Example usage for com.google.common.collect Range upperEndpoint

List of usage examples for com.google.common.collect Range upperEndpoint

  1. HOME
  2. Java
  3. com.google.common
  4. com.google.common.collect.*
  5. Range
  6. upperEndpoint

Introduction

In this page you can find the example usage for com.google.common.collect Range upperEndpoint.

Prototype

public C upperEndpoint()

Source Link

Document

Returns the upper endpoint of this range.

Usage

From source file:com.google.googlejavaformat.java.JavaOutput.java

/**
 * Expand a token range to start and end on acceptable boundaries for re-formatting.
 *
 * @param iRange the {@link Range} of tokens
 * @return the expanded token range//from   ww w.j a  v  a2 s.  com
 */
private Range<Integer> expandToBreakableRegions(Range<Integer> iRange) {
    // The original line range.
    int loTok = iRange.lowerEndpoint();
    int hiTok = iRange.upperEndpoint() - 1;

    // Expand the token indices to formattable boundaries (e.g. edges of statements).
    if (!partialFormatRanges.contains(loTok) || !partialFormatRanges.contains(hiTok)) {
        return EMPTY_RANGE;
    }
    loTok = partialFormatRanges.rangeContaining(loTok).lowerEndpoint();
    hiTok = partialFormatRanges.rangeContaining(hiTok).upperEndpoint();
    return Range.closedOpen(loTok, hiTok + 1);
}

From source file:com.yahoo.gondola.container.client.ZookeeperShardManagerClient.java

@Override
public void migrateBuckets(Range<Integer> splitRange, String fromShardId, String toShardId, long timeoutMs)
        throws ShardManagerException, InterruptedException {
    // Enable special mode on destination shard.
    sendActionToShard(toShardId, MIGRATE_1, splitRange.lowerEndpoint(), splitRange.upperEndpoint(), fromShardId,
            toShardId, timeoutMs);//w w w  .  ja  va 2 s  .  c om
    waitCondition(fromShardId, ZookeeperStat::isMigrating1Operational, timeoutMs);

    // set all nodes in migrating mode, traffic to the original shard will route to new shard in this state.
    setBuckets(splitRange, fromShardId, toShardId, false);

    // set all nodes migration complete, all traffic will route to new shard.
    setBuckets(splitRange, fromShardId, toShardId, true);

    // done, mark operation as completed
    sendActionToAll(Action.NOOP);
}

From source file:net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.ADAPpeakpicking.ADAPDetector.java

@Override
public Feature[] resolvePeaks(final Feature chromatogram, final ParameterSet parameters,
        RSessionWrapper rSession, double msmsRange, double rTRangeMSMS) throws RSessionWrapperException {

    int scanNumbers[] = chromatogram.getScanNumbers();
    final int scanCount = scanNumbers.length;
    double retentionTimes[] = new double[scanCount];
    double intensities[] = new double[scanCount];
    RawDataFile dataFile = chromatogram.getDataFile();
    for (int i = 0; i < scanCount; i++) {
        final int scanNum = scanNumbers[i];
        retentionTimes[i] = dataFile.getScan(scanNum).getRetentionTime();
        DataPoint dp = chromatogram.getDataPoint(scanNum);
        if (dp != null)
            intensities[i] = dp.getIntensity();
        else/*from   w  ww.  j  a v a 2  s  .co  m*/
            intensities[i] = 0.0;
    }

    //List<PeakInfo> ADAPPeaks = new ArrayList<PeakInfo>();
    List<PeakInfo> ADAPPeaks = null;

    Range<Double> peakDuration = parameters.getParameter(PEAK_DURATION).getValue();

    final MZmineProcessingStep<SNEstimatorChoice> signalNoiseEstimator = parameters.getParameter(SN_ESTIMATORS)
            .getValue();
    String SNCode = signalNoiseEstimator.getModule().getSNCode();

    double signalNoiseWindowMult = -1.0;
    boolean absWavCoeffs = false;
    Map<String, Object> informationSN = new HashMap<String, Object>();
    if (SNCode == "Wavelet Coefficient Estimator") {
        informationSN.put("code", "Wavelet Coefficient Estimator");
        signalNoiseWindowMult = signalNoiseEstimator.getParameterSet().getParameter(HALF_WAVELET_WINDOW)
                .getValue();
        absWavCoeffs = signalNoiseEstimator.getParameterSet().getParameter(ABS_WAV_COEFFS).getValue();
        informationSN.put("multiplier", signalNoiseWindowMult);
        informationSN.put("absolutewavecoeffs", absWavCoeffs);
    }
    if (SNCode == "Intensity Window Estimator") {
        informationSN.put("code", "Intensity Window Estimator");
    }

