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

Introduction

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

Prototype

public C lowerEndpoint() 

Source Link

Document

Returns the lower endpoint of this range.

Usage

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/*www  .  j  a v  a2 s  .c  o  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: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 av  a 2  s  . c  o  m
 */
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.zulily.omicron.crontab.ExpressionPart.java

ExpressionPart(final Range<Integer> allowedRange, final String[] stringValues) {
    this.allowedRange = allowedRange;

    final HashMap<String, Integer> stringValuesMap = Maps.newHashMap();

    if (stringValues != null && allowedRange != null) {

        for (int index = 0; index < stringValues.length; index++) {
            stringValuesMap.put(stringValues[index], index + allowedRange.lowerEndpoint()); // correct for 1-based month/d-o-m
        }//www . ja  v a2s .c  o  m

    }

    this.stringNameMap = ImmutableMap.copyOf(stringValuesMap);
}

---

From source file:org.apache.drill.exec.record.RecordIterator.java

public void forward(long delta) {
    if (!enableMarkAndReset) {
        throw new UnsupportedOperationException("mark and reset disabled for this RecordIterator");
    }//from www.  j  a v  a 2s .co  m
    assert delta >= 0;
    assert (delta + outerPosition) < totalRecordCount;
    final long nextOuterPosition = delta + outerPosition;
    final RecordBatchData rbdNew = batches.get(nextOuterPosition);
    final RecordBatchData rbdOld = batches.get(outerPosition);
    assert rbdNew != null;
    assert rbdOld != null;
    container.transferOut(rbdOld.getContainer());
    // Get vectors from new position.
    container.transferIn(rbdNew.getContainer());
    outerPosition = nextOuterPosition;
    final Range<Long> markedBatchRange = batches.getEntry(outerPosition).getKey();
    startBatchPosition = markedBatchRange.lowerEndpoint();
    innerPosition = (int) (outerPosition - startBatchPosition);
    innerRecordCount = (int) (markedBatchRange.upperEndpoint() - startBatchPosition);
}

---

From source file:org.apache.drill.exec.record.RecordIterator.java

public void reset() {
    if (!enableMarkAndReset) {
        throw new UnsupportedOperationException("mark and reset disabled for this RecordIterator");
    }/*w w w  . j  a va2  s  .  c  o  m*/
    if (markedOuterPosition >= 0) {
        // Move to rbd for markedOuterPosition.
        final RecordBatchData rbdNew = batches.get(markedOuterPosition);
        final RecordBatchData rbdOld = batches.get(startBatchPosition);
        assert rbdOld != null;
        assert rbdNew != null;
        if (rbdNew != rbdOld) {
            container.transferOut(rbdOld.getContainer());
            container.transferIn(rbdNew.getContainer());
        }
        innerPosition = markedInnerPosition;
        outerPosition = markedOuterPosition;
        final Range<Long> markedBatchRange = batches.getEntry(outerPosition).getKey();
        startBatchPosition = markedBatchRange.lowerEndpoint();
        innerRecordCount = (int) (markedBatchRange.upperEndpoint() - startBatchPosition);
        markedInnerPosition = -1;
        markedOuterPosition = -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);/*from  w  w  w .  ja  v a  2  s .  c o  m*/
    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.projectmethods.projectsave.RawDataFileSaveHandler.java

/**
 * Create the part of the XML document related to the scans
 * // w w  w  . j  av  a 2  s  .  com
 * @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: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  ww  w. ja  v a2 s .  com
        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: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 v a2 s. co  m*/
    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);
}

---

From source file:org.openmhealth.dsu.repository.MongoDataPointRepositoryImpl.java

void addCreationTimestampCriteria(Query query, Range<OffsetDateTime> timestampRange) {

    if (timestampRange.hasLowerBound() || timestampRange.hasUpperBound()) {

        Criteria timestampCriteria = where("header.creation_date_time");

        if (timestampRange.hasLowerBound()) {
            if (timestampRange.lowerBoundType() == CLOSED) {
                timestampCriteria = timestampCriteria.gte(timestampRange.lowerEndpoint());
            } else {
                timestampCriteria = timestampCriteria.gt(timestampRange.lowerEndpoint());
            }/*from  w w w  . ja v a 2  s  .c  o  m*/
        }

        if (timestampRange.hasUpperBound()) {
            if (timestampRange.upperBoundType() == CLOSED) {
                timestampCriteria = timestampCriteria.lte(timestampRange.upperEndpoint());
            } else {
                timestampCriteria = timestampCriteria.lt(timestampRange.upperEndpoint());
            }
        }

        query.addCriteria(timestampCriteria);
    }
}

---

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