lphy.base.function.tree.TreeLength Maven / Gradle / Ivy

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The standard library of LPhy, which contains the required generative distributions and basic functions.

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package lphy.base.function.tree;

import lphy.base.evolution.tree.TimeTree;
import lphy.core.model.DeterministicFunction;
import lphy.core.model.Value;
import lphy.core.model.annotation.GeneratorCategory;
import lphy.core.model.annotation.GeneratorInfo;
import lphy.core.model.annotation.ParameterInfo;
import lphy.core.model.datatype.DoubleValue;

/**
 * use {@link TimeTree#treeLength()}
 */
@Deprecated
public class TreeLength extends DeterministicFunction {

    final String paramName;

    public TreeLength(@ParameterInfo(name = "tree", description = "the tree.") Value x) {
        paramName = getParamName(0);
        setParam(paramName, x);
    }

    @GeneratorInfo(name="treeLength",
            category = GeneratorCategory.TREE, examples = {"simpleCalibratedYule.lphy","simpleExtantBirthDeath.lphy"},
            description = "The sum of all the branch lengths in the tree.")
    public Value apply() {
        Value v = (Value)getParams().get(paramName);
        return new DoubleValue(v.value().treeLength(), this);
    }
}