    // get the average rt spacing
    double rtSum = 0.0;
    for (int i = 0; i < retentionTimes.length - 1; i++) {
        rtSum += retentionTimes[i + 1] - retentionTimes[i];
    }
    double avgRTInterval = rtSum / ((double) (retentionTimes.length - 1));
    // Change the lower and uper bounds for the wavelet scales from retention times to number of scans.
    Range<Double> rtRangeForCWTScales = parameters.getParameter(RT_FOR_CWT_SCALES_DURATION).getValue();
    double rtLow = rtRangeForCWTScales.lowerEndpoint();
    double rtHigh = rtRangeForCWTScales.upperEndpoint();
    int numScansRTLow = (int) Math.round(rtLow / avgRTInterval);
    int numScansRTHigh = (int) Math.round(rtHigh / avgRTInterval);

    if (numScansRTLow < 1) {
        numScansRTLow = 1;
    }
    if (numScansRTHigh >= retentionTimes.length) {
        numScansRTHigh = retentionTimes.length;
    }

    ADAPPeaks = DeconvoluteSignal(retentionTimes, intensities, chromatogram.getMZ(),
            parameters.getParameter(SN_THRESHOLD).getValue(),
            parameters.getParameter(MIN_FEAT_HEIGHT).getValue(), peakDuration,
            parameters.getParameter(COEF_AREA_THRESHOLD).getValue(), numScansRTLow, numScansRTHigh,
            informationSN);

    final List<ResolvedPeak> resolvedPeaks;

    if (ADAPPeaks == null) {
        resolvedPeaks = new ArrayList<ResolvedPeak>(0);

    } else {

        LOG.finest("Processing peak matrix...");

        // Process peak matrix.
        resolvedPeaks = new ArrayList<ResolvedPeak>(ADAPPeaks.size());

        // The old way could detect the same peak more than once if the wavlet scales were too large.
        // If the left bounds were the same and there was a null point before the right bounds it would
        //make the same peak twice.
        // To avoid the above see if the peak duration range is met before going into
        // the loop

        //for (final double[] peakRow : peakMatrix) {
        for (int i = 0; i < ADAPPeaks.size(); i++) {

            PeakInfo curPeak = ADAPPeaks.get(i);

            SimplePeakInformation information = new SimplePeakInformation();
            information.addProperty("Signal-to-Noise", Double.toString(curPeak.signalToNoiseRatio));
            information.addProperty("Coefficient-over-area", Double.toString(curPeak.coeffOverArea));
            //                information.addProperty("index", 
            //                        //Integer.toString(scans[(int) peakIndex[j] - 1])); // Substract one because r-indices start from 1
            //                        Integer.toString((int) curPeak.peakIndex));
            //                information.addProperty("sharpness", 
            //                        Double.toString(curPeak.sharpness));
            //                information.addProperty("signalToNoiseRatio", 
            //                        Double.toString(curPeak.signalToNoiseRatio));
            //                information.addProperty("isShared", 
            //                        Boolean.toString(curPeak.isShared));
            //                        //Boolean.toString(1.0 == curPeak.isShared));
            //                information.addProperty("offset", 
            //                        Integer.toString((int) curPeak.offset));

            ResolvedPeak peak = new ResolvedPeak(chromatogram, curPeak.leftApexIndex, curPeak.rightApexIndex,
                    msmsRange, rTRangeMSMS);
            peak.setPeakInformation(information);

            resolvedPeaks.add(peak);
            //resolvedPeaks.add(new ResolvedPeak(chromatogram,curPeak.leftApexIndex, curPeak.rightApexIndex));
        }
    }

    return resolvedPeaks.toArray(new ResolvedPeak[resolvedPeaks.size()]);
}

From source file:net.sf.mzmine.modules.projectmethods.projectsave.RawDataFileSaveHandler.java

