Examples with TaxonSet beast.evolution.alignment.TaxonSet used on opensource projects

Example 1 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class BeautiDoc method createTaxonSet.

/**
 * create taxonset, one taxon for each sequence in the alignment
 * and assign taxonset to the alignment
 * *
 */
static void createTaxonSet(Alignment a, BeautiDoc doc) {
    List<String> taxaNames = a.getTaxaNames();
    TaxonSet taxonset = new TaxonSet();
    for (final String taxaName : taxaNames) {
        taxonset.taxonsetInput.get().add(doc.getTaxon(taxaName));
    }
    taxonset.setID("TaxonSet0." + a.getID());
    try {
        taxonset.initAndValidate();
    } catch (Exception e) {
        e.printStackTrace();
    }
    doc.registerPlugin(taxonset);
}

Example 2 with TaxonSet

use of beast.evolution.alignment.TaxonSet 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;
        }
    }
}

Example 3 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class CalibratedYuleModel method initAndValidate.

@Override
public void initAndValidate() {
    super.initAndValidate();
    type = correctionTypeInput.get();
    final TreeInterface tree = treeInput.get();
    // shallow copy. we shall change cals later
    final List<CalibrationPoint> cals = new ArrayList<>(calibrationsInput.get());
    int calCount = cals.size();
    final List<TaxonSet> taxaSets = new ArrayList<>(calCount);
    if (cals.size() > 0) {
        xclades = new int[calCount][];
        // convenience
        for (final CalibrationPoint cal : cals) {
            taxaSets.add(cal.taxa());
        }
    } else {
        // find calibration points from prior
        for (final Object beastObject : getOutputs()) {
            if (beastObject instanceof CompoundDistribution) {
                final CompoundDistribution prior = (CompoundDistribution) beastObject;
                for (final Distribution distr : prior.pDistributions.get()) {
                    if (distr instanceof MRCAPrior) {
                        final MRCAPrior _MRCAPrior = (MRCAPrior) distr;
                        // make sure MRCAPrior is monophyletic
                        if (_MRCAPrior.distInput.get() != null) {
                            // make sure MRCAPrior is monophyletic
                            if (!_MRCAPrior.isMonophyleticInput.get()) {
                                throw new IllegalArgumentException("MRCAPriors must be monophyletic for Calibrated Yule prior");
                            }
                            // create CalibrationPoint from MRCAPrior
                            final CalibrationPoint cal = new CalibrationPoint();
                            cal.distInput.setValue(_MRCAPrior.distInput.get(), cal);
                            cal.taxonsetInput.setValue(_MRCAPrior.taxonsetInput.get(), cal);
                            cal.forParentInput.setValue(_MRCAPrior.useOriginateInput.get(), cal);
                            cal.initAndValidate();
                            cals.add(cal);
                            taxaSets.add(cal.taxa());
                            cal.taxa().initAndValidate();
                            calCount++;
                            calcCalibrations = false;
                        } else {
                            if (_MRCAPrior.isMonophyleticInput.get()) {
                                Log.warning.println("WARNING: MRCAPriors (" + _MRCAPrior.getID() + ") must have a distribution when monophyletic. Ignored for Calibrated Yule prior");
                            } else {
                                Log.warning.println("WARNING: MRCAPriors (" + _MRCAPrior.getID() + ") found that is not monophyletic. Ignored for Calibrated Yule prior");
                            }
                        }
                    }
                }
            }
        }
        xclades = new int[calCount][];
    }
    if (calCount == 0) {
        Log.warning.println("WARNING: Calibrated Yule prior could not find any properly configured calibrations. Expect this to crash in a BEAST run.");
        // assume we are in beauti, back off for now
        return;
    }
    for (int k = 0; k < calCount; ++k) {
        final TaxonSet tk = taxaSets.get(k);
        for (int i = k + 1; i < calCount; ++i) {
            final TaxonSet ti = taxaSets.get(i);
            if (ti.containsAny(tk)) {
                if (!(ti.containsAll(tk) || tk.containsAll(ti))) {
                    throw new IllegalArgumentException("Overlapping taxaSets??");
                }
            }
        }
    }
    orderedCalibrations = new CalibrationPoint[calCount];
