import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
public TaxonSet generateSuperset() {
    List<Taxon> superSetList = new ArrayList<>();
    for (int i = 0; i < nSpecies; i++) {
        final String speciesName = String.format("s%d", i);
        List<Taxon> taxonList = new ArrayList<>();
        for (int j = 0; j < individualsPerSpecies; j++) {
            final String taxonName = String.format("s%d_tip%d", i, j);
            taxonList.add(new Taxon(taxonName));
        }
        superSetList.add(new TaxonSet(speciesName, taxonList));
    }

    TaxonSet speciesSuperset = new TaxonSet(superSetList);
    
    return speciesSuperset;
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
private void initialize(TaxonSet speciesSuperset) throws Exception {
    speciesTree = new SpeciesTreeParser();
    speciesTree.initByName("newick", newickSpeciesTree, "IsLabelledNewick", true, "taxonset", speciesSuperset);

    for (String geneTreeNewick: newickGeneTrees) {
        TreeParser geneTree = new TreeParser();
        geneTree.initByName("newick", geneTreeNewick, "IsLabelledNewick", true);
        geneTrees.add(geneTree);

        GeneTree geneTreeWrapper = new GeneTree();
        geneTreeWrapper.initByName("tree", geneTree, "ploidy", ploidy, "speciesTree", speciesTree);
        geneTreeWrappers.add(geneTreeWrapper);
    }

    state.initByName("stateNode", alphaParameter);
    state.initByName("stateNode", meanParameter);

    msc = new MultispeciesCoalescent();
    msc.initByName("populationShape", alphaParameter, "populationMean", meanParameter, "distribution", geneTreeWrappers);

    for (GeneTree gt: geneTreeWrappers) gt.calculateLogP();
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
public TaxonSet generateSuperset() throws Exception {
    List<Taxon> superSetList = new ArrayList<>();
    for (int i = 0; i < nSpecies; i++) {
        final String speciesName = String.format("s%d", i);
        List<Taxon> taxonList = new ArrayList<>();
        for (int j = 0; j < individualsPerSpecies; j++) {
            final String taxonName = String.format("s%d_tip%d", i, j);
            taxonList.add(new Taxon(taxonName));
        }
        superSetList.add(new TaxonSet(speciesName, taxonList));
    }

    TaxonSet speciesSuperSet = new TaxonSet(superSetList);

    return speciesSuperSet;
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
@Test
public void testLogP() throws Exception {
    TaxonSet speciesSuperset = generateSuperset();
    speciesTree = new SpeciesTreeParser();
    speciesTree.initByName("newick", newickSpeciesTree, "IsLabelledNewick", true, "taxonset", speciesSuperset);

    final int nBranches = nSpecies * 2 - 1;
    popsizeParameter.initByName("value", String.valueOf(popSize), "dimension", String.valueOf(nBranches));
    state.initByName("stateNode", popsizeParameter);

    popModel = new ConstantPopulations();
    popModel.initByName("populationSizes", popsizeParameter, "speciesTree", speciesTree);

    double calculatedLogP = 0.0;
    for (String geneTreeNewick: newickGeneTrees) {
        TreeParser geneTree = new TreeParser();
        geneTree.initByName("newick", geneTreeNewick, "IsLabelledNewick", true);

        GeneTree geneTreeWrapper = new GeneTree();
        geneTreeWrapper.initByName("tree", geneTree, "ploidy", ploidy, "speciesTree", speciesTree, "populationModel", popModel);
        calculatedLogP += geneTreeWrapper.calculateLogP();
    }

    // System.out.println(String.format("expected %f, calculated %f", expectedLogP, calculatedLogP));
    assertEquals(expectedLogP, calculatedLogP, allowedError);
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
public TaxonSet generateSuperset() {
    List<Taxon> superSetList = new ArrayList<>();
    for (int i = 0; i < nSpecies; i++) {
        final String speciesName = String.format("T%d", i + 1);
        List<Taxon> taxonList = new ArrayList<>();
        for (int j = 0; j < individualsPerSpecies; j++) {
            final String taxonName = String.format("T%d_%d", i + 1, j + 1);
            taxonList.add(new Taxon(taxonName));
        }
        superSetList.add(new TaxonSet(speciesName, taxonList));
    }

