Example usage for org.apache.commons.lang ArrayUtils toObject

Introduction

In this page you can find the example usage for org.apache.commons.lang ArrayUtils toObject.

Prototype

public static Boolean[] toObject(boolean[] array) 

Source Link

Document

Converts an array of primitive booleans to objects.

Usage

From source file:parquet.column.statistics.bloomfilter.BloomFilter.java

public List<Long> getBitSet() {
    return Arrays.asList(ArrayUtils.toObject(bitSet.getData()));
}

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From source file:sf.net.experimaestro.manager.plans.GroupBy.java

@Override
protected String getName() {
    if (indices != null)
        return String.format("GroupBy(%s)", Output.toString(", ", ArrayUtils.toObject(indices)));
    return "GroupBy";
}

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From source file:sf.net.experimaestro.manager.plans.OrderBy.java

@Override
protected String getName() {
    if (contextOrder != null) {
        return String.format("OrderBy (%s)", Output.toString(", ", ArrayUtils.toObject(contextOrder)));
    }//  ww w.j  a v  a  2  s  .  c  o  m
    return String.format("OrderBy (%d contexts)", order.size());
}

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From source file:sf.net.experimaestro.manager.plans.ReorderNodes.java

@Override
protected String getName() {
    return String.format("reorder [%s]", Output.toString(", ", ArrayUtils.toObject(mapping)));
}

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From source file:tachyon.worker.block.TieredBlockStoreTestUtils.java

/**
 * Sets up a specific tier's {@link TachyonConf} for a {@link TieredBlockStore}.
 *
 * @param ordinal Ordinal value of the tier
 * @param tierAlias Alias of the tier/*from   w  w  w.j  a  va 2s  .  co m*/
 * @param tierPath Absolute path of the tier
 * @param tierCapacity Capacity of the tier
 */
private static void setupTachyonConfTier(int ordinal, String tierAlias, String[] tierPath,
        long[] tierCapacity) {
    Preconditions.checkNotNull(tierPath);
    Preconditions.checkNotNull(tierCapacity);
    Preconditions.checkArgument(tierPath.length == tierCapacity.length,
            String.format("tierPath and tierCapacity should have the same length"));

    sTachyonConf.set(String.format(Constants.WORKER_TIERED_STORE_LEVEL_ALIAS_FORMAT, ordinal), tierAlias);

    String tierPathString = StringUtils.join(tierPath, ",");
    sTachyonConf.set(String.format(Constants.WORKER_TIERED_STORE_LEVEL_DIRS_PATH_FORMAT, ordinal),
            tierPathString);

    String tierCapacityString = StringUtils.join(ArrayUtils.toObject(tierCapacity), ",");
    sTachyonConf.set(String.format(Constants.WORKER_TIERED_STORE_LEVEL_DIRS_QUOTA_FORMAT, ordinal),
            tierCapacityString);
}

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From source file:tools.descartes.wcf.forecasting.AbstractRForecaster.java

@Override
public final IForecastResult forecast(final int numForecastSteps) {
    if (rBridge == null)
        return null;

    final ITimeSeries<Double> history = this.getTsOriginal();

    final String varNameValues = RServerBridgeControl.uniqueVarname();
    final String varNameModel = RServerBridgeControl.uniqueVarname();
    final String varNameForecast = RServerBridgeControl.uniqueVarname();

    final double[] values;
    List<Double> allHistory = new ArrayList<Double>(history.getValues());

    // remove NullValues only if strategy is not "Croston" (forecasting for intermitted demands)
    if (strategy == ForecastStrategyEnum.CROST) {
        Double[] histValues = new Double[allHistory.size()];
        histValues = allHistory.toArray(histValues);
        values = ArrayUtils.toPrimitive(histValues);
    } else {/*from  ww  w. j av a 2 s .c  om*/
        Double[] histValuesNotNull = removeNullValues(allHistory);
        values = ArrayUtils.toPrimitive(histValuesNotNull);
    }

    /*
     * 0. Assign values to temporal variable
     */
    long startFC = System.currentTimeMillis();
    AbstractRForecaster.rBridge.assign(varNameValues, values);

