Examples with PopulationFunction beast.evolution.tree.coalescent.PopulationFunction used on opensource projects

Example 1 with PopulationFunction

use of beast.evolution.tree.coalescent.PopulationFunction in project beast2 by CompEvol.

the class RandomTree method initStateNodes.

// taxonset intersection test
// private boolean intersects(final BitSet bitSet, final BitSet bitSet2) {
// for (int k = bitSet.nextSetBit(0); k >= 0; k = bitSet.nextSetBit(k + 1)) {
// if (bitSet2.get(k)) {
// return true;
// }
// }
// return false;
// }
// returns true if bitSet is a subset of bitSet2
// private boolean isSubset(final BitSet bitSet, final BitSet bitSet2) {
// boolean isSubset = true;
// for (int k = bitSet.nextSetBit(0); isSubset && k >= 0; k = bitSet.nextSetBit(k + 1)) {
// isSubset = bitSet2.get(k);
// }
// return isSubset;
// }
@SuppressWarnings("unchecked")
@Override
public void initStateNodes() {
    // find taxon sets we are dealing with
    taxonSets = new ArrayList<>();
    m_bounds = new ArrayList<>();
    distributions = new ArrayList<>();
    taxonSetIDs = new ArrayList<>();
    lastMonophyletic = 0;
    if (taxaInput.get() != null) {
        taxa.addAll(taxaInput.get().getTaxaNames());
    } else {
        taxa.addAll(m_taxonset.get().asStringList());
    }
    // pick up constraints from outputs, m_inititial input tree and output tree, if any
    List<MRCAPrior> calibrations = new ArrayList<>();
    calibrations.addAll(calibrationsInput.get());
    // pick up constraints in m_initial tree
    for (final Object beastObject : getOutputs()) {
        if (beastObject instanceof MRCAPrior && !calibrations.contains(beastObject)) {
            calibrations.add((MRCAPrior) beastObject);
        }
    }
    if (m_initial.get() != null) {
        for (final Object beastObject : m_initial.get().getOutputs()) {
            if (beastObject instanceof MRCAPrior && !calibrations.contains(beastObject)) {
                calibrations.add((MRCAPrior) beastObject);
            }
        }
    }
    for (final MRCAPrior prior : calibrations) {
        final TaxonSet taxonSet = prior.taxonsetInput.get();
        if (taxonSet != null && !prior.onlyUseTipsInput.get()) {
            final Set<String> usedTaxa = new LinkedHashSet<>();
            if (taxonSet.asStringList() == null) {
                taxonSet.initAndValidate();
            }
            for (final String taxonID : taxonSet.asStringList()) {
                if (!taxa.contains(taxonID)) {
                    throw new IllegalArgumentException("Taxon <" + taxonID + "> could not be found in list of taxa. Choose one of " + taxa);
                }
                usedTaxa.add(taxonID);
            }
            final ParametricDistribution distr = prior.distInput.get();
            final Bound bounds = new Bound();
            if (distr != null) {
                List<BEASTInterface> beastObjects = new ArrayList<>();
                distr.getPredecessors(beastObjects);
                for (int i = beastObjects.size() - 1; i >= 0; i--) {
                    beastObjects.get(i).initAndValidate();
                }
                try {
                    bounds.lower = distr.inverseCumulativeProbability(0.0) + distr.offsetInput.get();
                    bounds.upper = distr.inverseCumulativeProbability(1.0) + distr.offsetInput.get();
                } catch (MathException e) {
                    Log.warning.println("At RandomTree::initStateNodes, bound on MRCAPrior could not be set " + e.getMessage());
                }
            }
            if (prior.isMonophyleticInput.get()) {
                // add any monophyletic constraint
                taxonSets.add(lastMonophyletic, usedTaxa);
                distributions.add(lastMonophyletic, distr);
                m_bounds.add(lastMonophyletic, bounds);
                taxonSetIDs.add(prior.getID());
                lastMonophyletic++;
            } else {
                // only calibrations with finite bounds are added
                if (!Double.isInfinite(bounds.lower) || !Double.isInfinite(bounds.upper)) {
                    taxonSets.add(usedTaxa);
                    distributions.add(distr);
                    m_bounds.add(bounds);
                    taxonSetIDs.add(prior.getID());
                }
            }
        }
    }
    // assume all calibration constraints are MonoPhyletic