    {
        int loc = taxaSets.size() - 1;
        while (loc >= 0) {
            assert loc == taxaSets.size() - 1;
            // place maximal taxaSets at end one at a time
            int k = 0;
            for (; /**/
            k < taxaSets.size(); ++k) {
                if (isMaximal(taxaSets, k)) {
                    break;
                }
            }
            final List<String> tk = taxaSets.get(k).asStringList();
            final int tkcount = tk.size();
            this.xclades[loc] = new int[tkcount];
            for (int nt = 0; nt < tkcount; ++nt) {
                final int taxonIndex = getTaxonIndex(tree, tk.get(nt));
                this.xclades[loc][nt] = taxonIndex;
                if (taxonIndex < 0) {
                    throw new IllegalArgumentException("Taxon not found in tree: " + tk.get(nt));
                }
            }
            orderedCalibrations[loc] = cals.remove(k);
            taxaSets.remove(k);
            // cals and taxaSets should match
            --loc;
        }
    }
    // tio[i] will contain all taxaSets contained in the i'th clade, in the form of thier index into orderedCalibrations
    @SuppressWarnings("unchecked") final List<Integer>[] tio = new List[orderedCalibrations.length];
    for (int k = 0; k < orderedCalibrations.length; ++k) {
        tio[k] = new ArrayList<>();
    }
    for (int k = 0; k < orderedCalibrations.length; ++k) {
        final TaxonSet txk = orderedCalibrations[k].taxa();
        for (int i = k + 1; i < orderedCalibrations.length; ++i) {
            if (orderedCalibrations[i].taxa().containsAll(txk)) {
                tio[i].add(k);
                break;
            }
        }
    }
    this.taxaPartialOrder = new int[orderedCalibrations.length][];
    for (int k = 0; k < orderedCalibrations.length; ++k) {
        final List<Integer> tiok = tio[k];
        this.taxaPartialOrder[k] = new int[tiok.size()];
        for (int j = 0; j < tiok.size(); ++j) {
            this.taxaPartialOrder[k][j] = tiok.get(j);
        }
    }
    // true if clade is not contained in any other clade
    final boolean[] maximal = new boolean[calCount];
    for (int k = 0; k < calCount; ++k) {
        maximal[k] = true;
    }
    for (int k = 0; k < calCount; ++k) {
        for (final int i : this.taxaPartialOrder[k]) {
            maximal[i] = false;
        }
    }
    userPDF = userMarInput.get();
    if (userPDF == null) {
        if (type == Type.OVER_ALL_TOPOS) {
            if (calCount == 1) {
            // closed form formula
            } else {
                boolean anyParent = false;
                for (final CalibrationPoint c : orderedCalibrations) {
                    if (c.forParentInput.get()) {
                        anyParent = true;
                    }
                }
                if (anyParent) {
                    throw new IllegalArgumentException("Sorry, not implemented: calibration on parent for more than one clade.");
                }
                if (calCount == 2 && orderedCalibrations[1].taxa().containsAll(orderedCalibrations[0].taxa())) {
                // closed form formulas
                } else {
                    setUpTables(tree.getLeafNodeCount() + 1);
                    linsIter = new CalibrationLineagesIterator(this.xclades, this.taxaPartialOrder, maximal, tree.getLeafNodeCount());
                    lastHeights = new double[calCount];
                }
            }
        } else if (type == Type.OVER_RANKED_COUNTS) {
            setUpTables(tree.getLeafNodeCount() + 1);
        }
    }
    final List<Node> leafs = tree.getExternalNodes();
    final double height = leafs.get(0).getHeight();
    for (final Node leaf : leafs) {
        if (Math.abs(leaf.getHeight() - height) > 1e-8) {
            Log.warning.println("WARNING: Calibrated Yule Model cannot handle dated tips. Use for example a coalescent prior instead.");
            break;
        }
    }
}

Example 4 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class TraitSetTest method taxonSet.

public TaxonSet taxonSet(int Nleaves) {
    List<Sequence> seqList = new ArrayList<Sequence>();
    for (int i = 0; i < Nleaves; i++) {
        String taxonID = "t" + i;
        seqList.add(new Sequence(taxonID, "?"));
    }
    Alignment alignment = new Alignment(seqList, "nucleotide");
    TaxonSet taxonSet = new TaxonSet(alignment);
    return taxonSet;
}

Example 5 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class NodeReheight method initAndValidate.

@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();
}