    //frequency for time series object in R --> needed for MASE calculation.
    AbstractRForecaster.rBridge.toTS(varNameValues, history.getFrequency());
    /*
     * 1. Compute stochastic model for forecast
     */
    if (this.modelFunc == null) {
        // In this case, the values are the model ...
        AbstractRForecaster.rBridge.assign(varNameModel, values);
        AbstractRForecaster.rBridge.toTS(varNameModel, history.getFrequency());
    } else {
        final String[] additionalModelParams = this.getModelFuncParams();

        StringBuffer params = new StringBuffer();
        params.append(varNameValues);
        if (null != additionalModelParams) {
            for (String param : additionalModelParams) {
                params.append(",");
                params.append(param);
            }
        }
        AbstractRForecaster.rBridge.e(String.format("%s<<-%s(%s)", varNameModel, this.modelFunc, params));
    }

    /*
     * 2. Perform forecast based on stochastic model
     */
    if (this.getConfidenceLevel() == 0) {
        AbstractRForecaster.rBridge.e(String.format("%s<<-%s(%s,h=%d)", varNameForecast, this.forecastFunc,
                varNameModel, numForecastSteps));
    } else {
        AbstractRForecaster.rBridge.e(String.format("%s<<-%s(%s,h=%d,level=c(%d))", varNameForecast,
                this.forecastFunc, varNameModel, numForecastSteps, this.getConfidenceLevel()));
    }
    /*
     * 3. Calculate Forecast Quality Metric
     */
    double fcQuality;
    if (this.modelFunc == null || this.strategy == ForecastStrategyEnum.TBATS) {
        fcQuality = AbstractRForecaster.rBridge.eDbl("accuracy(" + varNameForecast + ")[6]");
    } else {
        fcQuality = AbstractRForecaster.rBridge.eDbl("accuracy(" + varNameModel + ")[6]");
    }
    final double[] lowerValues = AbstractRForecaster.rBridge.eDblArr(lowerOperationOnResult(varNameForecast));
    final double[] forecastValues = AbstractRForecaster.rBridge
            .eDblArr(forecastOperationOnResult(varNameForecast));
    final double[] upperValues = AbstractRForecaster.rBridge.eDblArr(upperOperationOnResult(varNameForecast));

    // remove temporal variable:
    AbstractRForecaster.rBridge.e(String.format("rm(%s)", varNameModel));
    AbstractRForecaster.rBridge.e(String.format("rm(%s)", varNameValues));
    AbstractRForecaster.rBridge.e(String.format("rm(%s)", varNameForecast));

    long endFC = System.currentTimeMillis();

    ITimeSeries<Double> tsForecast = this.prepareForecastTS();
    ITimeSeries<Double> tsLower;
    ITimeSeries<Double> tsUpper;
    tsForecast.appendAll(ArrayUtils.toObject(forecastValues));

    if (this.getConfidenceLevel() == 0) {
        tsLower = tsForecast;
        tsUpper = tsForecast;
    } else {
        tsLower = this.prepareForecastTS();
        tsLower.appendAll(ArrayUtils.toObject(lowerValues));
        tsUpper = this.prepareForecastTS();
        tsUpper.appendAll(ArrayUtils.toObject(upperValues));
    }
    return new ForecastResult(tsForecast, this.getTsOriginal(), this.getConfidenceLevel(), fcQuality, tsLower,
            tsUpper, strategy, endFC - startFC);
}

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From source file:ubic.basecode.util.r.JRIClientTest.java

/**
 * With a continuous covariate as well a categorical one.
 * //from   w  w  w . jav  a2  s.c o m
 * @throws Exception
 */
public void testLinearModelB() throws Exception {
    if (!connected) {
        log.warn("Cannot load JRI, skipping test");
        return;
    }

    /*
     * dat<-c( 3.2969, 3.1856, 3.1638, NA, 3.2342, 3.3533, 3.4347, 3.3074); a<-factor(c( "A", "A", "A", "A", "B",
     * "B", "B", "B" )); b<-c(1, 2, 3, 4, 5, 6, 7, 8) bar<-lm(dat ~ a + b); summary(bar) anova(bar)
     */

    double[] data = new double[] { 3.2969, 3.1856, 3.1638, Double.NaN, 3.2342, 3.3533, 3.4347, 3.3074 };
    String[] f1 = new String[] { "A", "A", "A", "A", "B", "B", "B", "B" };