    TaxonSet speciesSuperset = new TaxonSet(superSetList);
    
    return speciesSuperset;
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
private TaxonSet generateSuperset() {
    List<Taxon> superSetList = new ArrayList<>();
    for (int i = 0; i < nSpecies; i++) {
        final String speciesName = String.format("s%d", i);
        List<Taxon> taxonList = new ArrayList<>();
        for (int j = 0; j < individualsPerSpecies; j++) {
            final String taxonName = String.format("s%d_tip%d", i, j);
            taxonList.add(new Taxon(taxonName));
        }
        superSetList.add(new TaxonSet(speciesName, taxonList));
    }

    TaxonSet speciesSuperset = new TaxonSet(superSetList);

    return speciesSuperset;
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
private void initialize(TaxonSet speciesSuperset) throws Exception {
    speciesTree = new SpeciesTreeParser();
    speciesTree.initByName("newick", newickSpeciesTree, "IsLabelledNewick", true, "taxonset", speciesSuperset);

    for (String geneTreeNewick: newickGeneTrees) {
        TreeParser geneTree = new TreeParser();
        geneTree.initByName("newick", geneTreeNewick, "IsLabelledNewick", true);
        geneTrees.add(geneTree);

        GeneTree geneTreeWrapper = new GeneTree();
        geneTreeWrapper.initByName("tree", geneTree, "ploidy", ploidy, "speciesTree", speciesTree);
        geneTreeWrappers.add(geneTreeWrapper);
    }

    state.initByName("stateNode", alphaParameter);
    state.initByName("stateNode", meanParameter);

    msc = new MultispeciesCoalescent();
    msc.initByName("populationShape", alphaParameter, "populationMean", meanParameter, "distribution", geneTreeWrappers);
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
public TaxonSet generateSuperset() throws Exception {
    List<Taxon> superSetList = new ArrayList<>();

    List<Taxon> taxonListA = new ArrayList<>();
    List<Taxon> taxonListB = new ArrayList<>();
    List<Taxon> taxonListC = new ArrayList<>();

    taxonListA.add(new Taxon("A1"));
    taxonListA.add(new Taxon("A2"));
    taxonListB.add(new Taxon("B1"));
    taxonListB.add(new Taxon("B2"));
    taxonListC.add(new Taxon("C1"));

    superSetList.add(new TaxonSet("A", taxonListA));
    superSetList.add(new TaxonSet("B", taxonListB));
    superSetList.add(new TaxonSet("C", taxonListC));


    TaxonSet speciesSuperSet = new TaxonSet(superSetList);

    return speciesSuperSet;
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
private TaxonSet generateSuperset() throws Exception {
    String speciesCodes = "abc";
    List<Taxon> superSetList = new ArrayList<>();
    for (int i = 0; i < nSpecies; i++) {
        final String speciesName = speciesCodes.substring(i, i + 1);
        List<Taxon> taxonList = new ArrayList<>();
        for (int j = 0; j < individualsPerSpecies; j++) {
            final String taxonName = String.format("%s%d", speciesName, j + 1);
            taxonList.add(new Taxon(taxonName));
        }
        superSetList.add(new TaxonSet(speciesName, taxonList));
    }

    TaxonSet speciesSuperSet = new TaxonSet(superSetList);
    
    return speciesSuperSet;
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
public TaxonSet generateSuperset() throws Exception {
    List<Taxon> superSetList = new ArrayList<>();

    List<Taxon> taxonListA = new ArrayList<>();
    List<Taxon> taxonListB = new ArrayList<>();
    List<Taxon> taxonListC = new ArrayList<>();

    taxonListA.add(new Taxon("A1"));
    taxonListA.add(new Taxon("A2"));
    taxonListB.add(new Taxon("B1"));
    taxonListB.add(new Taxon("B2"));
    taxonListC.add(new Taxon("C1"));

    superSetList.add(new TaxonSet("A", taxonListA));
    superSetList.add(new TaxonSet("B", taxonListB));
    superSetList.add(new TaxonSet("C", taxonListC));

