Examples with CompoundDistribution beast.core.util.CompoundDistribution used on opensource projects

Example 6 with CompoundDistribution

use of beast.core.util.CompoundDistribution 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 7 with CompoundDistribution

use of beast.core.util.CompoundDistribution in project beast2 by CompEvol.

the class AlignmentListInputEditor method initTableData.

void initTableData() {
    this.likelihoods = new GenericTreeLikelihood[partitionCount];
    if (tableData == null) {
        tableData = new Object[partitionCount][NR_OF_COLUMNS];
    }
    CompoundDistribution likelihoods = (CompoundDistribution) doc.pluginmap.get("likelihood");
    for (int i = 0; i < partitionCount; i++) {
        Alignment data = alignments.get(i);
        // partition name
        tableData[i][NAME_COLUMN] = data;
        // alignment name
        if (data instanceof FilteredAlignment) {
            tableData[i][FILE_COLUMN] = ((FilteredAlignment) data).alignmentInput.get();
        } else {
            tableData[i][FILE_COLUMN] = data;
        }
        // # taxa
        tableData[i][TAXA_COLUMN] = data.getTaxonCount();
        // # sites
        tableData[i][SITES_COLUMN] = data.getSiteCount();
        // Data type
        tableData[i][TYPE_COLUMN] = data.getDataType();
        // site model
        GenericTreeLikelihood likelihood = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(i);
        assert (likelihood != null);
        this.likelihoods[i] = likelihood;
        tableData[i][SITEMODEL_COLUMN] = getPartition(likelihood.siteModelInput);
        // clock model
        tableData[i][CLOCKMODEL_COLUMN] = getPartition(likelihood.branchRateModelInput);
        // tree
        tableData[i][TREE_COLUMN] = getPartition(likelihood.treeInput);
        // useAmbiguities
        tableData[i][USE_AMBIGUITIES_COLUMN] = null;
        try {
            if (hasUseAmbiguitiesInput(i)) {
                tableData[i][USE_AMBIGUITIES_COLUMN] = likelihood.getInputValue("useAmbiguities");
            }
        } catch (Exception e) {
        // ignore
        }
    }
}

Example 8 with CompoundDistribution

use of beast.core.util.CompoundDistribution in project beast2 by CompEvol.

the class SiteModelInputEditor method customConnector.

public static boolean customConnector(BeautiDoc doc) {
    try {
        DeltaExchangeOperator operator = (DeltaExchangeOperator) doc.pluginmap.get("FixMeanMutationRatesOperator");
        if (operator == null) {
            return false;
        }
        List<RealParameter> parameters = operator.parameterInput.get();
        parameters.clear();
        // String weights = "";
        CompoundDistribution likelihood = (CompoundDistribution) doc.pluginmap.get("likelihood");
        boolean hasOneEstimatedRate = false;
        List<String> rateIDs = new ArrayList<>();
        List<Integer> weights = new ArrayList<>();
        for (Distribution d : likelihood.pDistributions.get()) {
            GenericTreeLikelihood treelikelihood = (GenericTreeLikelihood) d;
            Alignment data = treelikelihood.dataInput.get();
            int weight = data.getSiteCount();
            if (data.isAscertained) {
                weight -= data.getExcludedPatternCount();
            }
            if (treelikelihood.siteModelInput.get() instanceof SiteModel) {
                SiteModel siteModel = (SiteModel) treelikelihood.siteModelInput.get();
                RealParameter mutationRate = siteModel.muParameterInput.get();
                // clockRate.m_bIsEstimated.setValue(true, clockRate);
                if (mutationRate.isEstimatedInput.get()) {
                    hasOneEstimatedRate = true;
                    if (rateIDs.indexOf(mutationRate.getID()) == -1) {
                        parameters.add(mutationRate);
                        weights.add(weight);
                        rateIDs.add(mutationRate.getID());
                    } else {
                        int k = rateIDs.indexOf(mutationRate.getID());
                        weights.set(k, weights.get(k) + weight);
                    }
                }
            }
        }
        IntegerParameter weightParameter;
        if (weights.size() == 0) {
            weightParameter = new IntegerParameter();
        } else {
            String weightString = "";
            for (int k : weights) {
                weightString += k + " ";
            }
            weightParameter = new IntegerParameter(weightString);
            weightParameter.setID("weightparameter");
        }
        weightParameter.isEstimatedInput.setValue(false, weightParameter);
        operator.parameterWeightsInput.setValue(weightParameter, operator);
        return hasOneEstimatedRate;
    } catch (Exception e) {
    }
    return false;
}

Example 9 with CompoundDistribution

use of beast.core.util.CompoundDistribution in project beast2 by CompEvol.

the class MRCAPriorInputEditor method customConnector.

