Examples with DoubleArrayList cern.colt.list.DoubleArrayList used on opensource projects

Example 31 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class ExpressionExperimentQCController method getCorrelHistFromFile.

/**
 * For backwards compatibility - read from the file. Remove this method when no longer needed.
 */
private XYSeries getCorrelHistFromFile(ExpressionExperiment ee) throws IOException {
    File file = this.locateProbeCorrFile(ee);
    // Current format is to have just one file for each analysis.
    if (file == null) {
        return null;
    } else if (!file.canRead()) {
        return null;
    }
    try (BufferedReader in = new BufferedReader(new FileReader(file))) {
        XYSeries series = new XYSeries(ee.getId(), true, true);
        DoubleArrayList counts = new DoubleArrayList();
        while (in.ready()) {
            String line = in.readLine().trim();
            if (line.startsWith("#"))
                continue;
            String[] split = StringUtils.split(line);
            if (split.length < 2)
                continue;
            try {
                double x = Double.parseDouble(split[0]);
                double y = Double.parseDouble(split[1]);
                series.add(x, y);
                counts.add(y);
            } catch (NumberFormatException e) {
            // line wasn't useable.. no big deal. Heading is included.
            }
        }
        if (!counts.isEmpty()) {
            // Backfill.
            this.corrDistFileToPersistent(file, ee, counts);
        }
        return series;
    }
}

Example 32 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class ExpressionExperimentQCController method getEigenGene.

/**
 * Get the eigengene for the given component.
 * The values are rescaled so that jfreechart can cope. Small numbers give it fits.
 */
private Double[] getEigenGene(SVDValueObject svdo, Integer component) {
    DoubleArrayList eigenGeneL = new DoubleArrayList(ArrayUtils.toPrimitive(svdo.getvMatrix().getColObj(component)));
    DescriptiveWithMissing.standardize(eigenGeneL);
    return ArrayUtils.toObject(eigenGeneL.elements());
}

Example 33 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project beast-mcmc by beast-dev.

the class KernelDensityEstimator2D method bandwidthNRD.

// bandwidth.nrd =
// function (x)
// {
// r <- quantile(x, c(0.25, 0.75))
// h <- (r[2] - r[1])/1.34
// 4 * 1.06 * min(sqrt(var(x)), h) * length(x)^(-1/5)
// }
public double bandwidthNRD(double[] in) {
    DoubleArrayList inList = new DoubleArrayList(in.length);
    for (double d : in) inList.add(d);
    inList.sort();
    final double h = (Descriptive.quantile(inList, 0.75) - Descriptive.quantile(inList, 0.25)) / 1.34;
    return 4 * 1.06 * Math.min(Math.sqrt(DiscreteStatistics.variance(in)), h) * Math.pow(in.length, -0.2);
}

Example 34 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project EnrichmentMapApp by BaderLab.

the class HeatMapTableModel method median.

private static double median(double[] vals) {
    if (vals.length == 0)
        return 0.0;
    // DoubleArrayList is just a wrapper for vals, we must make a copy of the array 
    // before sorting or else the expression values will be moved to the wrong order.
    double[] copy = Arrays.copyOf(vals, vals.length);
    Arrays.sort(copy);
    return Descriptive.median(new DoubleArrayList(copy));
}

Example 35 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class ProcessedExpressionDataVectorCreateHelperServiceImpl method computeRanks.

private Collection<ProcessedExpressionDataVector> computeRanks(Collection<ProcessedExpressionDataVector> processedDataVectors, ExpressionDataDoubleMatrix intensities) {
    DoubleArrayList ranksByMean = this.getRanks(intensities, ProcessedExpressionDataVectorDao.RankMethod.mean);
    assert ranksByMean != null;
    DoubleArrayList ranksByMax = this.getRanks(intensities, ProcessedExpressionDataVectorDao.RankMethod.max);
    assert ranksByMax != null;
    for (ProcessedExpressionDataVector vector : processedDataVectors) {
        CompositeSequence de = vector.getDesignElement();
        if (intensities.getRow(de) == null) {
            ProcessedExpressionDataVectorCreateHelperServiceImpl.log.warn("No intensity value for " + de + ", rank for vector will be null");
            vector.setRankByMean(null);
            vector.setRankByMax(null);
            continue;
        }
        Integer i = intensities.getRowIndex(de);
        double rankByMean = ranksByMean.get(i) / ranksByMean.size();
        double rankByMax = ranksByMax.get(i) / ranksByMax.size();
        vector.setRankByMean(rankByMean);
        vector.setRankByMax(rankByMax);
    }
    return processedDataVectors;
}