Examples with AncestralStatesComponentOptions dr.app.beauti.components.ancestralstates.AncestralStatesComponentOptions used on opensource projects

Example 6 with AncestralStatesComponentOptions

use of dr.app.beauti.components.ancestralstates.AncestralStatesComponentOptions in project beast-mcmc by beast-dev.

the class BeautiOptions method updateTraitParameters.

private void updateTraitParameters(AbstractPartitionData partition) {
    if (partition.isCreatedFromTrait()) {
        ContinuousComponentOptions comp = (ContinuousComponentOptions) getComponentOptions(ContinuousComponentOptions.class);
        comp.createParameters(this);
        DiscreteTraitsComponentOptions comp2 = (DiscreteTraitsComponentOptions) getComponentOptions(DiscreteTraitsComponentOptions.class);
        comp2.createParameters(this);
        AncestralStatesComponentOptions comp3 = (AncestralStatesComponentOptions) getComponentOptions(AncestralStatesComponentOptions.class);
        comp3.setReconstructAtNodes(partition, true);
        comp3.setReconstructAtMRCA(partition, false);
    }
}

Example 7 with AncestralStatesComponentOptions

use of dr.app.beauti.components.ancestralstates.AncestralStatesComponentOptions in project beast-mcmc by beast-dev.

the class DiscreteTraitsComponentGenerator method writeTreeLikelihoodReferences.

private void writeTreeLikelihoodReferences(XMLWriter writer) {
    for (AbstractPartitionData partition : options.dataPartitions) {
        if (partition.getTraits() != null) {
            AncestralStatesComponentOptions ancestralStatesOptions = (AncestralStatesComponentOptions) options.getComponentOptions(AncestralStatesComponentOptions.class);
            String treeLikelihoodTag = TreeLikelihoodParser.ANCESTRAL_TREE_LIKELIHOOD;
            if (ancestralStatesOptions.isCountingStates(partition)) {
                treeLikelihoodTag = MarkovJumpsTreeLikelihoodParser.MARKOV_JUMP_TREE_LIKELIHOOD;
            }
            TraitData trait = partition.getTraits().get(0);
            String prefix = partition.getName() + ".";
            if (trait.getTraitType() == TraitData.TraitType.DISCRETE) {
                writer.writeIDref(treeLikelihoodTag, prefix + TreeLikelihoodParser.TREE_LIKELIHOOD);
            }
        }
    }
}