    // TODO: verify that this is a reasonable assumption
    lastMonophyletic = taxonSets.size();
    // sort constraints such that if taxon set i is subset of taxon set j, then i < j
    for (int i = 0; i < lastMonophyletic; i++) {
        for (int j = i + 1; j < lastMonophyletic; j++) {
            Set<String> intersection = new LinkedHashSet<>(taxonSets.get(i));
            intersection.retainAll(taxonSets.get(j));
            if (intersection.size() > 0) {
                final boolean isSubset = taxonSets.get(i).containsAll(taxonSets.get(j));
                final boolean isSubset2 = taxonSets.get(j).containsAll(taxonSets.get(i));
                // o taxonset1 does not intersect taxonset2
                if (!(isSubset || isSubset2)) {
                    throw new IllegalArgumentException("333: Don't know how to generate a Random Tree for taxon sets that intersect, " + "but are not inclusive. Taxonset " + taxonSetIDs.get(i) + " and " + taxonSetIDs.get(j));
                }
                // swap i & j if b1 subset of b2
                if (isSubset) {
                    swap(taxonSets, i, j);
                    swap(distributions, i, j);
                    swap(m_bounds, i, j);
                    swap(taxonSetIDs, i, j);
                }
            }
        }
    }
    // build tree of mono constraints such that j is parent of i if i is a subset of j but i+1,i+2,...,j-1 are not.
    // The last one, standing for the virtual "root" of all monophyletic clades is not associated with an actual clade
    final int[] parent = new int[lastMonophyletic];
    children = new List[lastMonophyletic + 1];
    for (int i = 0; i < lastMonophyletic + 1; i++) {
        children[i] = new ArrayList<>();
    }
    for (int i = 0; i < lastMonophyletic; i++) {
        int j = i + 1;
        while (j < lastMonophyletic && !taxonSets.get(j).containsAll(taxonSets.get(i))) {
            j++;
        }
        parent[i] = j;
        children[j].add(i);
    }
    // make sure upper bounds of a child does not exceed the upper bound of its parent
    for (int i = lastMonophyletic - 1; i >= 0; --i) {
        if (parent[i] < lastMonophyletic) {
            if (m_bounds.get(i).upper > m_bounds.get(parent[i]).upper) {
                m_bounds.get(i).upper = m_bounds.get(parent[i]).upper - 1e-100;
            }
        }
    }
    final PopulationFunction popFunction = populationFunctionInput.get();
    simulateTree(taxa, popFunction);
    if (rootHeightInput.get() != null) {
        scaleToFit(rootHeightInput.get() / root.getHeight(), root);
    }
    nodeCount = 2 * taxa.size() - 1;
    internalNodeCount = taxa.size() - 1;
    leafNodeCount = taxa.size();
    HashMap<String, Integer> taxonToNR = null;
    // preserve node numbers where possible
    if (m_initial.get() != null) {
        if (leafNodeCount == m_initial.get().getLeafNodeCount()) {
            // dont ask me how the initial tree is rubbish  (i.e. 0:0.0)
            taxonToNR = new HashMap<>();
            for (Node n : m_initial.get().getExternalNodes()) {
                taxonToNR.put(n.getID(), n.getNr());
            }
        }
    } else {
        taxonToNR = new HashMap<>();
        String[] taxa = getTaxaNames();
        for (int k = 0; k < taxa.length; ++k) {
            taxonToNR.put(taxa[k], k);
        }
    }
    // multiple simulation tries may produce an excess of nodes with invalid nr's. reset those.
    setNodesNrs(root, 0, new int[1], taxonToNR);
    initArrays();
    if (m_initial.get() != null) {
        m_initial.get().assignFromWithoutID(this);
    }
    for (int k = 0; k < lastMonophyletic; ++k) {
        final MRCAPrior p = calibrations.get(k);
        if (p.isMonophyleticInput.get()) {
            final TaxonSet taxonSet = p.taxonsetInput.get();
            if (taxonSet == null) {
                throw new IllegalArgumentException("Something is wrong with constraint " + p.getID() + " -- a taxonset must be specified if a monophyletic constraint is enforced.");
            }
            final Set<String> usedTaxa = new LinkedHashSet<>();
            if (taxonSet.asStringList() == null) {
                taxonSet.initAndValidate();
            }
            usedTaxa.addAll(taxonSet.asStringList());
            /* int c = */
            traverse(root, usedTaxa, taxonSet.getTaxonCount(), new int[1]);
        // boolean b = c == nrOfTaxa + 127;
        }
    }
}