/**
 * Create the part of the XML document related to the scans
 * //from ww w .j  a  v a  2 s  .c om
 * @param scan
 * @param element
 */
private void fillScanElement(Scan scan, TransformerHandler hd) throws SAXException, IOException {
    // <SCAN_ID>
    AttributesImpl atts = new AttributesImpl();
    hd.startElement("", "", RawDataElementName.SCAN_ID.getElementName(), atts);
    hd.characters(String.valueOf(scan.getScanNumber()).toCharArray(), 0,
            String.valueOf(scan.getScanNumber()).length());
    hd.endElement("", "", RawDataElementName.SCAN_ID.getElementName());

    // <MS_LEVEL>
    hd.startElement("", "", RawDataElementName.MS_LEVEL.getElementName(), atts);
    hd.characters(String.valueOf(scan.getMSLevel()).toCharArray(), 0,
            String.valueOf(scan.getMSLevel()).length());
    hd.endElement("", "", RawDataElementName.MS_LEVEL.getElementName());

    if (scan.getMSLevel() >= 2) {
        // <PRECURSOR_MZ>
        hd.startElement("", "", RawDataElementName.PRECURSOR_MZ.getElementName(), atts);
        hd.characters(String.valueOf(scan.getPrecursorMZ()).toCharArray(), 0,
                String.valueOf(scan.getPrecursorMZ()).length());
        hd.endElement("", "", RawDataElementName.PRECURSOR_MZ.getElementName());

        // <PRECURSOR_CHARGE>
        hd.startElement("", "", RawDataElementName.PRECURSOR_CHARGE.getElementName(), atts);
        hd.characters(String.valueOf(scan.getPrecursorCharge()).toCharArray(), 0,
                String.valueOf(scan.getPrecursorCharge()).length());
        hd.endElement("", "", RawDataElementName.PRECURSOR_CHARGE.getElementName());
    }

    // <RETENTION_TIME>
    hd.startElement("", "", RawDataElementName.RETENTION_TIME.getElementName(), atts);
    // In the project file, retention time is represented in seconds, for
    // historical reasons
    double rt = scan.getRetentionTime() * 60d;
    hd.characters(String.valueOf(rt).toCharArray(), 0, String.valueOf(rt).length());
    hd.endElement("", "", RawDataElementName.RETENTION_TIME.getElementName());

    // <CENTROIDED>
    hd.startElement("", "", RawDataElementName.CENTROIDED.getElementName(), atts);
    hd.characters(String.valueOf(scan.getSpectrumType()).toCharArray(), 0,
            String.valueOf(scan.getSpectrumType()).length());
    hd.endElement("", "", RawDataElementName.CENTROIDED.getElementName());

    // <QUANTITY_DATAPOINTS>
    hd.startElement("", "", RawDataElementName.QUANTITY_DATAPOINTS.getElementName(), atts);
    hd.characters(String.valueOf((scan.getNumberOfDataPoints())).toCharArray(), 0,
            String.valueOf((scan.getNumberOfDataPoints())).length());
    hd.endElement("", "", RawDataElementName.QUANTITY_DATAPOINTS.getElementName());

    // <FRAGMENT_SCAN>
    if (scan.getFragmentScanNumbers() != null) {
        int[] fragmentScans = scan.getFragmentScanNumbers();
        atts.addAttribute("", "", RawDataElementName.QUANTITY.getElementName(), "CDATA",
                String.valueOf(fragmentScans.length));
        hd.startElement("", "", RawDataElementName.QUANTITY_FRAGMENT_SCAN.getElementName(), atts);
        atts.clear();
        for (int i : fragmentScans) {
            hd.startElement("", "", RawDataElementName.FRAGMENT_SCAN.getElementName(), atts);
            hd.characters(String.valueOf(i).toCharArray(), 0, String.valueOf(i).length());
            hd.endElement("", "", RawDataElementName.FRAGMENT_SCAN.getElementName());
        }
        hd.endElement("", "", RawDataElementName.QUANTITY_FRAGMENT_SCAN.getElementName());

