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

Introduction

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

Prototype

public boolean contains(C value) 

Source Link

Document

Returns true if value is within the bounds of this range.

Usage

From source file:net.sf.mzmine.modules.peaklistmethods.alignment.path.scorer.RTScore.java

public double calculateScore(AlignmentPath path, PeakListRow peak, ParameterSet parameters) {
    try {/* w  w  w.  ja  v a 2 s.c  o  m*/
        rtTolerance = parameters.getParameter(PathAlignerParameters.RTTolerance).getValue();
        mzTolerance = parameters.getParameter(PathAlignerParameters.MZTolerance).getValue();
        Range<Double> rtRange = rtTolerance.getToleranceRange(path.getRT());
        Range<Double> mzRange = mzTolerance.getToleranceRange(path.getMZ());

        if (!rtRange.contains(peak.getAverageRT()) || !mzRange.contains(peak.getAverageMZ())) {
            return WORST_SCORE;
        }

        double mzDiff = Math.abs(path.getMZ() - peak.getAverageMZ());

        double rtDiff = Math.abs(path.getRT() - peak.getAverageRT());

        double score = ((mzDiff / (RangeUtils.rangeLength(mzRange) / 2.0)))
                + ((rtDiff / (RangeUtils.rangeLength(rtRange) / 2.0)));

        if (parameters.getParameter(PathAlignerParameters.SameChargeRequired).getValue()) {
            if (!PeakUtils.compareChargeState(path.convertToAlignmentRow(0), peak)) {
                return WORST_SCORE;
            }
        }

        if (parameters.getParameter(PathAlignerParameters.SameIDRequired).getValue()) {
            if (!PeakUtils.compareIdentities(path.convertToAlignmentRow(0), peak)) {
                return WORST_SCORE;
            }
        }

        if (parameters.getParameter(PathAlignerParameters.compareIsotopePattern).getValue()) {
            IsotopePattern ip1 = path.convertToAlignmentRow(0).getBestIsotopePattern();
            IsotopePattern ip2 = peak.getBestIsotopePattern();

            if ((ip1 != null) && (ip2 != null)) {
                ParameterSet isotopeParams = parameters
                        .getParameter(PathAlignerParameters.compareIsotopePattern).getEmbeddedParameters();

                if (!IsotopePatternScoreCalculator.checkMatch(ip1, ip2, isotopeParams)) {
                    return WORST_SCORE;
                }
            }
        }

        return score;
    } catch (NullPointerException e) {
        e.printStackTrace();
        return WORST_SCORE;
    }
}

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From source file:org.apache.cassandra.dht.BootStrapper.java

/** get potential sources for each range, ordered by proximity (as determined by EndpointSnitch) */
Multimap<Range, InetAddress> getRangesWithSources(String table) {
    assert tokenMetadata.sortedTokens().size() > 0;
    final AbstractReplicationStrategy strat = Table.open(table).getReplicationStrategy();
    Collection<Range> myRanges = strat.getPendingAddressRanges(tokenMetadata, token, address);

    Multimap<Range, InetAddress> myRangeAddresses = ArrayListMultimap.create();
    Multimap<Range, InetAddress> rangeAddresses = strat.getRangeAddresses(tokenMetadata);
    for (Range myRange : myRanges) {
        for (Range range : rangeAddresses.keySet()) {
            if (range.contains(myRange)) {
                List<InetAddress> preferred = DatabaseDescriptor.getEndpointSnitch()
                        .getSortedListByProximity(address, rangeAddresses.get(range));
                myRangeAddresses.putAll(myRange, preferred);
                break;
            }//from   ww w . ja  va2s  .co m
        }
        assert myRangeAddresses.keySet().contains(myRange);
    }
    return myRangeAddresses;
}

---

From source file:net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.HighestDataPointConnector.java

public void addScan(int scanNumber, DataPoint mzValues[]) {

    // Sort m/z peaks by descending intensity
    Arrays.sort(mzValues, new DataPointSorter(SortingProperty.Intensity, SortingDirection.Descending));

    // Set of already connected chromatograms in each iteration
    Set<Chromatogram> connectedChromatograms = new LinkedHashSet<Chromatogram>();

