Example usage for java.lang Math log10

Introduction

In this page you can find the example usage for java.lang Math log10.

Prototype

@HotSpotIntrinsicCandidate
public static double log10(double a) 

Source Link

Document

Returns the base 10 logarithm of a double value.

Usage

From source file:org.broadinstitute.gatk.tools.walkers.variantrecalibration.MultivariateGaussian.java

public void precomputeDenominatorForEvaluation() {
    precomputeInverse();//  w  w w . j av a  2  s . c  om
    cachedDenomLog10 = Math.log10(Math.pow(2.0 * Math.PI, -1.0 * ((double) mu.length) / 2.0))
            + Math.log10(Math.pow(sigma.det(), -0.5));
}

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From source file:org.opensha.sha.magdist.IncrementalMagFreqDist.java

/**
* This computes the b-value (the slope of the line of a linear-log plot, meaning
 * after computing log10 of all y-axis values) between the the given x-axis values.
 * If Double.NaN is passed in, then the first (or last) non-zero rate is used for
 * min_bValMag (or max_bValMag)./*from  ww  w .j  a  v a  2  s.c  o m*/
 * @param min_bValMag
 * @param max_bValMag
 * @return
 */
public double compute_bValue(double min_bValMag, double max_bValMag) {
    int firstIndex, lastIndex;

    if (Double.isNaN(min_bValMag))
        firstIndex = getClosestXIndex(getMinMagWithNonZeroRate());
    else
        firstIndex = getClosestXIndex(min_bValMag);

    if (Double.isNaN(max_bValMag))
        lastIndex = getClosestXIndex(getMaxMagWithNonZeroRate());
    else
        lastIndex = getClosestXIndex(max_bValMag);

    SimpleRegression regression = new SimpleRegression();
    for (int i = firstIndex; i <= lastIndex; i++) {
        if (getY(i) > 0.0) // avoid taking log of zero
            regression.addData(getX(i), Math.log10(getY(i)));
    }

    //      if(getX(lastIndex)-getX(firstIndex) <1.0)
    //         return Double.NaN;

    return regression.getSlope();
}

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From source file:org.broadinstitute.gatk.tools.walkers.cancer.m2.TumorPowerCalculator.java

private double calculateLogLikelihood(final int numReads, final int numAlts, final double alleleFraction) {
    return ((numReads - numAlts)
            * Math.log10(alleleFraction * errorProbability + (1 - alleleFraction) * (1 - errorProbability))
            + numAlts * Math//from   w w  w . j  a  v a2  s.  c  o  m
                    .log10(alleleFraction * (1 - errorProbability) + (1 - alleleFraction) * errorProbability));
}

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From source file:org.processmining.analysis.performance.advanceddottedchartanalysis.ui.DottedChartPanel.java

public void adjustSlideBar() {
    int value = (int) (Math.log10(updWidth / dca.getViewportSize().getWidth()) * 1000.0);

    if (value > 3000)
        value = 3000;/*from   w  w w .  j a v  a  2  s  .  c  o m*/
    dca.getDottedChartOptionPanel().getZoomSliderX().setValue(value);
    dca.getDottedChartOptionPanel().getZoomSliderX().repaint();

    value = (int) (Math.log10(updHight / dca.getViewportSize().getHeight()) * 1000.0);
    if (value > 3000)
        value = 3000;
    dca.getDottedChartOptionPanel().getZoomSliderY().setValue(value);
    dca.getDottedChartOptionPanel().getZoomSliderY().repaint();
}

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From source file:com.glanznig.beepme.data.DataExporter.java

public static String getReadableFileSize(double size, int decimals) {
    if (size <= 0) {
        return "0 KB";
    }/*from www .  j  a  va2  s. c o  m*/

    final String[] units = new String[] { "B", "KB", "MB", "GB", "TB" };
    int digitGroups = (int) (Math.log10(size) / Math.log10(1024));
    NumberFormat numFormat = DecimalFormat.getInstance();
    numFormat.setMaximumFractionDigits(decimals);

    return numFormat.format(size / Math.pow(1024, digitGroups)) + " " + units[digitGroups];
}

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From source file:org.broadinstitute.gatk.utils.MathUtilsUnitTest.java

