
    Gene a_center = new Gene(1, -1, Arrays.copyOf(neighborhood.get(a_start).data, samples));
    Gene b_center = new Gene(1, -1, Arrays.copyOf(neighborhood.get(b_start).data, samples));
    float[] a_center_pong = new float[samples];
    Arrays.fill(a_center_pong, Float.NaN);
    float[] b_center_pong = new float[samples];
    Arrays.fill(b_center_pong, Float.NaN);

    float[] tmp;
    BitSet partOf_a = new BitSet(n);

    double d_old = 0;
    for (int i = 0; i < maxit; ++i) {
        int j = 0;
        int changed = 0;
        double d_new = 0;
        for (Gene gene : neighborhood) {
            final double a_distance = distance(a_center, gene);
            final double b_distance = distance(b_center, gene);
            final boolean in_a = a_distance < b_distance;
            if (partOf_a.get(j) != in_a) {
                changed++;
                partOf_a.set(j, in_a);
            }
            d_new += in_a ? a_distance : b_distance;
            tmp = in_a ? a_center_pong : b_center_pong;
            // shift new center
            for (int k = 0; k < samples; ++k) {
                if (!gene.isNaN(k)) {
                    if (Float.isNaN(tmp[k]))
                        tmp[k] = gene.get(k);
                    else
                        tmp[k] += gene.get(k);
                }
            }
            j++;
        }
        if (changed == 0 || d_new == 0)
            break;
        final double ratio = Math.abs(d_new - d_old) / d_old;
        if (i > 0 && ratio < eps)
            break;
        d_old = d_new;
        int a_n = partOf_a.cardinality();
        int b_n = n - a_n;
        if (a_n == 0 || b_n == 0) {
            // FIXME
        }
        updateCenter(a_center, a_center_pong, a_n);
        updateCenter(b_center, b_center_pong, b_n);
    }

    return split(neighborhood, partOf_a);
}

From source file:srebrinb.compress.sevenzip.SevenZFile.java

private BitSet readAllOrBits(final ByteBuffer header, final int size) throws IOException {
    final int areAllDefined = getUnsignedByte(header);
    final BitSet bits;
    if (areAllDefined != 0) {
        bits = new BitSet(size);
        for (int i = 0; i < size; i++) {
            bits.set(i, true);
        }/*w  w  w .ja  va2 s.co  m*/
    } else {
        bits = readBits(header, size);
    }
    return bits;
}

From source file:bobs.is.compress.sevenzip.SevenZFile.java

private BitSet readAllOrBits(final DataInput header, final int size) throws IOException {
    final int areAllDefined = header.readUnsignedByte();
    final BitSet bits;
    if (areAllDefined != 0) {
        bits = new BitSet(size);
        for (int i = 0; i < size; i++) {
            bits.set(i, true);
        }//w  w  w  .  ja v a  2s.  c  o  m
    } else {
        bits = readBits(header, size);
    }
    return bits;
}

From source file:srebrinb.compress.sevenzip.SevenZFile.java

private BitSet readBits(final ByteBuffer header, final int size) throws IOException {
    final BitSet bits = new BitSet(size);
    int mask = 0;
    int cache = 0;
    for (int i = 0; i < size; i++) {
        if (mask == 0) {
            mask = 0x80;//from w  w w.  ja va 2  s.c  o  m
            cache = getUnsignedByte(header);
        }
        bits.set(i, (cache & mask) != 0);
        mask >>>= 1;
    }
    return bits;
}

From source file:bobs.is.compress.sevenzip.SevenZFile.java

private BitSet readBits(final DataInput header, final int size) throws IOException {
    final BitSet bits = new BitSet(size);
    int mask = 0;
    int cache = 0;
    for (int i = 0; i < size; i++) {
        if (mask == 0) {
            mask = 0x80;// w ww  . j a  v a2  s.c o m
            cache = header.readUnsignedByte();
        }
        bits.set(i, (cache & mask) != 0);
        mask >>>= 1;
    }
    return bits;
}

From source file:org.alfresco.module.org_alfresco_module_rm.capability.RMAfterInvocationProvider.java

private Object[] decide(Authentication authentication, Object object, ConfigAttributeDefinition config,
        Object[] returnedObject) {
    // Assumption: value is not null
    BitSet incudedSet = new BitSet(returnedObject.length);

