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

Example 16 with Taxon

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

the class StarBeastStartState method fullInit.

private void fullInit() {
    // Build gene trees from  alignments
    final Function muInput = this.muInput.get();
    final double mu = (muInput != null) ? muInput.getArrayValue() : 1;
    final Tree stree = speciesTreeInput.get();
    final TaxonSet species = stree.m_taxonset.get();
    final List<String> speciesNames = species.asStringList();
    final int speciesCount = speciesNames.size();
    final List<Tree> geneTrees = genes.get();
    // final List<Alignment> alignments = genes.get();
    // final List<Tree> geneTrees = new ArrayList<>(alignments.size());
    double maxNsites = 0;
    // for( final Alignment alignment : alignments)  {
    for (final Tree gtree : geneTrees) {
        // final Tree gtree = new Tree();
        final Alignment alignment = gtree.m_taxonset.get().alignmentInput.get();
        final ClusterTree ctree = new ClusterTree();
        ctree.initByName("initial", gtree, "clusterType", "upgma", "taxa", alignment);
        gtree.scale(1 / mu);
        maxNsites = max(maxNsites, alignment.getSiteCount());
    }
    final Map<String, Integer> geneTips2Species = new HashMap<>();
    final List<Taxon> taxonSets = species.taxonsetInput.get();
    for (int k = 0; k < speciesNames.size(); ++k) {
        final Taxon nx = taxonSets.get(k);
        final List<Taxon> taxa = ((TaxonSet) nx).taxonsetInput.get();
        for (final Taxon n : taxa) {
            geneTips2Species.put(n.getID(), k);
        }
    }
    final double[] dg = new double[(speciesCount * (speciesCount - 1)) / 2];
    final double[][] genesDmins = new double[geneTrees.size()][];
    for (int ng = 0; ng < geneTrees.size(); ++ng) {
        final Tree g = geneTrees.get(ng);
        final double[] dmin = firstMeetings(g, geneTips2Species, speciesCount);
        genesDmins[ng] = dmin;
        for (int i = 0; i < dmin.length; ++i) {
            dg[i] += dmin[i];
            if (dmin[i] == Double.MAX_VALUE) {
                // this happens when a gene tree has no taxa for some species-tree taxon.
                // TODO: ensure that if this happens, there will always be an "infinite"
                // distance between species-taxon 0 and the species-taxon with missing lineages,
                // so i < speciesCount - 1.
                // What if lineages for species-taxon 0 are missing? Then all entries will be 'infinite'.
                String id = (i < speciesCount - 1 ? stree.getExternalNodes().get(i + 1).getID() : "unknown taxon");
                if (i == 0) {
                    // test that all entries are 'infinite', which implies taxon 0 has lineages missing
                    boolean b = true;
                    for (int k = 1; b && k < speciesCount - 1; k++) {
                        b = (dmin[k] == Double.MAX_VALUE);
                    }
                    if (b) {
                        // if all entries have 'infinite' distances, it is probably the first taxon that is at fault
                        id = stree.getExternalNodes().get(0).getID();
                    }
                }
                throw new RuntimeException("Gene tree " + g.getID() + " has no lineages for species taxon " + id + " ");
            }
        }
    }
    for (int i = 0; i < dg.length; ++i) {
        double d = dg[i] / geneTrees.size();
        if (d == 0) {
            d = (0.5 / maxNsites) * (1 / mu);
        } else {
            // heights to distances
            d *= 2;
        }
        dg[i] = d;
    }
    final ClusterTree ctree = new ClusterTree();
    final Distance distance = new Distance() {

        @Override
        public double pairwiseDistance(final int s1, final int s2) {
            final int i = getDMindex(speciesCount, s1, s2);
            return dg[i];
        }
    };
    ctree.initByName("initial", stree, "taxonset", species, "clusterType", "upgma", "distance", distance);
    final Map<String, Integer> sptips2SpeciesIndex = new HashMap<>();
    for (int i = 0; i < speciesNames.size(); ++i) {
        sptips2SpeciesIndex.put(speciesNames.get(i), i);
    }
    final double[] spmin = firstMeetings(stree, sptips2SpeciesIndex, speciesCount);
    for (int ng = 0; ng < geneTrees.size(); ++ng) {
        final double[] dmin = genesDmins[ng];
        boolean compatible = true;
        for (int i = 0; i < spmin.length; ++i) {
            if (dmin[i] <= spmin[i]) {
                compatible = false;
                break;
            }
        }
        if (!compatible) {
            final Tree gtree = geneTrees.get(ng);
            final TaxonSet gtreeTaxa = gtree.m_taxonset.get();
            final Alignment alignment = gtreeTaxa.alignmentInput.get();
            final List<String> taxaNames = alignment.getTaxaNames();
            final int taxonCount = taxaNames.size();
            // speedup
            final Map<Integer, Integer> g2s = new HashMap<>();
            for (int i = 0; i < taxonCount; ++i) {
                g2s.put(i, geneTips2Species.get(taxaNames.get(i)));
            }
            final JukesCantorDistance jc = new JukesCantorDistance();
            jc.setPatterns(alignment);
            final Distance gdistance = new Distance() {