@Test
public void testLog10Factorial() {
    logger.warn("Executing testLog10Factorial");
    Assert.assertEquals(MathUtils.log10Factorial(4), 1.380211, 1e-6);
    Assert.assertEquals(MathUtils.log10Factorial(10), 6.559763, 1e-6);
    Assert.assertEquals(MathUtils.log10Factorial(12), 8.680337, 1e-6);
    Assert.assertEquals(MathUtils.log10Factorial(200), 374.8969, 1e-3);
    Assert.assertEquals(MathUtils.log10Factorial(12342), 45138.26, 1e-1);
    double log10factorial_small = 0;
    double log10factorial_middle = 374.8969;
    double log10factorial_large = 45138.26;
    int small_start = 1;
    int med_start = 200;
    int large_start = 12342;
    for (int i = 1; i < 1000; i++) {
        log10factorial_small += Math.log10(i + small_start);
        log10factorial_middle += Math.log10(i + med_start);
        log10factorial_large += Math.log10(i + large_start);
        Assert.assertEquals(MathUtils.log10Factorial(small_start + i), log10factorial_small, 1e-6);
        Assert.assertEquals(MathUtils.log10Factorial(med_start + i), log10factorial_middle, 1e-3);
        Assert.assertEquals(MathUtils.log10Factorial(large_start + i), log10factorial_large, 1e-1);
    }// w w w.j av a2 s .  com
}

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From source file:edu.cornell.med.icb.goby.modes.SplitTranscriptsMode.java

/**
 * Get a number formatter to print leading zeros up to n.
 *
 * @param n The largest number that will be formatted
 * @return the NumberFormat for n/*from   w w  w  .  j  a  v  a  2  s . com*/
 */
public NumberFormat getNumberFormatter(final int n) {
    assert n >= 0 : "n must be non-negative";
    final int numDigits;
    if (n == 0) {
        numDigits = 1;
    } else {
        numDigits = 1 + (int) (Math.log10(n));
    }

    final NumberFormat numberFormat = NumberFormat.getInstance();
    numberFormat.setGroupingUsed(false);
    numberFormat.setMinimumIntegerDigits(numDigits);
    return numberFormat;
}

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From source file:hms.hwestra.interactionrebuttal2.InteractionRebuttal2.java

private void determineInteractionPvalueAndMerge(String normal1, String robust1, String out) throws IOException {

    InteractionRebuttal a = new InteractionRebuttal();
    HashMap<String, Double> normalSE = a.loadSE(normal1);
    HashMap<String, Double> robustSE = a.loadSE(robust1);

    HashMap<String, Double> normalZ = loadZ(normal1);
    HashMap<String, Double> robustZ = loadZ(robust1);

    Set<String> eqtls = normalZ.keySet();
    TextFile tf = new TextFile(out, TextFile.W);
    SpearmansCorrelation corr = new SpearmansCorrelation();
    tf.writeln("SNP-Probe\tZNorm\tZRobust\tPNorm\tPRobust\tSENorm\tSERobust");
    ArrayList<Double> x = new ArrayList<Double>();
    ArrayList<Double> y = new ArrayList<Double>();
    ArrayList<Double> x2 = new ArrayList<Double>();
    ArrayList<Double> y2 = new ArrayList<Double>();

    ArrayList<Double> x3 = new ArrayList<Double>();
    ArrayList<Double> y3 = new ArrayList<Double>();
    for (String s : eqtls) {
        if (robustZ.containsKey(s)) {
            if (!Double.isNaN(normalZ.get(s))) {
                x.add(normalZ.get(s));/*from   w w  w .  j  a  v  a 2 s. c o m*/
                y.add(robustZ.get(s));
                x2.add(-Math.log10(ZScores.zToP(normalZ.get(s))));
                y2.add(-Math.log10(ZScores.zToP(robustZ.get(s))));
                x3.add(normalSE.get(s));
                y3.add(robustSE.get(s));
            }
            String ln = s + "\t" + normalZ.get(s) + "\t" + robustZ.get(s) + "\t"
                    + -Math.log10(ZScores.zToP(normalZ.get(s))) + "\t"
                    + -Math.log10(ZScores.zToP(robustZ.get(s))) + "\t" + normalSE.get(s) + "\t"
                    + robustSE.get(s);
            tf.writeln(ln);
        }
    }
    tf.close();
    System.out.println(x.size());
    double c = corr.correlation(Primitives.toPrimitiveArr(x.toArray(new Double[0])),
            Primitives.toPrimitiveArr(y.toArray(new Double[0])));
    double c2 = corr.correlation(Primitives.toPrimitiveArr(x2.toArray(new Double[0])),
            Primitives.toPrimitiveArr(y2.toArray(new Double[0])));

    double c3 = Correlation.correlate(Primitives.toPrimitiveArr(x.toArray(new Double[0])),
            Primitives.toPrimitiveArr(y.toArray(new Double[0])));
    double c4 = Correlation.correlate(Primitives.toPrimitiveArr(x2.toArray(new Double[0])),
            Primitives.toPrimitiveArr(y2.toArray(new Double[0])));

    double c5 = corr.correlation(Primitives.toPrimitiveArr(x3.toArray(new Double[0])),
            Primitives.toPrimitiveArr(y3.toArray(new Double[0])));
    double c6 = Correlation.correlate(Primitives.toPrimitiveArr(x3.toArray(new Double[0])),
            Primitives.toPrimitiveArr(y3.toArray(new Double[0])));

