Examples with TreeModel dr.evomodel.tree.TreeModel used on opensource projects

Example 6 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class RandomBranchModelParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Logger.getLogger("dr.evomodel").info("\nUsing random assignment branch model.");
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    GY94CodonModel baseSubstitutionModel = (GY94CodonModel) xo.getElementFirstChild(BASE_MODEL);
    long seed = -1;
    boolean hasSeed = false;
    if (xo.hasAttribute(SEED)) {
        seed = xo.getLongIntegerAttribute(SEED);
        hasSeed = true;
    }
    double rate = 1;
    if (xo.hasAttribute(RATE)) {
        rate = xo.getDoubleAttribute(RATE);
    }
    return new RandomBranchModel(treeModel, baseSubstitutionModel, rate, hasSeed, seed);
}

Example 7 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class BranchCategoriesParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter allocationParameter = (Parameter) xo.getElementFirstChild(ALLOCATION);
    CountableBranchCategoryProvider cladeModel;
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    if (!xo.getAttribute(RANDOMIZE, true)) {
        CountableBranchCategoryProvider.CladeBranchCategoryModel cm = new CountableBranchCategoryProvider.CladeBranchCategoryModel(treeModel, allocationParameter);
        for (int i = 0; i < xo.getChildCount(); ++i) {
            if (xo.getChild(i) instanceof XMLObject) {
                XMLObject xoc = (XMLObject) xo.getChild(i);
                if (xoc.getName().equals(LocalClockModelParser.CLADE)) {
                    TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                    boolean includeStem = xoc.getAttribute(LocalClockModelParser.INCLUDE_STEM, false);
                    boolean excludeClade = xoc.getAttribute(LocalClockModelParser.EXCLUDE_CLADE, false);
                    // XML index-start = 1 not 0
                    int rateCategory = xoc.getIntegerAttribute(CATEGORY) - 1;
                    try {
                        cm.setClade(taxonList, rateCategory, includeStem, excludeClade, false);
                    } catch (TreeUtils.MissingTaxonException e) {
                        throw new XMLParseException("Unable to find taxon for clade in countable mixture model: " + e.getMessage());
                    }
                } else if (xoc.getName().equals(LocalClockModelParser.TRUNK)) {
                    TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                    boolean includeStem = xoc.getAttribute(LocalClockModelParser.INCLUDE_STEM, false);
                    boolean excludeClade = xoc.getAttribute(LocalClockModelParser.EXCLUDE_CLADE, false);
                    // XML index-start = 1 not 0
                    int rateCategory = xoc.getIntegerAttribute(CATEGORY) - 1;
                    try {
                        cm.setClade(taxonList, rateCategory, includeStem, excludeClade, true);
                    } catch (TreeUtils.MissingTaxonException e) {
                        throw new XMLParseException("Unable to find taxon for trunk in countable mixture model: " + e.getMessage());
                    }
                }
            }
        }
        cladeModel = cm;
    } else {
        CountableBranchCategoryProvider.IndependentBranchCategoryModel cm = new CountableBranchCategoryProvider.IndependentBranchCategoryModel(treeModel, allocationParameter);
        cm.randomize();
        cladeModel = cm;
    }
    return cladeModel;
}

Example 8 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class AncestralSequenceAnnotator method sampleTree.