                @Override
                public double pairwiseDistance(final int t1, final int t2) {
                    final int s1 = g2s.get(t1);
                    final int s2 = g2s.get(t2);
                    double d = jc.pairwiseDistance(t1, t2) / mu;
                    if (s1 != s2) {
                        final int i = getDMindex(speciesCount, s1, s2);
                        final double minDist = 2 * spmin[i];
                        if (d <= minDist) {
                            d = minDist * 1.001;
                        }
                    }
                    return d;
                }
            };
            final ClusterTree gtreec = new ClusterTree();
            gtreec.initByName("initial", gtree, "taxonset", gtreeTaxa, "clusterType", "upgma", "distance", gdistance);
        }
    }
    {
        final RealParameter lambda = birthRate.get();
        if (lambda != null) {
            final double rh = stree.getRoot().getHeight();
            double l = 0;
            for (int i = 2; i < speciesCount + 1; ++i) {
                l += 1. / i;
            }
            setParameterValue(lambda, (1 / rh) * l);
        }
        double totBranches = 0;
        final Node[] streeNodeas = stree.getNodesAsArray();
        for (final Node n : streeNodeas) {
            if (!n.isRoot()) {
                totBranches += n.getLength();
            }
        }
        totBranches /= 2 * (streeNodeas.length - 1);
        final RealParameter popm = popMean.get();
        if (popm != null) {
            setParameterValue(popm, totBranches);
        }
        final SpeciesTreePrior speciesTreePrior = speciesTreePriorInput.get();
        if (speciesTreePrior != null) {
            final RealParameter popb = speciesTreePrior.popSizesBottomInput.get();
            if (popb != null) {
                for (int i = 0; i < popb.getDimension(); ++i) {
                    setParameterValue(popb, i, 2 * totBranches);
                }
            }
            final RealParameter popt = speciesTreePrior.popSizesTopInput.get();
            if (popt != null) {
                for (int i = 0; i < popt.getDimension(); ++i) {
                    setParameterValue(popt, i, totBranches);
                }
            }
        }
    }
}

Example 17 with Taxon

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

the class BeautiDoc method addMRCAPrior.

public void addMRCAPrior(MRCAPrior mrcaPrior) {
    Tree tree = (Tree) pluginmap.get("Tree.t:" + alignments.get(0).getID());
    if (tree == null) {
        for (String key : pluginmap.keySet()) {
            if (key.startsWith("Tree.t:")) {
                tree = (Tree) pluginmap.get(key);
                break;
            }
        }
    }
    // make sure we have the appropriate tree:
    if (alignments.size() > 1) {
        String testTaxon = mrcaPrior.taxonsetInput.get().toString().split("\n")[1].trim();
        // = tree.getTaxaNames();
        String[] taxaNames;
        int index = -1;
        int j = 0;
        while (index < 0 && j++ < alignments.size()) {
            tree = (Tree) pluginmap.get("Tree.t:" + alignments.get(j - 1).getID());
            taxaNames = tree.getTaxaNames();
            for (int i = 0; i < taxaNames.length && index < 0; i++) if (testTaxon.equals(taxaNames[i]))
                index = i;
        }
    }
    CompoundDistribution prior = (CompoundDistribution) pluginmap.get("prior");
    mrcaPrior.treeInput.setValue(tree, mrcaPrior);
    ParametricDistribution distr = mrcaPrior.distInput.get();
    TaxonSet t = mrcaPrior.taxonsetInput.get();
    if (taxaset.keySet().contains(t.getID())) {
        Log.warning.println("taxonset " + t.getID() + " already exists: MRCAPrior " + mrcaPrior.getID() + " can not be added");
    } else {
        taxaset.put(t.getID(), t);
        // ensure TaxonSets are not duplicated
        List<Taxon> taxa = t.taxonsetInput.get();
        for (int i = 0; i < taxa.size(); i++) {
            if (taxaset.containsKey(taxa.get(i).getID())) {
                taxa.set(i, taxaset.get(taxa.get(i).getID()));
            } else {
                taxaset.put(taxa.get(i).getID(), taxa.get(i));
            }
        }
        if (distr instanceof Normal && (Double.isInfinite(((Normal) distr).sigmaInput.get().getValue()))) {
        // it is a 'fixed' calibration, no need to add a distribution
        } else {
            prior.pDistributions.setValue(mrcaPrior, prior);
            connect(mrcaPrior, "tracelog", "log");
        }
    }
    if (t.taxonsetInput.get().size() == 1 && distr != null) {
        // only add operators if it is NOT a 'fixed' calibration
        if (!(distr instanceof Normal && (Double.isInfinite(((Normal) distr).sigmaInput.get().getValue())))) {
            TipDatesRandomWalker operator = new TipDatesRandomWalker();
            t.initAndValidate();
            operator.initByName("taxonset", t, "weight", 1.0, "tree", tree, "windowSize", 1.0);
            operator.setID("TipDatesRandomWalker." + t.getID());
            MCMC mcmc = (MCMC) this.mcmc.get();
            mcmc.operatorsInput.setValue(operator, mcmc);
        }
        // set up date trait
        double date = distr.getMean();
        TraitSet dateTrait = null;
        for (TraitSet ts : tree.m_traitList.get()) {
            if (ts.isDateTrait()) {
                dateTrait = ts;
            }
        }
        if (dateTrait == null) {
            dateTrait = new TraitSet();
            dateTrait.setID("traitsetDate");
            registerPlugin(dateTrait);
            dateTrait.initByName("traitname", TraitSet.DATE_BACKWARD_TRAIT, "taxa", tree.getTaxonset(), "value", t.taxonsetInput.get().get(0).getID() + "=" + date);
            tree.m_traitList.setValue(dateTrait, tree);
            tree.initAndValidate();
        } else {
            dateTrait.traitsInput.setValue(dateTrait.traitsInput.get() + ",\n" + t.taxonsetInput.get().get(0).getID() + "=" + date, dateTrait);
        }
        mrcaPrior.onlyUseTipsInput.setValue(true, mrcaPrior);
    }
}