    TaxonSet speciesSuperSet = new TaxonSet(superSetList);

    return speciesSuperSet;
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
@Override
public void initAndValidate() {
    /** maps gene taxa names to species number **/
    final Map<String, Integer> taxonMap = new HashMap<>();
    final List<Taxon> list = taxonSetInput.get().taxonsetInput.get();
    
    if (list.size() <= 1) {
    	Log.err.println("NodeReheight operator requires at least 2 taxa while the taxon set (id=" + taxonSetInput.get().getID() +") has only " + list.size() + " taxa. "
    			+ "If the XML file was set up in BEAUti, this probably means a taxon assignment needs to be set up in the taxonset panel.");
    	// assume we are in BEAUti, back off for now
    	return;
    }
    
    for (int i = 0; i < list.size(); i++) {
        final Taxon taxa = list.get(i);
        // cast should be ok if taxon-set is the set for the species tree
        final TaxonSet set = (TaxonSet) taxa;
        for (final Taxon taxon : set.taxonsetInput.get()) {
            taxonMap.put(taxon.getID(), i);
        }
    }

    /** build the taxon map for each gene tree **/
    m_taxonMap = new ArrayList<>();
    for (final Tree tree : geneTreesInput.get()) {
        final Map<Integer, Integer> map = new HashMap<>();
        setupTaxaMap(tree.getRoot(), map, taxonMap);
        m_taxonMap.add(map);
    }

    nrOfGeneTrees = geneTreesInput.get().size();
    nrOfSpecies = treeInput.get().getLeafNodeCount();
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
private void randomInit() {
        double lam = 1;
        final RealParameter lambda = birthRate.get();
        if( lambda != null ) {
            lam = lambda.getArrayValue();
        }
        final Tree stree = speciesTreeInput.get();
        final TaxonSet species = stree.m_taxonset.get();
        final int speciesCount = species.asStringList().size();
        double s = 0;
        for(int k = 2; k <= speciesCount; ++k) {
            s += 1.0/k;
        }
        final double rootHeight = (1/lam) * s;
        stree.scale(rootHeight/stree.getRoot().getHeight());
        randomInitGeneTrees(rootHeight);
//        final List<Tree> geneTrees = genes.get();
//        for (final Tree gtree : geneTrees) {
//            gtree.makeCaterpillar(rootHeight, rootHeight/gtree.getInternalNodeCount(), true);
//        }
    }
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
Set<Taxon> getTaxonCandidates(MRCAPrior prior) {
     Set<Taxon> candidates = new HashSet<>();
     Tree tree = prior.treeInput.get();
     String [] taxa = null;
     if (tree.m_taxonset.get() != null) {
     	try {
         	TaxonSet set = tree.m_taxonset.get();
     		set.initAndValidate();
         	taxa = set.asStringList().toArray(new String[0]);
     	} catch (Exception e) {
         	taxa = prior.treeInput.get().getTaxaNames();
}
     } else {
     	taxa = prior.treeInput.get().getTaxaNames();
     }
     
     for (String taxon : taxa) {
         candidates.add(doc.getTaxon(taxon));
     }
     return candidates;
 }
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
private void enableTipSampling() {
   	// First, create/find the operator
   	TipDatesRandomWalker operator = null;
   	MRCAPrior prior = (MRCAPrior) m_beastObject;
   	TaxonSet taxonset = prior.taxonsetInput.get();
   	taxonset.initAndValidate();
   	
   	// see if an old operator still hangs around -- happens when toggling the TipsOnly checkbox a few times
   	for (BEASTInterface o : taxonset.getOutputs()) {
   		if (o instanceof TipDatesRandomWalker) {
   			operator = (TipDatesRandomWalker) o;
   		}
   	}
   	
   	if (operator == null) {
   		operator = new TipDatesRandomWalker();
   		operator.initByName("tree", prior.treeInput.get(), "taxonset", taxonset, "windowSize", 1.0, "weight", 1.0);
   	}
  		operator.setID("tipDatesSampler." + taxonset.getID());
  	    	
   	doc.mcmc.get().setInputValue("operator", operator);
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
/**
 * Create a tree from the given newick format
 *
 * @param taxaNames a list of taxa names to use, or null.
 *                  If null then IsLabelledNewick will be set to true
 * @param newick    the newick of the tree
 * @param offset    the offset to map node numbers in newick format to indices in taxaNames.
 *                  so, name(node with nodeNumber) = taxaNames[nodeNumber-offset]
 * @param adjustTipHeightsWhenMissingDateTraits
 *                  true if tip heights should be adjusted to zero
 */
public TreeParser(final List<String> taxaNames,
                  final String newick,
                  final int offset,
                  final boolean adjustTipHeightsWhenMissingDateTraits) {