private FlexibleTree sampleTree(Tree tree, PatternList alignment, GammaSiteRateModel siteModel, BranchRateModel rateModel) {
    FlexibleTree flexTree = new FlexibleTree(tree, true);
    flexTree.adoptTreeModelOrdering();
    FlexibleTree finalTree = new FlexibleTree(tree);
    finalTree.adoptTreeModelOrdering();
    TreeModel treeModel = new TreeModel(tree);
    // Turn off noisy logging by TreeLikelihood constructor
    Logger logger = Logger.getLogger("dr.evomodel");
    boolean useParentHandlers = logger.getUseParentHandlers();
    logger.setUseParentHandlers(false);
    //        AncestralStateTreeLikelihood likelihood = new AncestralStateTreeLikelihood(
    //                alignment,
    //                treeModel,
    //                siteModel,
    //                rateModel,
    //                false, true,
    //                alignment.getDataType(),
    //                TAG,
    //                false);
    AncestralStateBeagleTreeLikelihood likelihood = new AncestralStateBeagleTreeLikelihood(alignment, treeModel, new HomogeneousBranchModel(siteModel.getSubstitutionModel()), siteModel, rateModel, null, false, PartialsRescalingScheme.DEFAULT, true, null, alignment.getDataType(), TAG, false, true);
    //        PatternList patternList, TreeModel treeModel,
    //                                              BranchSiteModel branchSiteModel,
    // SiteRateModel siteRateModel,
    //                                              BranchRateModel branchRateModel,
    // boolean useAmbiguities,
    //                                              PartialsRescalingScheme scalingScheme,
    //                                              Map<Set<String>, Parameter> partialsRestrictions,
    //                                              final DataType dataType,
    //                                              final String tag,
    //                                              SubstitutionModel substModel,
    //                                              boolean useMAP,
    //                                              boolean returnML) {
    //        PatternList patternList, TreeModel treeModel,
    //                                        SiteModel siteModel, BranchRateModel branchRateModel,
    //                                        boolean useAmbiguities, boolean storePartials,
    //                                        final DataType dataType,
    //                                        final String tag,
    //                                        boolean forceRescaling,
    //                                        boolean useMAP,
    //                                        boolean returnML) {
    logger.setUseParentHandlers(useParentHandlers);
    // Sample internal nodes
    likelihood.makeDirty();
    double logLikelihood = likelihood.getLogLikelihood();
    System.out.println("The new and old Likelihood (this value should be roughly the same, debug?): " + logLikelihood + ", " + Double.parseDouble(tree.getAttribute(LIKELIHOOD).toString()));
    if (Double.parseDouble(tree.getAttribute(LIKELIHOOD).toString()) != logLikelihood) {
    /* Newly written check, not sure if this is correct. May need to round values at least */
    //throw new RuntimeException("The values of likelihood are not identical");
    }
    //		System.err.printf("New logLikelihood = %4.1f\n", logLikelihood);
    flexTree.setAttribute(LIKELIHOOD, logLikelihood);
    TreeTrait ancestralStates = likelihood.getTreeTrait(TAG);
    for (int i = 0; i < treeModel.getNodeCount(); i++) {
        NodeRef node = treeModel.getNode(i);
        String sample = ancestralStates.getTraitString(treeModel, node);
        String oldSeq = (String) flexTree.getNodeAttribute(flexTree.getNode(i), SEQ_STRING);
        if (oldSeq != null) {
            char[] seq = (sample.substring(1, sample.length() - 1)).toCharArray();
            int length = oldSeq.length();
            for (int j = 0; j < length; j++) {
                if (oldSeq.charAt(j) == GAP)
                    seq[j] = GAP;
            }
            String newSeq = new String(seq);
            //				if( newSeq.contains("MMMMMMM") ) {
            //					System.err.println("bad = "+newSeq);
            //					System.exit(-1);
            //				}
            finalTree.setNodeAttribute(finalTree.getNode(i), NEW_SEQ, newSeq);
        }
    //			Taxon taxon = finalTree.getNodeTaxon(finalTree.getNode(i));
    //			System.err.println("node: "+(taxon == null ? "null" : taxon.getId())+" "+
    //					finalTree.getNodeAttribute(finalTree.getNode(i),NEW_SEQ));
    }
    return finalTree;
}

Example 9 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class GMRFMultilocusSkyrideLikelihood method handleModelChangedEvent.

protected void handleModelChangedEvent(Model model, Object object, int index) {
    if (model instanceof TreeModel) {
        TreeModel treeModel = (TreeModel) model;
        int tn = treeList.indexOf(treeModel);
        if (tn >= 0) {
            //   intervalsList.get(tn).setIntervalsUnknown();  // TODO Why is this slower (?) than remaking whole list?
            makeTreeIntervalList(treeList, false);
            intervalsKnown = false;
            likelihoodKnown = false;
        } else {
            throw new RuntimeException("Unknown tree modified in GMRFMultilocusSkyrideLikelihood");
        }
    } else {
        throw new RuntimeException("Unknown object modified in GMRFMultilocusSkyrideLikelihood");
    }
}

Example 10 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class GaussianProcessMultilocusSkytrackLikelihood method handleModelChangedEvent.

//
//    protected int getCorrectOldFieldLength() {
//        int tips = 0;
//        for (Tree tree : treeList) {
//            tips += tree.getExternalNodeCount();
//        }
//        return tips - treeList.size();
//    }
protected void handleModelChangedEvent(Model model, Object object, int index) {
    if (model instanceof TreeModel) {
        TreeModel treeModel = (TreeModel) model;
        int tn = treeList.indexOf(treeModel);
        if (tn >= 0) {
            //   intervalsList.get(tn).setIntervalsUnknown();  // TODO Why is this slower (?) than remaking whole list?
            makeTreeIntervalList(treeList, false);
            intervalsKnown = false;
            likelihoodKnown = false;
        } else {
            throw new RuntimeException("Unknown tree modified in GMRFMultilocusSkyrideLikelihood");
        }
    } else {
        throw new RuntimeException("Unknown object modified in GMRFMultilocusSkyrideLikelihood");
    }
}