/*
 * BranchRateGradientForDiscreteTrait.java
 *
 * Copyright (c) 2002-2017 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.discrete;

import dr.evolution.tree.*;
import dr.evomodel.treedatalikelihood.*;
import dr.inference.hmc.GradientWrtParameterProvider;
import dr.inference.hmc.HessianWrtParameterProvider;
import dr.inference.loggers.Loggable;
import dr.inference.model.Parameter;
import dr.xml.Reportable;

import static dr.math.MachineAccuracy.SQRT_EPSILON;

/**
 * @author Xiang Ji
 * @author Marc A. Suchard
 */
public class BranchRateGradientForDiscreteTrait extends DiscreteTraitBranchRateGradient
        implements GradientWrtParameterProvider, HessianWrtParameterProvider, Reportable, Loggable {

    public BranchRateGradientForDiscreteTrait(String traitName,
                                              TreeDataLikelihood treeDataLikelihood,
                                              BeagleDataLikelihoodDelegate likelihoodDelegate,
                                              Parameter rateParameter,
                                              boolean useHessian) {
        super(traitName, treeDataLikelihood, likelihoodDelegate, rateParameter, useHessian);
    }

    @Override
    protected double getChainGradient(Tree tree, NodeRef node) {
        final double differential = branchRateModel.getBranchRateDifferential(tree, node);
        return differential * tree.getBranchLength(node);
    }

    @Override
    protected double getChainSecondDerivative(Tree tree, NodeRef node) {
        final double branchLength = tree.getBranchLength(node);
        return branchRateModel.getBranchRateSecondDifferential(tree, node) * branchLength;
    }

}

@@ -1149,248 +1149,25 @@
 nce.
-hmc.GradientWrtParameterProvider;%0Aimport dr.inference.hmc.HessianWrtParameterProvider;%0Aimport dr.inference.loggers.Loggable;%0Aimport dr.inference.model.Parameter;%0Aimport dr.xml.Reportable;%0A%0Aimport static dr.math.MachineAccuracy.SQRT_EPSILON;
+model.Parameter;%0A
 %0A%0A/*
@@ -1310,107 +1310,8 @@
 ient
-%0A        implements GradientWrtParameterProvider, HessianWrtParameterProvider, Reportable, Loggable
  %7B%0A%0A
@@ -1884,35 +1884,14 @@
     
-final double differential =
+return
  bra
@@ -1944,37 +1944,8 @@
 ode)
-;%0A        return differential
  * t
@@ -2069,72 +2069,8 @@
 ) %7B%0A
-        final double branchLength = tree.getBranchLength(node);%0A
     
@@ -2142,17 +2142,25 @@
 node) * 
-b
+tree.getB
 ranchLen
@@ -2162,19 +2162,25 @@
 chLength
+(node)
 ;%0A    %7D%0A
 %0A%7D%0A
@@ -2176,11 +2176,10 @@
 ;%0A    %7D%0A
-%0A
 %7D%0A

clean up class