    if (taxaNames == null) {
        isLabelledNewickInput.setValue(true, this);
    } else {
        m_taxonset.setValue(new TaxonSet(Taxon.createTaxonList(taxaNames)), this);
    }
    newickInput.setValue(newick, this);
    offsetInput.setValue(offset, this);
    adjustTipHeightsInput.setValue(adjustTipHeightsWhenMissingDateTraits, this);
    labels = taxaNames;
    initAndValidate();
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
protected void processSets() {
   	// create monophyletic MRCAPrior for each taxon set that 
   	// does not already have a calibration associated with it
   	for (TaxonSet taxonset : taxonsets) {
   		boolean found = false;
   		for (BEASTInterface o : taxonset.getOutputs()) {
   			if (o instanceof MRCAPrior) {
   				found = true;
   				break;
   			}
   		}
   		if (!found) {
       		MRCAPrior prior = new MRCAPrior();
       		prior.isMonophyleticInput.setValue(true, prior);
       		prior.taxonsetInput.setValue(taxonset, prior);
       		prior.setID(taxonset.getID() + ".prior");
       		// should set Tree before initialising, but we do not know the tree yet...
       		if (calibrations == null) {
       			calibrations = new ArrayList<>();
       		}
       		calibrations.add(prior);
   		}
   	}
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
public void testWeightedSitesReordered() throws Exception {

        // reorder taxa
        Alignment data = getAlignmentNoTInHuman();
        data.setID("data");

        List<Taxon> taxa = new ArrayList<>();
        taxa.add(new Taxon("1chimp"));
        taxa.add(new Taxon("0human"));
        TaxonSet set = new TaxonSet(taxa);

        data.taxonSetInput.setValue(set, data);
        data.siteWeightsInput.setValue("11232, 2, 3, 4 ,1123,2,3,4,112,2,3,4,11,2,3,	4 ", data);
        data.initAndValidate();

        String weights = Arrays.toString(data.getWeights());

        System.out.println(weights + "\n0human\t" + alignmentToString(data, data.getTaxonIndex("0human")) + "\n1chimp\t"
                + alignmentToString(data, data.getTaxonIndex("1chimp")));
        assertEquals("[11243, 1123, 112, 4, 2, 2, 6, 3, 3, 8, 4, 4]", weights);

    }
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
@Test
public void testLogP() throws Exception {
    TaxonSet speciesSuperset = generateSuperset();
    initialize(speciesSuperset);

    final double calculatedLogP = msc.calculateLogP();
    // System.out.println(String.format("expected %f, calculated %f", expectedLogP, calculatedLogP));
    assertEquals(expectedLogP, calculatedLogP, allowedError);
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
@Test
public void testRates() throws Exception {
    TaxonSet speciesSuperSet = generateSuperset();
    initializeTrees(speciesSuperSet);

    meanRateParameter = new RealParameter();
    stdevParameter = new RealParameter();
    branchRatesParameter = new IntegerParameter();

    meanRateParameter.initByName("value", String.valueOf(meanRate));
    stdevParameter.initByName("value", String.valueOf(1.0));
    branchRatesParameter.initByName("value", String.valueOf(initialBranchRate));

    // Create dummy state to allow statenode editing
    State state = new State();
    state.initByName("stateNode", meanRateParameter);
    state.initByName("stateNode", branchRatesParameter);
    state.initialise();

    speciesTreeClock = new UncorrelatedRates();
    speciesTreeClock.initByName("tree", speciesTree, "rates", branchRatesParameter, "stdev", stdevParameter, "estimateRoot", true);
    initializeRates();

    geneTreeClock = new StarBeastClock();
    geneTreeClock.initByName("geneTree", geneTreeWrapper, "speciesTreeRates", speciesTreeClock, "clock.rate", meanRateParameter);
    checkRates();
}
 

import beast.evolution.alignment.TaxonSet; //导入依赖的package包/类
public void initializeTrees(TaxonSet speciesSuperSet) throws Exception {
    speciesTree = new SpeciesTreeParser();
    speciesTree.initByName("newick", newickSpeciesTree, "IsLabelledNewick", true, "taxonset", speciesSuperSet);

    geneTree = new TreeParser();
    geneTree.initByName("newick", newickGeneTree, "IsLabelledNewick", true);

    geneTreeWrapper = new GeneTree();
    geneTreeWrapper.initByName("tree", geneTree, "ploidy", ploidy, "speciesTree", speciesTree);
}