    }

    // <MASS_LIST>
    MassList massLists[] = scan.getMassLists();
    for (MassList massList : massLists) {
        StorableMassList stMassList = (StorableMassList) massList;
        atts.addAttribute("", "", RawDataElementName.NAME.getElementName(), "CDATA", stMassList.getName());
        atts.addAttribute("", "", RawDataElementName.STORAGE_ID.getElementName(), "CDATA",
                String.valueOf(stMassList.getStorageID()));
        hd.startElement("", "", RawDataElementName.MASS_LIST.getElementName(), atts);
        atts.clear();
        hd.endElement("", "", RawDataElementName.MASS_LIST.getElementName());
    }

    // <POLARITY>
    hd.startElement("", "", RawDataElementName.POLARITY.getElementName(), atts);
    String pol = scan.getPolarity().toString();
    hd.characters(pol.toCharArray(), 0, pol.length());
    hd.endElement("", "", RawDataElementName.POLARITY.getElementName());

    // <SCAN_DESCRIPTION>
    hd.startElement("", "", RawDataElementName.SCAN_DESCRIPTION.getElementName(), atts);
    String scanDesc = scan.getScanDefinition();
    hd.characters(scanDesc.toCharArray(), 0, scanDesc.length());
    hd.endElement("", "", RawDataElementName.SCAN_DESCRIPTION.getElementName());

    // <SCAN_MZ_RANGE>
    hd.startElement("", "", RawDataElementName.SCAN_MZ_RANGE.getElementName(), atts);
    Range<Double> mzRange = scan.getScanningMZRange();
    String mzRangeStr = mzRange.lowerEndpoint() + "-" + mzRange.upperEndpoint();
    hd.characters(mzRangeStr.toCharArray(), 0, mzRangeStr.length());
    hd.endElement("", "", RawDataElementName.SCAN_MZ_RANGE.getElementName());

}

From source file:it.units.malelab.ege.ge.mapper.HierarchicalMapper.java

public Node<T> mapIteratively(BitsGenotype genotype, int[] bitUsages) throws MappingException {
    Node<EnhancedSymbol<T>> enhancedTree = new Node<>(
            new EnhancedSymbol<>(grammar.getStartingSymbol(), Range.closedOpen(0, genotype.size())));
    while (true) {
        Node<EnhancedSymbol<T>> nodeToBeReplaced = null;
        for (Node<EnhancedSymbol<T>> node : enhancedTree.leafNodes()) {
            if (grammar.getRules().keySet().contains(node.getContent().getSymbol())) {
                nodeToBeReplaced = node;
                break;
            }/*from  www  . j  a va 2  s.  c  om*/
        }
        if (nodeToBeReplaced == null) {
            break;
        }
        //get genotype
        T symbol = nodeToBeReplaced.getContent().getSymbol();
        Range<Integer> symbolRange = nodeToBeReplaced.getContent().getRange();
        List<List<T>> options = grammar.getRules().get(symbol);
        //get option
        List<T> symbols;
        if ((symbolRange.upperEndpoint() - symbolRange.lowerEndpoint()) < options.size()) {
            int count = (symbolRange.upperEndpoint() - symbolRange.lowerEndpoint() > 0)
                    ? genotype.slice(symbolRange).count()
                    : genotype.count();
            int index = shortestOptionIndexesMap.get(symbol)
                    .get(count % shortestOptionIndexesMap.get(symbol).size());
            symbols = options.get(index);
        } else {
            symbols = chooseOption(genotype, symbolRange, options);
            for (int i = symbolRange.lowerEndpoint(); i < symbolRange.upperEndpoint(); i++) {
                bitUsages[i] = bitUsages[i] + 1;
            }
        }
        //add children
        List<Range<Integer>> childRanges = getChildrenSlices(symbolRange, symbols);
        for (int i = 0; i < symbols.size(); i++) {
            Range<Integer> childRange = childRanges.get(i);
            if (childRanges.get(i).equals(symbolRange)
                    && (childRange.upperEndpoint() - childRange.lowerEndpoint() > 0)) {
                childRange = Range.closedOpen(symbolRange.lowerEndpoint(), symbolRange.upperEndpoint() - 1);
            }
            Node<EnhancedSymbol<T>> newChild = new Node<>(new EnhancedSymbol<>(symbols.get(i), childRange));
            nodeToBeReplaced.getChildren().add(newChild);
        }
    }
    //convert
    return extractFromEnhanced(enhancedTree);
}