    // TODO: these two nested cycles should be optimized for speed
    for (DataPoint mzPeak : mzValues) {

        // Search for best chromatogram, which has highest last data point
        Chromatogram bestChromatogram = null;

        for (Chromatogram testChrom : buildingChromatograms) {

            DataPoint lastMzPeak = testChrom.getLastMzPeak();
            Range<Double> toleranceRange = mzTolerance.getToleranceRange(lastMzPeak.getMZ());
            if (toleranceRange.contains(mzPeak.getMZ())) {
                if ((bestChromatogram == null) || (testChrom.getLastMzPeak().getIntensity() > bestChromatogram
                        .getLastMzPeak().getIntensity())) {
                    bestChromatogram = testChrom;
                }//from   w ww . ja  v a 2 s  .c  om
            }

        }

        // If we found best chromatogram, check if it is already connected.
        // In such case, we may discard this mass and continue. If we
        // haven't found a chromatogram, we may create a new one.
        if (bestChromatogram != null) {
            if (connectedChromatograms.contains(bestChromatogram)) {
                continue;
            }
        } else {
            bestChromatogram = new Chromatogram(dataFile, allScanNumbers);
        }

        // Add this mzPeak to the chromatogram
        bestChromatogram.addMzPeak(scanNumber, mzPeak);

        // Move the chromatogram to the set of connected chromatograms
        connectedChromatograms.add(bestChromatogram);

    }

    // Process those chromatograms which were not connected to any m/z peak
    for (Chromatogram testChrom : buildingChromatograms) {

        // Skip those which were connected
        if (connectedChromatograms.contains(testChrom)) {
            continue;
        }

        // Check if we just finished a long-enough segment
        if (testChrom.getBuildingSegmentLength() >= minimumTimeSpan) {
            testChrom.commitBuildingSegment();

            // Move the chromatogram to the set of connected chromatograms
            connectedChromatograms.add(testChrom);
            continue;
        }

        // Check if we have any committed segments in the chromatogram
        if (testChrom.getNumberOfCommittedSegments() > 0) {
            testChrom.removeBuildingSegment();

            // Move the chromatogram to the set of connected chromatograms
            connectedChromatograms.add(testChrom);
            continue;
        }

    }

    // All remaining chromatograms in buildingChromatograms are discarded
    // and buildingChromatograms is replaced with connectedChromatograms
    buildingChromatograms = connectedChromatograms;

}

---

From source file:net.sf.mzmine.modules.masslistmethods.ADAPchromatogrambuilder.ADAPHighestDataPointConnector.java

public void addScan(int scanNumber, DataPoint mzValues[]) {

    // Sort m/z peaks by descending intensity
    Arrays.sort(mzValues, new DataPointSorter(SortingProperty.Intensity, SortingDirection.Descending));

    // Set of already connected chromatograms in each iteration
    Set<ADAPChromatogram> connectedChromatograms = new LinkedHashSet<ADAPChromatogram>();

    // TODO: these two nested cycles should be optimized for speed
    for (DataPoint mzPeak : mzValues) {

        // Search for best chromatogram, which has highest last data point
        ADAPChromatogram bestChromatogram = null;

        for (ADAPChromatogram testChrom : buildingChromatograms) {

            DataPoint lastMzPeak = testChrom.getLastMzPeak();
            Range<Double> toleranceRange = mzTolerance.getToleranceRange(lastMzPeak.getMZ());
            if (toleranceRange.contains(mzPeak.getMZ())) {
                if ((bestChromatogram == null) || (testChrom.getLastMzPeak().getIntensity() > bestChromatogram
                        .getLastMzPeak().getIntensity())) {
                    bestChromatogram = testChrom;
                }/*from   w ww .j av  a2 s.com*/
            }

        }

        // If we found best chromatogram, check if it is already connected.
        // In such case, we may discard this mass and continue. If we
        // haven't found a chromatogram, we may create a new one.
        if (bestChromatogram != null) {
            if (connectedChromatograms.contains(bestChromatogram)) {
                continue;
            }
        } else {
            bestChromatogram = new ADAPChromatogram(dataFile, allScanNumbers);
        }

        // Add this mzPeak to the chromatogram
        bestChromatogram.addMzPeak(scanNumber, mzPeak);

