PrecisionType.java

/*
 * PrecisionType.java
 *
 * Copyright (c) 2002-2016 Alexei Drummond, Andrew Rambaut and Marc Suchard
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.evomodel.treedatalikelihood.continuous.cdi;

/**
 * @author Marc A. Suchard
 */
public enum PrecisionType {
    SCALAR("proportional scaling per branch", 0) {
        @Override
        public void fillPrecisionInPartials(double[] partial, int offset, int index, double precision,
                                            int dimTrait) {
            if (index == 0) {
                partial[offset + dimTrait] = precision;
            } else {
                if (partial[offset + dimTrait] != 0.0) {
                    partial[offset + dimTrait] = precision;
                }
            }
        }

        @Override
        public void copyObservation(double[] partial, int pOffset, double[] data, int dOffset, int dimTrait) {
            for (int i = 0; i < dimTrait; ++i) {
                data[dOffset + i] = Double.isInfinite(partial[pOffset + dimTrait]) ?
                        partial[pOffset + i] : Double.NaN;
            }
        }
    },
    MIXED("mixed method", 1) {
        @Override
        public void fillPrecisionInPartials(double[] partial, int offset, int index, double precision,
                                            int dimTrait) {
            partial[offset + dimTrait + index] = precision;
        }

        @Override
        public void copyObservation(double[] partial, int pOffset, double[] data, int dOffset, int dimTrait) {
            for (int i = 0; i < dimTrait; ++i) {
                data[dOffset + i] = Double.isInfinite(partial[pOffset + dimTrait + i]) ?
                        partial[pOffset + i] : Double.NaN;
            }
        }
    },
    FULL("full precision matrix per branch", 2) {
        @Override
        public void fillPrecisionInPartials(double[] partial, int offset, int index, double precision,
                                            int dimTrait) {
            final int offs = offset + dimTrait + index * dimTrait + index;
            partial[offs] = precision;
            partial[offs+ dimTrait * dimTrait] = Double.isInfinite(precision) ? 0.0 : 1.0 / precision;
            partial[offset + dimTrait + 2 * dimTrait * dimTrait] = Double.POSITIVE_INFINITY;
        }

        @Override
        public void copyObservation(double[] partial, int pOffset, double[] data, int dOffset, int dimTrait) {
            for (int i = 0; i < dimTrait; ++i) {
                data[dOffset + i] = Double.isInfinite(partial[pOffset + dimTrait + i * dimTrait + i]) ?
                        partial[pOffset + i] : Double.NaN;
            }
        }

        @Override
        public int getMatrixLength(int dimTrait) {
            return 2 * super.getMatrixLength(dimTrait) + 1;
        }
    };

    private final int power;
    private final String name;

    PrecisionType(String name, int power) {
        this.name = name;
        this.power = power;
    }

    public String toString() {
        return name;
    }

    public int getPower() {
        return power;
    }

    public int getMatrixLength(int dimTrait) {
        int length = 1;
        final int pow = getPower();
        for (int i = 0; i < pow; ++i) {
            length *= dimTrait;
        }
        return length;
    }

    public static double getObservedPrecisionValue(final boolean missing) {
        return missing ? 0.0 : Double.POSITIVE_INFINITY;
    }

    abstract public void fillPrecisionInPartials(double[] partial, int offset, int index, double precision,
                                                 int dimTrait);

    abstract public void copyObservation(double[] partial, int pOffset, double[] data, int dOffset, int dimTrait);

}