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

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

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Introduction

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

Prototype

public static <C extends Comparable<?>> Range<C> closed(C lower, C upper)

Source Link

Document

Returns a range that contains all values greater than or equal to lower and less than or equal to upper .

Usage

From source file:net.sf.mzmine.modules.peaklistmethods.msms.msmsscore.MSMSScoreCalculator.java

/**
 * Returns a calculated similarity score of
 *///from  w  ww.  j  a  v a  2  s . com
public static MSMSScore evaluateMSMS(IMolecularFormula parentFormula, Scan msmsScan, ParameterSet parameters) {

    MZTolerance msmsTolerance = parameters.getParameter(MSMSScoreParameters.msmsTolerance).getValue();
    String massListName = parameters.getParameter(MSMSScoreParameters.massList).getValue();

    MassList massList = msmsScan.getMassList(massListName);

    if (massList == null) {
        throw new IllegalArgumentException("Scan #" + msmsScan.getScanNumber()
                + " does not have a mass list called '" + massListName + "'");
    }

    DataPoint msmsIons[] = massList.getDataPoints();

    if (msmsIons == null) {
        throw new IllegalArgumentException(
                "Mass list " + massList + " does not contain data for scan #" + msmsScan.getScanNumber());
    }

    MolecularFormulaRange msmsElementRange = new MolecularFormulaRange();
    for (IIsotope isotope : parentFormula.isotopes()) {
        msmsElementRange.addIsotope(isotope, 0, parentFormula.getIsotopeCount(isotope));
    }

    int totalMSMSpeaks = 0, interpretedMSMSpeaks = 0;
    Map<DataPoint, String> msmsAnnotations = new Hashtable<DataPoint, String>();

    msmsCycle: for (DataPoint dp : msmsIons) {

        // Check if this is an isotope
        Range<Double> isotopeCheckRange = Range.closed(dp.getMZ() - 1.4, dp.getMZ() - 0.6);
        for (DataPoint dpCheck : msmsIons) {
            // If we have any MS/MS peak with 1 neutron mass smaller m/z
            // and higher intensity, it means the current peak is an
            // isotope and we should ignore it
            if (isotopeCheckRange.contains(dpCheck.getMZ()) && (dpCheck.getIntensity() > dp.getIntensity())) {
                continue msmsCycle;
            }
        }

        // If getPrecursorCharge() returns 0, it means charge is unknown. In
        // that case let's assume charge 1
        int precursorCharge = msmsScan.getPrecursorCharge();
        if (precursorCharge == 0)
            precursorCharge = 1;

        // We don't know the charge of the fragment, so we will simply
        // assume 1
        double neutralLoss = msmsScan.getPrecursorMZ() * precursorCharge - dp.getMZ();

        // Ignore negative neutral losses and parent ion, <5 may be a
        // good threshold
        if (neutralLoss < 5) {
            continue;
        }

        Range<Double> msmsTargetRange = msmsTolerance.getToleranceRange(neutralLoss);

        IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();

        MolecularFormulaGenerator msmsEngine;
        try {
            msmsEngine = new MolecularFormulaGenerator(builder, msmsTargetRange.lowerEndpoint(),
                    msmsTargetRange.upperEndpoint(), msmsElementRange);
        } catch (CDKException e) {
            e.printStackTrace();
            return null;
        }

        IMolecularFormula formula = msmsEngine.getNextFormula();
        if (formula != null) {
            String formulaString = MolecularFormulaManipulator.getString(formula);
            msmsAnnotations.put(dp, formulaString);
            interpretedMSMSpeaks++;
        }

        totalMSMSpeaks++;

    }

    // If we did not evaluate any MS/MS peaks, we cannot calculate a score
    if (totalMSMSpeaks == 0) {
        return null;
    }

    double msmsScore = (double) interpretedMSMSpeaks / totalMSMSpeaks;

    MSMSScore result = new MSMSScore(msmsScore, msmsAnnotations);

    return result;

}

From source file:com.ethlo.geodata.repository.GeoRepository.java

public Map.Entry<Long, Range<Long>> mapIpRange(Map<String, Object> rs) {
    final Long id = MapUtils.getLong(rs, "geoname_id");
    final long lower = MapUtils.getLong(rs, "first");
    final long upper = MapUtils.getLong(rs, "last");
    return new AbstractMap.SimpleEntry<>(id, Range.closed(lower, upper));
}

From source file:io.github.mzmine.parameters.parametertypes.ranges.IntegerRangeEditor.java

@Override
public Range<Integer> getValue() {
    String minValueS = minTxtField.getText();
    String maxValueS = maxTxtField.getText();
    try {//from  w  w  w. j a  va  2 s  .  co  m
        Integer minValue = Integer.parseInt(minValueS);
        Integer maxValue = Integer.parseInt(maxValueS);
        return Range.closed(minValue, maxValue);
    } catch (NumberFormatException e) {
        return null;
    }
}

From source file:io.github.msdk.util.MZTolerance.java

/**
 * <p>/*from   w  w  w  . j a v  a  2 s.c  o m*/
 * getToleranceRange.
 * </p>
 *
 * @param mzValue
 *            a {@link java.lang.Double} object.
 * @return a {@link com.google.common.collect.Range} object.
 */
@SuppressWarnings("null")
public @Nonnull Range<Double> getToleranceRange(final @Nonnull Double mzValue) {
    final @Nonnull Double absoluteTolerance = Math.max(mzTolerance, mzValue / MILLION * ppmTolerance);
    return Range.closed(mzValue - absoluteTolerance, mzValue + absoluteTolerance);
}