        // Move the chromatogram to the set of connected chromatograms
        connectedChromatograms.add(bestChromatogram);

    }

    // Process those chromatograms which were not connected to any m/z peak
    for (ADAPChromatogram testChrom : buildingChromatograms) {

        // Skip those which were connected
        if (connectedChromatograms.contains(testChrom)) {
            continue;
        }

        // Check if we just finished a long-enough segment
        if (testChrom.getBuildingSegmentLength() >= minimumTimeSpan) {
            testChrom.commitBuildingSegment();

            // Move the chromatogram to the set of connected chromatograms
            connectedChromatograms.add(testChrom);
            continue;
        }

        // Check if we have any committed segments in the chromatogram
        if (testChrom.getNumberOfCommittedSegments() > 0) {
            testChrom.removeBuildingSegment();

            // Move the chromatogram to the set of connected chromatograms
            connectedChromatograms.add(testChrom);
            continue;
        }

    }

    // All remaining chromatograms in buildingChromatograms are discarded
    // and buildingChromatograms is replaced with connectedChromatograms
    buildingChromatograms = connectedChromatograms;

}

---

From source file:yaphyre.core.shapes.SimpleSphere.java

@Override
@Nonnull/*from www . j  a  va 2s .c o m*/
public Optional<CollisionInformation> intersect(@Nonnull Ray ray) {
    final Ray objectSpaceRay = transformToObjectSpace(ray);
    final Vector3D originPositionVector = objectSpaceRay.getOrigin().asVector();
    final Vector3D direction = objectSpaceRay.getDirection();

    final double a = direction.dot(direction);
    final double b = originPositionVector.dot(direction) * 2;
    final double c = originPositionVector.dot(originPositionVector) - (RADIUS * RADIUS);

    final double[] solutions = quadraticSolver.solve(c, b, a);

    final OptionalDouble minSolution = Arrays.stream(solutions).filter(distance -> {
        Range<Double> tRange = ray.getTRange();
        LOGGER.trace(String.format("testing solution %.3f against range %s", distance, tRange));
        return tRange.contains(distance);
    }).min();

    LOGGER.trace("result: " + minSolution);

    if (minSolution.isPresent() && !Double.isNaN(minSolution.getAsDouble())) {
        final double distance = minSolution.getAsDouble();
        final Point3D intersectionPoint = objectSpaceRay.getPoint(distance);

        return Optional.of(
                new CollisionInformation(ray, this, distance, getObjectToWorld().transform(intersectionPoint),
                        getObjectToWorld().transform(calculateNormal(intersectionPoint, objectSpaceRay)),
                        mapToLocalUV(intersectionPoint)));

    } else {

        return Optional.empty();

    }

}

---

From source file:org.robotframework.ide.eclipse.main.plugin.project.build.fix.MetadataKeyInSameColumnFixer.java

@Override
public Optional<ICompletionProposal> asContentProposal(final IMarker marker, final IDocument document,
        final RobotSuiteFile suiteModel) {
    Optional<ICompletionProposal> proposal = Optional.empty();
    final Optional<RobotSettingsSection> section = suiteModel.findSection(RobotSettingsSection.class);
    if (section.isPresent()) {
        final Range<Integer> range = getRange(marker);
        final List<RobotKeywordCall> metadataSettings = section.get().getMetadataSettings();
        for (final RobotKeywordCall robotKeywordCall : metadataSettings) {
            if (range.contains(robotKeywordCall.getDefinitionPosition().getOffset())) {
                try {
                    proposal = createProposal(document, robotKeywordCall, suiteModel);
                } catch (final BadLocationException e) {
                    e.printStackTrace();
                }//from www .ja  v  a  2  s .c om
            }
        }
    }

    return proposal;
}

---

From source file:com.rockhoppertech.music.series.time.TimeEvent.java

public boolean overlaps(TimeEvent te) {
    // boolean b = this.getRange().overlaps(te.getRange());
    boolean b = false;
    Range<Double> range1 = this.getOpenRange();
    Range<Double> range2 = te.getOpenRange();
    if (range1.contains(range2.lowerEndpoint()) || range1.contains(range2.upperEndpoint())) {
        b = true;/*from w w  w.  j ava  2 s. c  o m*/
    }