From source file:org.noroomattheinn.visibletesla.Prefs.java

private Range<Long> getLoadPeriod() {
    Range<Long> range = Range.closed(Long.MIN_VALUE, Long.MAX_VALUE);

    long now = System.currentTimeMillis();
    LoadPeriod period = nameToLoadPeriod.get(loadPeriod.get());
    if (period == null) {
        period = LoadPeriod.All;//from w w w  .j  a  va  2 s  .co m
        loadPeriod.set(nameToLoadPeriod.inverse().get(period));
    }
    switch (period) {
    case None:
        range = Range.closed(now + 1000, now + 1000L); // Empty Range
        break;
    case Last7:
        range = Range.closed(now - (7 * 24 * 60 * 60 * 1000L), now);
        break;
    case Last14:
        range = Range.closed(now - (14 * 24 * 60 * 60 * 1000L), now);
        break;
    case Last30:
        range = Range.closed(now - (30 * 24 * 60 * 60 * 1000L), now);
        break;
    case ThisWeek:
        Range<Date> thisWeek = getThisWeek();
        range = Range.closed(thisWeek.lowerEndpoint().getTime(), thisWeek.upperEndpoint().getTime());
        break;
    case ThisMonth:
        Range<Date> thisMonth = getThisMonth();
        range = Range.closed(thisMonth.lowerEndpoint().getTime(), thisMonth.upperEndpoint().getTime());
        break;
    case All:
    default:
        break;

    }
    return range;
}

From source file:com.google.eclipse.protobuf.validation.ProtobufJavaValidator.java

private String rangeToString(Range<Long> range) {
    if (range.hasLowerBound() && range.hasUpperBound() && range.lowerEndpoint() == range.upperEndpoint()) {
        return String.valueOf(range.lowerEndpoint());
    }/*from w ww.  j a  v a  2 s. com*/

    String upper = range.hasUpperBound() ? String.valueOf(range.upperEndpoint()) : indexRanges.getMaxKeyword();
    return String.format("%d to %s", range.lowerEndpoint(), upper);
}

From source file:edu.cmu.lti.oaqa.framework.eval.passage.PassageMAPEvalAggregator.java

private float getAvgPsg2MAP(List<Passage> docs, List<Passage> gs) {
    if (gs.size() == 0) {
        return 0;
    }/* w w w. j  a  v a  2s .c om*/
    Map<String, RangeSet<Integer>> gsId2Spans = Maps.newHashMap();
    Map<String, RangeSet<Integer>> trackGsId2Spans = Maps.newHashMap();
    for (Passage g : gs) {
        String id = g.getUri();
        if (!gsId2Spans.containsKey(id)) {
            gsId2Spans.put(id, TreeRangeSet.<Integer>create());
            trackGsId2Spans.put(id, TreeRangeSet.<Integer>create());
        }
        gsId2Spans.get(g.getUri()).add(Range.closedOpen(g.getBegin(), g.getEnd()));
        trackGsId2Spans.get(g.getUri()).add(Range.closedOpen(g.getBegin(), g.getEnd()));
    }
    int totalChars = 0;
    int overlapLength = 0;
    float sumPrecision = 0;
    for (Passage doc : docs) {
        Range<Integer> docRange = Range.closedOpen(doc.getBegin(), doc.getEnd());
        String docId = doc.getUri();
        if (!gsId2Spans.containsKey(docId) || gsId2Spans.get(docId).encloses(docRange)) {
            totalChars += docRange.upperEndpoint() - docRange.lowerEndpoint();
            continue;
        }
        for (int offset = docRange.lowerEndpoint(); offset < docRange.upperEndpoint(); offset++) {
            if (gsId2Spans.containsKey(docId) && gsId2Spans.get(docId).contains(offset)) {
                if (trackGsId2Spans.get(docId).contains(offset)) {
                    trackGsId2Spans.get(docId).remove(Range.singleton(offset));
                    // +1
                    totalChars++;
                    overlapLength++;
                    sumPrecision += (float) overlapLength / (float) totalChars;
                }
            } else {
                // -1
                totalChars++;
            }
        }
    }
    int count = 0;
    for (RangeSet<Integer> spans : gsId2Spans.values()) {
        for (Range<Integer> span : spans.asRanges()) {
            count += span.upperEndpoint() - span.lowerEndpoint();
        }
    }
    return (float) sumPrecision / (float) count;
}