    List<ConfigAttributeDefintion> supportedDefinitions = extractSupportedDefinitions(config);

    if (supportedDefinitions.size() == 0) {
        return returnedObject;
    }/* w  w w .j a  v a 2s.c o  m*/

    for (int i = 0, l = returnedObject.length; i < l; i++) {
        Object current = returnedObject[i];

        int parentReadCheck = checkRead(getParentReadCheckNode(current));
        int childReadChek = checkRead(getChildReadCheckNode(current));

        for (ConfigAttributeDefintion cad : supportedDefinitions) {
            incudedSet.set(i, true);
            NodeRef testNodeRef = null;
            if (cad.parent) {
                if (StoreRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = null;
                } else if (NodeRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = nodeService.getPrimaryParent((NodeRef) current).getParentRef();
                } else if (ChildAssociationRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = ((ChildAssociationRef) current).getParentRef();
                } else if (PermissionCheckValue.class.isAssignableFrom(current.getClass())) {
                    NodeRef nodeRef = ((PermissionCheckValue) current).getNodeRef();
                    testNodeRef = nodeService.getPrimaryParent(nodeRef).getParentRef();
                } else {
                    throw new ACLEntryVoterException(
                            "The specified parameter is recognized: " + current.getClass());
                }
            } else {
                if (StoreRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = nodeService.getRootNode((StoreRef) current);
                } else if (NodeRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = (NodeRef) current;
                } else if (ChildAssociationRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = ((ChildAssociationRef) current).getChildRef();
                } else if (PermissionCheckValue.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = ((PermissionCheckValue) current).getNodeRef();
                } else {
                    throw new ACLEntryVoterException(
                            "The specified parameter is recognized: " + current.getClass());
                }
            }

            if (logger.isDebugEnabled()) {
                logger.debug("\t" + cad.typeString + " test on " + testNodeRef + " from "
                        + current.getClass().getName());
            }

            if (isUnfiltered(testNodeRef)) {
                continue;
            }

            int readCheck = childReadChek;
            if (cad.parent) {
                readCheck = parentReadCheck;
            }

            if (incudedSet.get(i) && (testNodeRef != null)
                    && (readCheck != AccessDecisionVoter.ACCESS_GRANTED)) {
                incudedSet.set(i, false);
            }

        }
    }

    if (incudedSet.cardinality() == returnedObject.length) {
        return returnedObject;
    } else {
        Object[] answer = new Object[incudedSet.cardinality()];
        for (int i = incudedSet.nextSetBit(0), p = 0; i >= 0; i = incudedSet.nextSetBit(++i), p++) {
            answer[p] = returnedObject[i];
        }
        return answer;
    }
}

From source file:org.alfresco.repo.security.permissions.impl.acegi.ACLEntryAfterInvocationProvider.java

@SuppressWarnings("rawtypes")
private Object[] decide(Authentication authentication, Object object, ConfigAttributeDefinition config,
        Object[] returnedObject) throws AccessDeniedException {
    // Assumption: value is not null
    BitSet incudedSet = new BitSet(returnedObject.length);

    List<ConfigAttributeDefintion> supportedDefinitions = extractSupportedDefinitions(config);

    if (supportedDefinitions.size() == 0) {
        return returnedObject;
    }//from   w w w.  j av  a  2s .  c o m