    System.out.println("Z Spearman: " + c + " Pearson: " + c3);
    System.out.println("P Spearman: " + c2 + " Pearson: " + c4);
    System.out.println("SE Spearman: " + c5 + " Pearson: " + c6);
}

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From source file:org.moeaframework.util.tree.NodeTest.java

@Test
public void testLog10() {
    Node node = new Log10().setArgument(0, new Constant(5));

    Assert.assertTrue(NumberArithmetic.equals(Math.log10(5), (Number) node.evaluate(new UnusedEnvironment())));
}

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From source file:com.bmwcarit.barefoot.markov.KStateTest.java

@Test
public void TestKStateJSON() throws JSONException {
    Map<Integer, MockElem> elements = new HashMap<>();

    KState<MockElem, StateTransition, Sample> state = new KState<>(1, -1);

    {//from w w  w  .ja  va  2  s.  c o m
        JSONObject json = state.toJSON();
        state = new KState<>(json, new MockFactory());
    }

    elements.put(0, new MockElem(0, Math.log10(0.3), 0.3, null));
    elements.put(1, new MockElem(1, Math.log10(0.2), 0.2, null));
    elements.put(2, new MockElem(2, Math.log10(0.5), 0.5, null));

    state.update(new HashSet<>(Arrays.asList(elements.get(0), elements.get(1), elements.get(2))),
            new Sample(0));

    {
        JSONObject json = state.toJSON();
        state = new KState<>(json, new MockFactory());

        elements.clear();

        for (MockElem element : state.vector()) {
            elements.put(element.numid(), element);
        }
    }

    elements.put(3, new MockElem(3, Math.log10(0.3), 0.3, elements.get(1)));
    elements.put(4, new MockElem(4, Math.log10(0.2), 0.2, elements.get(1)));
    elements.put(5, new MockElem(5, Math.log10(0.4), 0.4, elements.get(2)));
    elements.put(6, new MockElem(6, Math.log10(0.1), 0.1, elements.get(2)));

    state.update(
            new HashSet<>(Arrays.asList(elements.get(3), elements.get(4), elements.get(5), elements.get(6))),
            new Sample(1));

    {
        JSONObject json = state.toJSON();
        state = new KState<>(json, new MockFactory());

        elements.clear();

        for (MockElem element : state.vector()) {
            elements.put(element.numid(), element);
        }
    }

    elements.put(7, new MockElem(7, Math.log10(0.3), 0.3, elements.get(5)));
    elements.put(8, new MockElem(8, Math.log10(0.2), 0.2, elements.get(5)));
    elements.put(9, new MockElem(9, Math.log10(0.4), 0.4, elements.get(6)));
    elements.put(10, new MockElem(10, Math.log10(0.1), 0.1, elements.get(6)));

    state.update(
            new HashSet<>(Arrays.asList(elements.get(7), elements.get(8), elements.get(9), elements.get(10))),
            new Sample(2));

    {
        JSONObject json = state.toJSON();
        state = new KState<>(json, new MockFactory());

        elements.clear();

        for (MockElem element : state.vector()) {
            elements.put(element.numid(), element);
        }
    }

    elements.put(11, new MockElem(11, Math.log10(0.3), 0.3, null));
    elements.put(12, new MockElem(12, Math.log10(0.2), 0.2, null));
    elements.put(13, new MockElem(13, Math.log10(0.4), 0.4, null));
    elements.put(14, new MockElem(14, Math.log10(0.1), 0.1, null));

    state.update(
            new HashSet<>(
                    Arrays.asList(elements.get(11), elements.get(12), elements.get(13), elements.get(14))),
            new Sample(3));

    state.update(new HashSet<MockElem>(), new Sample(4));

    {
        JSONObject json = state.toJSON();
        KState<MockElem, StateTransition, Sample> state2 = new KState<>(json, new MockFactory());

        assertEquals(state.size(), state2.size());
        assertEquals(5, state2.size());
        assertEquals(state.estimate().numid(), state2.estimate().numid());
        assertEquals(13, state2.estimate().numid());
        assertEquals(state.sequence().size(), state2.sequence().size());
        assertEquals(2, state2.sequence().size());

        List<Integer> sequence = new LinkedList<>(Arrays.asList(9, 13));
        for (int i = 0; i < state.sequence().size() - 1; ++i) {
            assertEquals(state.sequence().get(i).numid(), state2.sequence().get(i).numid());
            assertEquals(sequence.get(i).longValue(), state2.sequence().get(i).numid());
        }
    }
}

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