    List<String> fac1 = Arrays.asList(f1);

    double[] fac2 = new double[] { 1, 2, 3, 4, 5, 6, 7, 8 };

    Map<String, List<?>> factors = new LinkedHashMap<String, List<?>>();
    factors.put("foo", fac1);
    factors.put("bar", Arrays.asList(ArrayUtils.toObject(fac2)));

    LinearModelSummary lms = rc.linearModel(data, factors);

    Double p = lms.getMainEffectP("foo");
    Double t = lms.getMainEffectT("foo")[0];

    Double pp = lms.getMainEffectP("bar");
    Double tt = lms.getMainEffectT("bar")[0];

    Double ip = lms.getInterceptP();
    Double it = lms.getInterceptT();

    assertEquals(0.1586, p, 0.0001);
    assertEquals(0.64117305, t, 0.0001);
    assertEquals(0.9443, pp, 0.0001);
    assertEquals(0.07432241, tt, 0.0001);
    assertEquals(2.821526e-06, ip, 0.0001);
    assertEquals(38.14344686, it, 0.0001);

}

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From source file:ubic.gemma.analysis.preprocess.normalize.ExpressionDataQuantileNormalizer.java

/**
 * Quantile normalize the matrix (in place)
 * //ww  w .  j  a va 2s .  com
 * @param matrix
 */
public static void normalize(ExpressionDataDoubleMatrix matrix) {

    DoubleMatrix<CompositeSequence, BioMaterial> rawMatrix = matrix.getMatrix();

    QuantileNormalizer<CompositeSequence, BioMaterial> normalizer = new QuantileNormalizer<CompositeSequence, BioMaterial>();
    DoubleMatrix<CompositeSequence, BioMaterial> normalized = normalizer.normalize(rawMatrix);

    for (int i = 0; i < normalized.rows(); i++) {
        matrix.setRow(i, ArrayUtils.toObject(normalized.getRow(i)));
    }

}

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From source file:ubic.gemma.datastructure.matrix.ExpressionDataDoubleMatrix.java

@Override
public Double[] getRow(Integer index) {
    double[] rawRow = matrix.getRow(index);
    return ArrayUtils.toObject(rawRow);
}

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From source file:ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl.java

@Override
@Transactional//from   ww  w .ja v  a  2  s .c o m
public GeneCoexpressionNodeDegreeValueObject updateNodeDegree(Gene g, GeneCoexpressionNodeDegree nd) {
    Session sess = this.getSessionFactory().getCurrentSession();

    List<CoexpressionValueObject> hits = this.getCoexpression(g);

    /*
     * We have to reset the support.
     */
    GeneCoexpressionNodeDegreeValueObject gcndvo = new GeneCoexpressionNodeDegreeValueObject(nd);
    gcndvo.clear();

    assert gcndvo.getMaxSupportNeg() == 0;

    for (CoexpressionValueObject hit : hits) {
        if (hit.isPositiveCorrelation()) {
            gcndvo.increment(hit.getNumDatasetsSupporting(), true);
        } else {
            gcndvo.increment(hit.getNumDatasetsSupporting(), false);
        }
    }

    assert gcndvo.total() == hits.size();

    GeneCoexpressionNodeDegree entity = gcndvo.toEntity();
    nd.setLinkCountsPositive(entity.getLinkCountsPositive());
    nd.setLinkCountsNegative(entity.getLinkCountsNegative());

    if (CoexpressionDaoImpl.log.isDebugEnabled())
        CoexpressionDaoImpl.log.debug("gene=" + g.getId() + " pos="
                + StringUtils.join(ArrayUtils.toObject(nd.getLinkCountsPositive()), " ") + " neg="
                + StringUtils.join(ArrayUtils.toObject(nd.getLinkCountsNegative()), " "));

    sess.update(nd);

    // might not be necessary, but presumption is data is stale now...
    this.gene2GeneCoexpressionCache.remove(g.getId());
    this.geneTestedInCache.remove(g.getId());

    return gcndvo;
}

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