    for (int i = 0, l = returnedObject.length; i < l; i++) {
        Object current = returnedObject[i];
        for (ConfigAttributeDefintion cad : supportedDefinitions) {
            incudedSet.set(i, true);
            NodeRef testNodeRef = null;
            if (cad.typeString.equals(AFTER_ACL_NODE)) {
                if (StoreRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = nodeService.getRootNode((StoreRef) current);
                } else if (NodeRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = (NodeRef) current;
                } else if (ChildAssociationRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = ((ChildAssociationRef) current).getChildRef();
                } else if (Pair.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = (NodeRef) ((Pair) current).getSecond();
                } else if (PermissionCheckValue.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = ((PermissionCheckValue) current).getNodeRef();
                } else {
                    throw new ACLEntryVoterException(
                            "The specified parameter is recognized: " + current.getClass());
                }
            } else if (cad.typeString.equals(AFTER_ACL_PARENT)) {
                if (StoreRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = null;
                } else if (NodeRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = nodeService.getPrimaryParent((NodeRef) current).getParentRef();
                } else if (ChildAssociationRef.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = ((ChildAssociationRef) current).getParentRef();
                } else if (Pair.class.isAssignableFrom(current.getClass())) {
                    testNodeRef = (NodeRef) ((Pair) current).getSecond();
                } else if (PermissionCheckValue.class.isAssignableFrom(current.getClass())) {
                    NodeRef nodeRef = ((PermissionCheckValue) current).getNodeRef();
                    testNodeRef = nodeService.getPrimaryParent(nodeRef).getParentRef();
                } else {
                    throw new ACLEntryVoterException(
                            "The specified parameter is recognized: " + current.getClass());
                }
            }

            if (log.isDebugEnabled()) {
                log.debug("\t" + cad.typeString + " test on " + testNodeRef + " from "
                        + current.getClass().getName());
            }

            if (isUnfiltered(testNodeRef)) {
                continue;
            }

            if (incudedSet.get(i) && (testNodeRef != null) && (permissionService.hasPermission(testNodeRef,
                    cad.required.toString()) == AccessStatus.DENIED)) {
                incudedSet.set(i, false);
            }

        }
    }

    if (incudedSet.cardinality() == returnedObject.length) {
        return returnedObject;
    } else {
        Object[] answer = new Object[incudedSet.cardinality()];
        for (int i = incudedSet.nextSetBit(0), p = 0; i >= 0; i = incudedSet.nextSetBit(++i), p++) {
            answer[p] = returnedObject[i];
        }
        return answer;
    }
}

From source file:org.apache.mele.embedded.HadoopQueueEmbedded.java

private boolean ackCheck() throws IOException {
    LOG.info("Starting ack check");
    BitSet bitSet = new BitSet();
    FileSystem fileSystem = null;
    try {//from   ww  w . ja  v a 2s  . c  o m
        _ackLock.lock();
        _ackOutputStream.close();
        fileSystem = newFileSystem(_file);
        FileStatus fileStatus = fileSystem.getFileStatus(_file);
        long dataLength = fileStatus.getLen();
        long totalAckLength = getTotalAckLength(fileSystem);
        if (!couldContainAllAcks(totalAckLength)) {
            LOG.info("Existing early [" + totalAckLength + "] because [" + totalAckLength % 12 + "]");
            return false;
        }
        for (Path ackFile : _ackFiles) {
            LOG.info("Starting ack check for file [" + ackFile + "]");
            DFSInputStream inputStream = null;
            try {
                inputStream = getDFS(fileSystem.open(ackFile));
                long length = inputStream.getFileLength();
                DataInputStream dataInputStream = new DataInputStream(inputStream);
                while (length > 0) {
                    int pos = (int) dataInputStream.readLong();
                    // @TODO check position
                    // 4 bytes for storing the length of the message
                    int len = dataInputStream.readInt() + 4;
                    bitSet.set(pos, pos + len);
                    length -= 12;
                }
                if (bitSet.cardinality() == dataLength) {
                    return true;
                }
            } finally {
                if (inputStream != null) {
                    inputStream.close();
                }
            }
        }
        return false;
    } finally {
        reopenAckFile(fileSystem);
        _ackLock.unlock();
        if (fileSystem != null) {
            fileSystem.close();
        }
    }
}

From source file:com.ibm.cics.ca1y.Emit.java

/**
 * Add name / value properties from the contents of CICS start data.
 * //from  w  ww.  j av  a2 s. co m
 * @param props
 *            - the properties to add to.
 * @return true if successful
 */
private static boolean addRetrieveData(Properties props) {
    BitSet bs = new BitSet();
    bs.set(RetrieveBits.DATA, true);
    RetrievedDataHolder rdh = new RetrievedDataHolder();

    try {
        Task.getTask().retrieve(bs, rdh);

    } catch (Exception e) {
        e.printStackTrace();
        return false;
    }

    String configuration;

    try {
        configuration = new String(rdh.getValue().getData(), LOCAL_CCSID);

