Java Code Examples for org.apache.commons.math3.util.MathArrays#distance()

The following examples show how to use org.apache.commons.math3.util.MathArrays#distance() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.

Example 1

Source File: LearnReadOrientationModelEngine.java From gatk with BSD 3-Clause "New" or "Revised" License

5 votes

public ArtifactPrior learnPriorForArtifactStates() {
    // Initialize the prior for artifact
    final double[] pseudocounts = getFlatPrior(refAllele);
    double[] statePrior = Arrays.copyOf(pseudocounts, F1R2FilterConstants.NUM_STATES);
    double l2Distance;

    do {
        final double[] oldStatePrior = Arrays.copyOf(statePrior, F1R2FilterConstants.NUM_STATES);

        // Responsibilities are updated by side effect to save space
        takeEstep(statePrior);
        statePrior = takeMstep(pseudocounts);

        // TODO: make sure EM increases the likelihood
        // newLikelihood >= oldLikelihood : "M step must increase the likelihood";
        l2Distance = MathArrays.distance(oldStatePrior, statePrior);

        numIterations.increment();
    } while (l2Distance > convergenceThreshold && numIterations.intValue() < maxEMIterations);

    if (numIterations.intValue() == maxEMIterations){
        logger.info(String.format("Context %s: with %s ref and %s alt examples, EM failed to converge within %d steps",
                referenceContext, numRefExamples, numAltExamples, maxEMIterations));
    } else {
        logger.info(String.format("Context %s: with %s ref and %s alt examples, EM converged in %d steps",
                referenceContext, numRefExamples, numAltExamples, numIterations.intValue()));
    }

    return new ArtifactPrior(referenceContext, statePrior, numExamples, numAltExamples);
}

Example 2

Source File: EuclideanDoublePoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanDoublePoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 3

Source File: EuclideanIntegerPoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanIntegerPoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 4

Source File: EuclideanDoublePoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanDoublePoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 5

Source File: EuclideanDistance.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double compute(double[] a, double[] b) {
    return MathArrays.distance(a, b);
}

Example 6

Source File: EuclideanIntegerPoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanIntegerPoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 7

Source File: EuclideanDoublePoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanDoublePoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 8

Source File: EuclideanDistance.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double compute(double[] a, double[] b) {
    return MathArrays.distance(a, b);
}

Example 9

Source File: EuclideanIntegerPoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanIntegerPoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 10

Source File: EuclideanDistance.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double compute(double[] a, double[] b) {
    return MathArrays.distance(a, b);
}

Example 11

Source File: EuclideanIntegerPoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanIntegerPoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 12

Source File: EuclideanIntegerPoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanIntegerPoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 13

Source File: EuclideanDoublePoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanDoublePoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 14

Source File: EuclideanDistance.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double compute(double[] a, double[] b) {
    return MathArrays.distance(a, b);
}

Example 15

Source File: EuclideanIntegerPoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanIntegerPoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 16

Source File: EuclideanIntegerPoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanIntegerPoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 17

Source File: EuclideanIntegerPoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanIntegerPoint p) {
    return MathArrays.distance(point, p.getPoint());
}

Example 18

Source File: EuclideanDoublePoint.java From astor with GNU General Public License v2.0

4 votes

/** {@inheritDoc} */
public double distanceFrom(final EuclideanDoublePoint p) {
    return MathArrays.distance(point, p.getPoint());
}