Example 18 with Taxon

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

the class BeautiDoc method registerPlugin.

public void registerPlugin(BEASTInterface beastObject) {
    // first make sure to remove plug-ins when the id of a beastObject changed
    unregisterPlugin(beastObject);
    pluginmap.put(beastObject.getID(), beastObject);
    reversePluginmap.put(beastObject, beastObject.getID());
    if (beastObject instanceof Taxon) {
        Taxon taxon = (Taxon) beastObject;
        taxaset.put(taxon.getID(), taxon);
    }
}

Example 19 with Taxon

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

the class TaxonSetInputEditor method modelToTaxonset.

/**
 * for convert table model to taxon sets *
 */
private void modelToTaxonset() {
    // update map
    for (int i = 0; i < m_model.getRowCount(); i++) {
        String lineageID = (String) ((Vector<?>) m_model.getDataVector().elementAt(i)).elementAt(0);
        String taxonSetID = (String) ((Vector<?>) m_model.getDataVector().elementAt(i)).elementAt(1);
        // new taxon set?
        if (!m_taxonMap.containsValue(taxonSetID)) {
            // create new taxon set
            TaxonSet taxonset = newTaxonSet(taxonSetID);
            m_taxonset.add(taxonset);
        }
        m_taxonMap.put(lineageID, taxonSetID);
    }
    // clear old taxon sets
    for (Taxon taxon : m_taxonset) {
        TaxonSet set = (TaxonSet) taxon;
        set.taxonsetInput.get().clear();
        doc.registerPlugin(set);
    }
    // group lineages with their taxon sets
    for (String lineageID : m_taxonMap.keySet()) {
        for (Taxon taxon : m_lineageset) {
            if (taxon.getID().equals(lineageID)) {
                String taxonSet = m_taxonMap.get(lineageID);
                for (Taxon taxon2 : m_taxonset) {
                    TaxonSet set = (TaxonSet) taxon2;
                    if (set.getID().equals(taxonSet)) {
                        try {
                            set.taxonsetInput.setValue(taxon, set);
                        } catch (Exception e) {
                            e.printStackTrace();
                        }
                    }
                }
            }
        }
    }
    // remove unused taxon sets
    for (int i = m_taxonset.size() - 1; i >= 0; i--) {
        if (((TaxonSet) m_taxonset.get(i)).taxonsetInput.get().size() == 0) {
            doc.unregisterPlugin(m_taxonset.get(i));
            m_taxonset.remove(i);
        }
    }
    TaxonSet taxonset = (TaxonSet) m_input.get();
    taxonset.taxonsetInput.get().clear();
    for (Taxon taxon : m_taxonset) {
        try {
            taxonset.taxonsetInput.setValue(taxon, taxonset);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
}

Example 20 with Taxon

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

the class TaxonSetDialog method showDialog.

// c'tor
public boolean showDialog() {
    JOptionPane optionPane = new JOptionPane(box, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null);
    optionPane.setBorder(new EmptyBorder(12, 12, 12, 12));
    Frame frame = (doc != null ? doc.getFrame() : Frame.getFrames()[0]);
    final JDialog dialog = optionPane.createDialog(frame, "Taxon set editor");
    dialog.pack();
    dialog.setVisible(true);
    int result = JOptionPane.CANCEL_OPTION;
    Integer value = (Integer) optionPane.getValue();
    if (value != null && value != -1) {
        result = value;
    }
    isOK = (result != JOptionPane.CANCEL_OPTION);
    if (isOK) {
        taxonSet.setID(id);
        List<Taxon> taxa = taxonSet.taxonsetInput.get();
        while (taxa.size() > 0) {
            taxa.remove(0);
        }
        for (int i = 0; i < listModel2.size(); i++) {
            taxa.add(listModel2.get(i));
        }
        isOK = true;
        dispose();
    }
    return isOK;
}