    logger.debug(String.format("overlaps %b %s %s", b, this.getOpenRange(), te.getOpenRange()));

    return b;
}

---

From source file:org.opendaylight.lispflowmapping.type.lisp.LocatorRecord.java

public LocatorRecord setPriority(short priority) {
    if (priority != 0) {
        boolean isValidRange = false;
        List<Range<Short>> rangeConstraints = new ArrayList<>();
        rangeConstraints.add(Range.closed(new Short("0"), new Short("255")));
        for (Range<Short> r : rangeConstraints) {
            if (r.contains(priority)) {
                isValidRange = true;//  www . j a v a  2  s.c  o m
            }
        }
        if (!isValidRange) {
            throw new IllegalArgumentException(
                    String.format("Invalid range: %s, expected: %s.", priority, rangeConstraints));
        }
    }
    this.priority = priority;
    return this;
}

---

From source file:org.opendaylight.lispflowmapping.type.lisp.LocatorRecord.java

public LocatorRecord setMulticastPriority(short value) {
    if (value != 0) {
        boolean isValidRange = false;
        List<Range<Short>> rangeConstraints = new ArrayList<>();
        rangeConstraints.add(Range.closed(new Short("0"), new Short("255")));
        for (Range<Short> r : rangeConstraints) {
            if (r.contains(value)) {
                isValidRange = true;/*from   w w  w.ja  v  a 2  s  .c  o  m*/
            }
        }
        if (!isValidRange) {
            throw new IllegalArgumentException(
                    String.format("Invalid range: %s, expected: %s.", value, rangeConstraints));
        }
    }
    this.multicastPriority = value;
    return this;
}

---

From source file:org.opentestsystem.authoring.testauth.validation.ScoringRuleParameterValidator.java

/**
 * validate scalar value//from   ww  w .  j  a v  a 2s. c  om
 */
private <N extends Number> void validateScalarValue(final ComputationRuleParameter computationRuleParameter,
        final String scalarValue, final Errors errors) {
    final ComputationRuleType fieldType = computationRuleParameter.getComputationRuleType();
    final String paramName = computationRuleParameter.getParameterName();
    final boolean valueIsNumeric = NUMERIC_TYPES.contains(fieldType);
    if (!rejectIfEmpty(scalarValue, errors, SCALAR, getErrorMessageRoot() + SCALAR,
            valueIsNumeric ? MAX_PARSEABLE_LENGTH : MAX_STRING_LENGTH, fieldType, paramName, scalarValue)
            && valueIsNumeric) {
        try {
            final String min = computationRuleParameter.getMinimumValue();
            final String max = computationRuleParameter.getMaximumValue();
            if (fieldType == ComputationRuleType.FLOAT) {
                final Float floatValue = Float.parseFloat(scalarValue);
                final Range<Float> floatRange = buildFloatRange(min, max);
                if (floatRange != null && !floatRange.contains(floatValue)) {
                    rejectValue(errors, SCALAR, getErrorMessageRoot() + SCALAR + MSG_RANGE, fieldType,
                            paramName, scalarValue, min, max);
                }
            } else {
                final Long longValue = Long.parseLong(scalarValue);
                final Range<Long> longRange = buildLongRange(min, max);
                if (longRange != null && !longRange.contains(longValue)) {
                    rejectValue(errors, SCALAR, getErrorMessageRoot() + SCALAR + MSG_RANGE, fieldType,
                            paramName, scalarValue, min, max);
                }
            }
        } catch (final NumberFormatException e) {
            rejectValue(errors, SCALAR, getErrorMessageRoot() + SCALAR + MSG_PARSEABLE_NUMBER, fieldType,
                    paramName, scalarValue);
        }
    } else if (ComputationRuleType.BOOLEAN.equals(fieldType)
            && !Boolean.FALSE.toString().equals(scalarValue.toString())
            && !Boolean.TRUE.toString().equals(scalarValue.toString())) {
        rejectValue(errors, SCALAR, getErrorMessageRoot() + SCALAR + MSG_PARSEABLE_BOOLEAN, fieldType,
                paramName, scalarValue);
    }
}

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