From source file:org.opendaylight.controller.cluster.datastore.persisted.FrontendClientMetadata.java

public static FrontendClientMetadata readFrom(final DataInput in) throws IOException, ClassNotFoundException {
    final ClientIdentifier id = ClientIdentifier.readFrom(in);

    final int purgedSize = in.readInt();
    final Builder<UnsignedLong> b = ImmutableRangeSet.builder();
    for (int i = 0; i < purgedSize; ++i) {
        final byte header = WritableObjects.readLongHeader(in);
        final UnsignedLong lower = UnsignedLong.fromLongBits(WritableObjects.readFirstLong(in, header));
        final UnsignedLong upper = UnsignedLong.fromLongBits(WritableObjects.readSecondLong(in, header));

        b.add(Range.closed(lower, upper));
    }/*w w w.j a va2s .c om*/

    final int currentSize = in.readInt();
    final Collection<FrontendHistoryMetadata> currentHistories = new ArrayList<>(currentSize);
    for (int i = 0; i < currentSize; ++i) {
        currentHistories.add(FrontendHistoryMetadata.readFrom(in));
    }

    return new FrontendClientMetadata(id, b.build(), currentHistories);
}

From source file:dollar.api.types.DollarVoid.java

@NotNull
@Override/*from   w  w  w .java 2 s  . com*/
public Value $as(@NotNull Type type) {
    if (type.is(Type._BOOLEAN)) {
        return DollarStatic.$(false);
    } else if (type.is(Type._STRING)) {
        return DollarStatic.$("");
    } else if (type.is(Type._LIST)) {
        return DollarStatic.$(Collections.emptyList());
    } else if (type.is(Type._MAP)) {
        return DollarStatic.$("value", this);
    } else if (type.is(Type._DECIMAL)) {
        return DollarStatic.$(0.0d);
    } else if (type.is(Type._INTEGER)) {
        return DollarStatic.$(0);
    } else if (type.is(Type._VOID)) {
        return this;
    } else if (type.is(Type._RANGE)) {
        return DollarFactory.fromValue(Range.closed($get(DollarStatic.$(0)), $get(DollarStatic.$(0))));
    } else {
        return DollarFactory.failure(ErrorType.INVALID_CAST, type.toString(), false);
    }
}

From source file:io.github.mzmine.parameters.parametertypes.ranges.MZRangeEditor.java

@Override
public Range<Double> getValue() {
    String minValueS = minTxtField.getText();
    String maxValueS = maxTxtField.getText();
    try {//from   w w w . j  a v  a2 s  .  c o m
        double minValue = Double.parseDouble(minValueS);
        double maxValue = Double.parseDouble(maxValueS);
        return Range.closed(minValue, maxValue);
    } catch (NumberFormatException e) {
        return null;
    }
}

From source file:org.apache.aurora.scheduler.base.Numbers.java

/**
 * Convert between range types./* ww  w . ja  v a  2  s.c o  m*/
 *
 * @param range Range to convert.
 * @return A closed range from the first to last of {@code range}.
 */
public static Range<Integer> toRange(IRange range) {
    return Range.closed(range.getFirst(), range.getLast());
}

From source file:org.apache.kylin.storage.cache.TsConditionExtractor.java

private static Range<Long> extractTsConditionInternal(TupleFilter filter, TblColRef colRef) {
    if (filter == null) {
        return Range.all();
    }//from   w  w  w  .  j  a  v a 2 s  . c  om

    if (filter instanceof LogicalTupleFilter) {
        if (filter.getOperator() == TupleFilter.FilterOperatorEnum.AND) {
            Range<Long> ret = Range.all();
            for (TupleFilter child : filter.getChildren()) {
                Range childRange = extractTsConditionInternal(child, colRef);
                if (childRange != null) {
                    if (ret.isConnected(childRange) && !ret.intersection(childRange).isEmpty()) {
                        ret = ret.intersection(childRange);
                    } else {
                        return null;
                    }
                } else {
                    return null;
                }
            }
            return ret.isEmpty() ? null : ret;
        } else {
            //for conditions like date > DATE'2000-11-11' OR date < DATE '1999-01-01'
            //we will use Ranges.all() rather than two ranges to represent them
            return Range.all();
        }
    }

    if (filter instanceof CompareTupleFilter) {
        CompareTupleFilter compareTupleFilter = (CompareTupleFilter) filter;
        if (compareTupleFilter.getColumn() == null)// column will be null at filters like " 1<>1"
            return Range.all();

        if (compareTupleFilter.getColumn().equals(colRef)) {
            Object firstValue = compareTupleFilter.getFirstValue();
            long t;
            switch (compareTupleFilter.getOperator()) {
            case EQ:
                t = DateFormat.stringToMillis((String) firstValue);
                return Range.closed(t, t);
            case LT:
                t = DateFormat.stringToMillis((String) firstValue);
                return Range.lessThan(t);
            case LTE:
                t = DateFormat.stringToMillis((String) firstValue);
                return Range.atMost(t);
            case GT:
                t = DateFormat.stringToMillis((String) firstValue);
                return Range.greaterThan(t);
            case GTE:
                t = DateFormat.stringToMillis((String) firstValue);
                return Range.atLeast(t);
            case NEQ:
            case IN://not handled for now
                break;
            default:
            }
        }
    }
    return Range.all();
}

From source file:org.apache.james.imap.api.message.UidRange.java

private static Range<MessageUid> mergeRanges(Range<MessageUid> range, Range<MessageUid> previous) {
    return Range.closed(previous.lowerEndpoint(), range.upperEndpoint());
}