Examples with Array2DRowRealMatrix org.apache.commons.math3.linear.Array2DRowRealMatrix used on opensource projects

Example 91 with Array2DRowRealMatrix

use of org.apache.commons.math3.linear.Array2DRowRealMatrix in project gatk by broadinstitute.

the class GATKProtectedMathUtilsTest method testRowMeans.

@Test
public void testRowMeans() {
    final double[][] array = { { 1, 2, 3 }, { 4, 5, 6 }, { 7, 8, 9 } };
    final double[] rowMeans = GATKProtectedMathUtils.rowMeans(new Array2DRowRealMatrix(array));
    Assert.assertEquals(rowMeans, new double[] { 2, 5, 8 });
}

Example 92 with Array2DRowRealMatrix

use of org.apache.commons.math3.linear.Array2DRowRealMatrix in project gatk by broadinstitute.

the class GATKProtectedMathUtilsTest method testRowNaN.

@Test
public void testRowNaN() {
    final double[][] array = { { 1, 2, Double.NaN }, { 5, 5, 5 }, { 7, 8, 9 }, { -15, 2, 12 } };
    final double[] guess = GATKProtectedMathUtils.rowSums(new Array2DRowRealMatrix(array));
    final double[] gt = { Double.NaN, 15, 24, -1 };
    Assert.assertEquals(guess.length, 4);
    Assert.assertEquals(guess[1], gt[1]);
    Assert.assertEquals(guess[2], gt[2]);
    Assert.assertEquals(guess[3], gt[3]);
    Assert.assertTrue(Double.isNaN(guess[0]));
}

Example 93 with Array2DRowRealMatrix

use of org.apache.commons.math3.linear.Array2DRowRealMatrix in project gatk by broadinstitute.

the class HDF5PCACoveragePoNCreationUtilsUnitTest method simpleEigensampleData.

@DataProvider(name = "singleEigensample")
public Object[][] simpleEigensampleData() {
    final List<Object[]> result = new ArrayList<>();
    final int NUM_TARGETS = 10;
    final int NUM_SAMPLES = 5;
    final List<Target> targets = IntStream.range(0, NUM_TARGETS).boxed().map(i -> new Target("target_" + i, new SimpleInterval("1", 100 * i + 1, 100 * i + 5))).collect(Collectors.toList());
    final List<String> columnNames = IntStream.range(0, NUM_SAMPLES).boxed().map(i -> "sample_" + i).collect(Collectors.toList());
    double[][] countsArray = new double[NUM_TARGETS][NUM_SAMPLES];
    final RealMatrix counts = new Array2DRowRealMatrix(countsArray);
    // All row data is the same (0,1,2,3,4...)
    final double[] rowData = IntStream.range(0, NUM_SAMPLES).boxed().mapToDouble(i -> i).toArray();
    for (int i = 0; i < NUM_TARGETS; i++) {
        counts.setRow(i, rowData);
    }
    new ReadCountCollection(targets, columnNames, counts);
    result.add(new Object[] { new ReadCountCollection(targets, columnNames, counts) });
    return result.toArray(new Object[result.size()][]);
}

Example 94 with Array2DRowRealMatrix

use of org.apache.commons.math3.linear.Array2DRowRealMatrix in project gatk by broadinstitute.

the class HDF5PCACoveragePoNCreationUtilsUnitTest method readCountOnlyWithDiverseShapeData.

@DataProvider(name = "readCountOnlyWithDiverseShapeData")
public Object[][] readCountOnlyWithDiverseShapeData() {
    final List<Object[]> result = new ArrayList<>(4);
    final Random rdn = new Random(31);
    final int[] columnCounts = new int[] { 10, 100, 100, 200 };
    final int[] targetCounts = new int[] { 100, 100, 200, 200 };
    for (int k = 0; k < columnCounts.length; k++) {
        final List<String> columnNames = IntStream.range(0, columnCounts[k]).mapToObj(i -> "sample_" + (i + 1)).collect(Collectors.toList());
        final List<Target> targets = IntStream.range(0, targetCounts[k]).mapToObj(i -> new Target("target_" + (i + 1))).collect(Collectors.toList());
        final double[][] counts = new double[targetCounts[k]][columnCounts[k]];
        for (int i = 0; i < counts.length; i++) {
            for (int j = 0; j < counts[0].length; j++) {
                counts[i][j] = rdn.nextDouble();
            }
        }
        final ReadCountCollection readCounts = new ReadCountCollection(targets, columnNames, new Array2DRowRealMatrix(counts, false));
        result.add(new Object[] { readCounts });
    }
    return result.toArray(new Object[result.size()][]);
}

Example 95 with Array2DRowRealMatrix

use of org.apache.commons.math3.linear.Array2DRowRealMatrix in project gatk by broadinstitute.

the class PCATangentNormalizationUtilsUnitTest method normalizeReadCountByTargetFactorsData.

@DataProvider(name = "normalizeReadCountByTargetFactorsData")
public Object[][] normalizeReadCountByTargetFactorsData() {
    final List<Object[]> result = new ArrayList<>(1);
    @SuppressWarnings("serial") final List<Target> targets = new ArrayList<Target>() {

        {
            add(new Target("A"));
            add(new Target("B"));
            add(new Target("C"));
        }
    };
    @SuppressWarnings("serial") final List<String> columnNames = new ArrayList<String>() {

        {
            add("1");
            add("2");
            add("3");
        }
    };
    result.add(new Object[] { new ReadCountCollection(targets, columnNames, new Array2DRowRealMatrix(new double[][] { new double[] { 1.1, 2.2, 3.3 }, new double[] { 0.1, 0.2, 0.3 }, new double[] { 11.1, 22.2, 33.3 } }, false)), new double[] { 100.0, 200.0, 300.0 } });
    return result.toArray(new Object[1][]);
}