    } catch (Exception e) {
        logger.warning(messages.getString("InvalidStartData") + " " + LOCAL_CCSID + ":" + e.getMessage());

        return false;
    }

    if (logger.isLoggable(Level.FINE)) {
        logger.fine(messages.getString("LoadingPropertiesFromStartData") + ":" + configuration);
    }

    return Util.loadProperties(props, configuration);
}

From source file:de.unijena.bioinf.FragmentationTreeConstruction.computation.FragmentationPatternAnalysis.java

/**
 * Step 3. Normalizing//  w  w  w.j a v  a 2  s.co m
 * Merge all peaks within a single spectrum
 * Return a list of peaks (from all spectra) with relative intensities
 */
public ProcessedInput performNormalization(ProcessedInput input) {
    final Ms2Experiment experiment = input.getExperimentInformation();
    final double parentMass = experiment.getIonMass();
    final ArrayList<ProcessedPeak> peaklist = new ArrayList<ProcessedPeak>(100);
    final Deviation mergeWindow = getDefaultProfile().getAllowedMassDeviation().divide(2d);
    final Ionization ion = experiment.getPrecursorIonType().getIonization();
    double globalMaxIntensity = 0d;
    for (Ms2Spectrum s : experiment.getMs2Spectra()) {
        // merge peaks: iterate them from highest to lowest intensity and remove peaks which
        // are in the mass range of a high intensive peak
        final MutableSpectrum<Peak> sortedByIntensity = new SimpleMutableSpectrum(s);
        Spectrums.sortSpectrumByDescendingIntensity(sortedByIntensity);
        // simple spectra are always ordered by mass
        final SimpleSpectrum sortedByMass = new SimpleSpectrum(s);
        final BitSet deletedPeaks = new BitSet(s.size());
        for (int i = 0; i < s.size(); ++i) {
            // get index of peak in mass-ordered spectrum
            final double mz = sortedByIntensity.getMzAt(i);
            final int index = Spectrums.binarySearch(sortedByMass, mz);
            assert index >= 0;
            if (deletedPeaks.get(index))
                continue; // peak is already deleted
            // delete all peaks within the mass range
            for (int j = index - 1; j >= 0 && mergeWindow.inErrorWindow(mz, sortedByMass.getMzAt(j)); --j)
                deletedPeaks.set(j, true);
            for (int j = index + 1; j < s.size() && mergeWindow.inErrorWindow(mz, sortedByMass.getMzAt(j)); ++j)
                deletedPeaks.set(j, true);
        }
        final int offset = peaklist.size();
        // add all remaining peaks to the peaklist
        for (int i = 0; i < s.size(); ++i) {
            if (!deletedPeaks.get(i)) {
                final ProcessedPeak propeak = new ProcessedPeak(
                        new MS2Peak(s, sortedByMass.getMzAt(i), sortedByMass.getIntensityAt(i)));
                propeak.setIon(ion);
                peaklist.add(propeak);

            }
        }
        // now performNormalization spectrum. Ignore peaks near to the parent peak
        final double lowerbound = parentMass - 0.1d;
        double scale = 0d;
        for (int i = offset; i < peaklist.size() && peaklist.get(i).getMz() < lowerbound; ++i) {
            scale = Math.max(scale, peaklist.get(i).getIntensity());
        }
        if (scale == 0)
            scale = peaklist.get(0).getIntensity(); // happens for spectra with only one peak
        // now set local relative intensities
        for (int i = offset; i < peaklist.size(); ++i) {
            final ProcessedPeak peak = peaklist.get(i);
            peak.setLocalRelativeIntensity(peak.getIntensity() / scale);
        }
        // and adjust global relative intensity
        globalMaxIntensity = Math.max(globalMaxIntensity, scale);
    }
    // now calculate global normalized intensities
    for (ProcessedPeak peak : peaklist) {
        peak.setGlobalRelativeIntensity(peak.getIntensity() / globalMaxIntensity);
        peak.setRelativeIntensity(
                normalizationType == NormalizationType.GLOBAL ? peak.getGlobalRelativeIntensity()
                        : peak.getLocalRelativeIntensity());
    }
    // finished!
    input.setMergedPeaks(peaklist);

    // postprocess
    postProcess(PostProcessor.Stage.AFTER_NORMALIZING, input);
    return input;
}