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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.taxa;

import lphy.base.evolution.Taxa;
import lphy.base.evolution.Taxon;
import lphy.core.model.DeterministicFunction;
import lphy.core.model.Value;
import lphy.core.model.annotation.GeneratorInfo;
import lphy.core.model.annotation.ParameterInfo;

import java.util.Arrays;

@Deprecated
public class TaxaFunction extends DeterministicFunction {

    final String paramName;

    public TaxaFunction(@ParameterInfo(name = "taxa", narrativeName="taxon list", verb="of", description = "the taxa value (i.e. alignment or tree).") Value x) {
        paramName = getParamName(0);
        setParam(paramName, x);
    }



    @Deprecated
    @GeneratorInfo(name="taxa",
            verbClause = "is",
            narrativeName = "taxon list",
            description = "The taxa of the given taxa-dimensioned object (e.g. alignment, tree et cetera).")
    public Value apply() {
        Value v = getParams().get(paramName);
        Object value = v.value();

        Taxa rawTaxa;
        if (value instanceof Taxa) {
            rawTaxa = (Taxa) value;
        } else if (value instanceof Taxa[]) {
            Taxa[] taxaArr = (Taxa[])value;
            rawTaxa = taxaArr[0];
            for (int i = 1; i < taxaArr.length; i++) {
                if (! Arrays.equals(rawTaxa.getTaxaNames(), taxaArr[i].getTaxaNames()))
                    throw new IllegalArgumentException("Taxa[] should have the same names and same order ! " + i);
            }

        } else throw new IllegalArgumentException("the taxa function can only take type Taxa or Taxa[] as a value input!");


        Taxa wrappedTaxa = new Taxa() {
            @Override
            public int ntaxa() {
                return rawTaxa.ntaxa();
            }

            @Override
            public Double[] getAges() {
                return rawTaxa.getAges();
            }

            @Override
            public String[] getSpecies() {
                return rawTaxa.getSpecies();
            }

            @Override
            public String[] getTaxaNames() {
                return rawTaxa.getTaxaNames();
            }

            public Taxon[] getTaxonArray() {
                return rawTaxa.getTaxonArray();
            }

            public Taxon getTaxon(int i) { return rawTaxa.getTaxon(i); };

            @Override
            public String toString() {
                StringBuilder builder = new StringBuilder();
                for (Taxon taxon : getTaxonArray()) {
                    builder.append(taxon.toString());
                    builder.append("\n");
                }
                return builder.toString();
            }
        };

        return new Value<>( null, wrappedTaxa, this);
    }
}