public static void customConnector(BeautiDoc doc) {
    Object o0 = doc.pluginmap.get("prior");
    if (o0 != null && o0 instanceof CompoundDistribution) {
        CompoundDistribution p = (CompoundDistribution) o0;
        for (Distribution p0 : p.pDistributions.get()) {
            if (p0 instanceof MRCAPrior) {
                MRCAPrior prior = (MRCAPrior) p0;
                if (prior.treeInput.get() != null) {
                    boolean isInState = false;
                    for (BEASTInterface o : prior.treeInput.get().getOutputs()) {
                        if (o instanceof State) {
                            isInState = true;
                            break;
                        }
                    }
                    if (!isInState) {
                        doc.disconnect(prior, "prior", "distribution");
                        doc.disconnect(prior, "tracelog", "log");
                        if (prior.onlyUseTipsInput.get()) {
                            disableTipSampling(prior, doc);
                        }
                        doc.unregisterPlugin(prior);
                        return;
                    }
                }
            }
        }
    }
}

Example 10 with CompoundDistribution

use of beast.core.util.CompoundDistribution in project beast2 by CompEvol.

the class BeautiPanel method cloneFrom.

/**
 * Clones partition identified by sourceID to targetID and type (Site/Clock/Tree model)
 * as stored in config.
 * @param sourceID
 * @param targetID
 */
public void cloneFrom(String sourceID, String targetID) {
    if (sourceID.equals(targetID)) {
        return;
    }
    String type = config.hasPartitionsInput.get().toString();
    java.util.List<BEASTInterface> list = doc.getPartitions(type);
    int source = -1, target = -1;
    for (int i = 0; i < list.size(); i++) {
        BEASTInterface partition = list.get(i);
        if (type.equals("SiteModel")) {
            partition = (BEASTInterface) ((GenericTreeLikelihood) partition).siteModelInput.get();
        } else if (type.equals("ClockModel")) {
            partition = ((GenericTreeLikelihood) partition).branchRateModelInput.get();
        } else if (type.equals("Tree")) {
            partition = (BEASTInterface) ((GenericTreeLikelihood) partition).treeInput.get();
        }
        String partitionID = partition.getID();
        partitionID = partitionID.substring(partitionID.lastIndexOf('.') + 1);
        if (partitionID.length() > 1 && partitionID.charAt(1) == ':') {
            partitionID = partitionID.substring(2);
        }
        if (partitionID.equals(sourceID)) {
            source = i;
        }
        if (partitionID.equals(targetID)) {
            target = i;
        }
    }
    if (target == -1) {
        throw new RuntimeException("Programmer error: sourceID and targetID should be in list");
    }
    CompoundDistribution likelihoods = (CompoundDistribution) doc.pluginmap.get("likelihood");
    GenericTreeLikelihood likelihoodSource = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(source);
    GenericTreeLikelihood likelihood = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(target);
    PartitionContext oldContext = doc.getContextFor(likelihoodSource);
    PartitionContext newContext = doc.getContextFor(likelihood);
    // this ensures the config.sync does not set any input value
    config._input.setValue(null, config);
    if (type.equals("SiteModel")) {
        SiteModelInterface siteModelSource = likelihoodSource.siteModelInput.get();
        SiteModelInterface siteModel = null;
        try {
            siteModel = (SiteModel.Base) BeautiDoc.deepCopyPlugin((BEASTInterface) siteModelSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (RuntimeException e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        likelihood.siteModelInput.setValue(siteModel, likelihood);
        return;
    } else if (type.equals("ClockModel")) {
        BranchRateModel clockModelSource = likelihoodSource.branchRateModelInput.get();
        BranchRateModel clockModel = null;
        try {
            clockModel = (BranchRateModel) BeautiDoc.deepCopyPlugin((BEASTInterface) clockModelSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (Exception e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        // make sure that *if* the clock model has a tree as input, it is
        // the same as for the likelihood
        TreeInterface tree = null;
        try {
            for (Input<?> input : ((BEASTInterface) clockModel).listInputs()) {
                if (input.getName().equals("tree")) {
                    tree = (TreeInterface) input.get();
                }
            }
        } catch (IllegalArgumentException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        if (tree != null && tree != likelihood.treeInput.get()) {
            // likelihood.treeInput.setValue(tree, likelihood);
            JOptionPane.showMessageDialog(null, "Cannot clone clock model with different trees");
            return;
        }
        likelihood.branchRateModelInput.setValue(clockModel, likelihood);
        return;
    } else if (type.equals("Tree")) {
        TreeInterface tree = null;
        TreeInterface treeSource = likelihoodSource.treeInput.get();
        try {
            tree = (TreeInterface) BeautiDoc.deepCopyPlugin((BEASTInterface) treeSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (Exception e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        // sanity check: make sure taxon sets are compatible
        Taxon.assertSameTaxa(tree.getID(), tree.getTaxonset().getTaxaNames(), likelihood.dataInput.get().getID(), likelihood.dataInput.get().getTaxaNames());
        likelihood.treeInput.setValue(tree, likelihood);
        return;
    } else {
        throw new RuntimeException("Programmer error calling cloneFrom: Should only clone Site/Clock/Tree model");
    }
}