From source file:org.dishevelled.bio.range.entrytree.CenteredRangeTree.java

/**
 * Depth first search.//w ww.  j a v  a 2 s.c  o m
 *
 * @param query query range
 * @param node node
 * @param result list of matching ranges
 * @param visited set of visited nodes
 */
private void depthFirstSearch(final Range<C> query, final Node node, final List<Entry<C, V>> result,
        final Set<Node> visited) {
    if (node == null || visited.contains(node) || query.isEmpty()) {
        return;
    }
    if (node.left() != null && Ranges.isLessThan(query, node.center())) {
        depthFirstSearch(query, node.left(), result, visited);
    } else if (node.right() != null && Ranges.isGreaterThan(query, node.center())) {
        depthFirstSearch(query, node.right(), result, visited);
    }
    if (Ranges.isGreaterThan(query, node.center())) {
        for (Entry<C, V> entry : node.overlapByUpperEndpoint()) {
            Range<C> range = entry.getRange();
            if (Ranges.intersect(range, query)) {
                result.add(entry);
            }
            if (Ranges.isGreaterThan(query, range.upperEndpoint())) {
                break;
            }
        }
    } else if (Ranges.isLessThan(query, node.center())) {
        for (Entry<C, V> entry : node.overlapByLowerEndpoint()) {
            Range<C> range = entry.getRange();
            if (Ranges.intersect(range, query)) {
                result.add(entry);
            }
            if (Ranges.isLessThan(query, range.lowerEndpoint())) {
                break;
            }
        }
    } else {
        result.addAll(node.overlapByLowerEndpoint());
    }
    visited.add(node);
}

From source file:de.tuberlin.uebb.jdae.llmsl.ExecutableDAE.java

public ExecutableDAE(final DataLayout layout, Causalisation causalisation,
        InitializationCausalisation iCausalisation, final ContinuousEvent[] continuousEvents,
        SimulationOptions options) {/* w ww  .  j  a va  2s. com*/
    this.options = options;
    this.logger = Logger.getLogger(this.getClass().toString());

    this.layout = layout;
    this.states = causalisation.states;
    data = layout.alloc();

    this.blocks = new IBlock[causalisation.computations.size()];
    int i = 0;
    for (TIntObjectMap<Range<Integer>> block : causalisation.computations) {

        final Set<DerivedEquation> deriveds = Sets.newHashSet();
        final TIntObjectIterator<Range<Integer>> blockIter = block.iterator();
        while (blockIter.hasNext()) {
            blockIter.advance();
            final int eq = blockIter.key();
            final Range<Integer> eqRange = blockIter.value();

            deriveds.add(new DerivedEquation(causalisation.equations[eq], eqRange.lowerEndpoint(),
                    eqRange.upperEndpoint()));
        }

        final IBlock block_i;
        /* always prepare a numerical fallback, just in case */
        final IBlock numericalSolution = new Block(data, layout, causalisation.iteratees.get(i), deriveds,
                options);

        if (causalisation.iteratees.get(i).size() == 1) {
            /* causalisation */
            final GlobalVariable var = causalisation.iteratees.get(i).iterator().next();
            final GlobalEquation eq = deriveds.iterator().next().eqn;

            if (eq.canSpecializeFor(var)) {
                block_i = eq.specializeFor(var, numericalSolution, this);
            } else {
                block_i = numericalSolution;
            }
        } else {
            block_i = numericalSolution;
        }

        blocks[i++] = block_i;

    }
    i = 0;

    this.initials = new IBlock[iCausalisation.computations.size()];
    for (Set<DerivedEquation> block : iCausalisation.computations)
        initials[i] = new Block(data, layout, iCausalisation.iteratees.get(i++), block, options);

    this.execCtxt = new ExecutionContext(0, new GlobalVariable[0], data);

    // must be last, calls methods here
    this.eventHandler = new EventEvaluator(this, continuousEvents);
}