Examples with TaxonList dr.evolution.util.TaxonList used on opensource projects

Example 6 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class BalancedBeagleTreeLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    boolean useAmbiguities = xo.getAttribute(BeagleTreeLikelihoodParser.USE_AMBIGUITIES, false);
    /*int instanceCount = xo.getAttribute(INSTANCE_COUNT, 1);
        if (instanceCount < 1) {
            instanceCount = 1;
        }

        String ic = System.getProperty(BEAGLE_INSTANCE_COUNT);
        if (ic != null && ic.length() > 0) {
            instanceCount = Integer.parseInt(ic);
        }*/
    PatternList patternList = (PatternList) xo.getChild(PatternList.class);
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    GammaSiteRateModel siteRateModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
    FrequencyModel rootFreqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
    BranchModel branchModel = (BranchModel) xo.getChild(BranchModel.class);
    if (branchModel == null) {
        SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
        if (substitutionModel == null) {
            substitutionModel = siteRateModel.getSubstitutionModel();
        }
        if (substitutionModel == null) {
            throw new XMLParseException("No substitution model available for TreeLikelihood: " + xo.getId());
        }
        branchModel = new HomogeneousBranchModel(substitutionModel, rootFreqModel);
    }
    BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    TipStatesModel tipStatesModel = (TipStatesModel) xo.getChild(TipStatesModel.class);
    //        if (xo.getChild(TipStatesModel.class) != null) {
    //            throw new XMLParseException("Sequence Error Models are not supported under BEAGLE yet. Please use Native BEAST Likelihood.");
    //        }
    PartialsRescalingScheme scalingScheme = PartialsRescalingScheme.DEFAULT;
    if (xo.hasAttribute(BeagleTreeLikelihoodParser.SCALING_SCHEME)) {
        //            scalingScheme = PartialsRescalingScheme.parseFromString(xo.getStringAttribute(BeagleTreeLikelihoodParser.SCALING_SCHEME));
        if (scalingScheme == null)
            throw new XMLParseException("Unknown scaling scheme '" + xo.getStringAttribute(BeagleTreeLikelihoodParser.SCALING_SCHEME) + "' in " + "OldBeagleTreeLikelihood object '" + xo.getId());
    }
    boolean delayScaling = true;
    Map<Set<String>, Parameter> partialsRestrictions = null;
    if (xo.hasChildNamed(PARTIALS_RESTRICTION)) {
        XMLObject cxo = xo.getChild(PARTIALS_RESTRICTION);
        TaxonList taxonList = (TaxonList) cxo.getChild(TaxonList.class);
        //            Parameter parameter = (Parameter) cxo.getChild(Parameter.class);
        try {
            TreeUtils.getLeavesForTaxa(treeModel, taxonList);
        } catch (TreeUtils.MissingTaxonException e) {
            throw new XMLParseException("Unable to parse taxon list: " + e.getMessage());
        }
        throw new XMLParseException("Restricting internal nodes is not yet implemented.  Contact Marc");
    }
    /*if (instanceCount == 1 || patternList.getPatternCount() < instanceCount) {
            return createTreeLikelihood(
                    patternList,
                    treeModel,
                    branchModel,
                    siteRateModel,
                    branchRateModel,
                    tipStatesModel,
                    useAmbiguities,
                    scalingScheme,
                    partialsRestrictions,
                    xo
            );
        }*/
    //first run a test for instanceCount == 1
    System.err.println("\nTesting instanceCount == 1");
    Likelihood baseLikelihood = createTreeLikelihood(patternList, treeModel, branchModel, siteRateModel, branchRateModel, tipStatesModel, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, xo);
    double start = System.nanoTime();
    for (int i = 0; i < TEST_RUNS; i++) {
        baseLikelihood.makeDirty();
        baseLikelihood.getLogLikelihood();
    }
    double end = System.nanoTime();
    double baseResult = end - start;
    System.err.println("Evaluation took: " + baseResult);
    if (!(patternList instanceof SitePatterns)) {
        throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with BEAUti-selected codon partitioning.");
    }
    if (tipStatesModel != null) {
        throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with a TipStateModel (i.e., a sequence error model).");
    }
    //List<Likelihood> likelihoods = new ArrayList<Likelihood>();
    List<Likelihood> likelihoods = null;
    CompoundLikelihood compound = null;
    int instanceCount = 2;
    boolean optimal = false;
    while (optimal == false) {
        System.err.println("\nCreating instanceCount == " + instanceCount);
        likelihoods = new ArrayList<Likelihood>();
        for (int i = 0; i < instanceCount; i++) {
            Patterns subPatterns = new Patterns((SitePatterns) patternList, 0, 0, 1, i, instanceCount);
            AbstractTreeLikelihood treeLikelihood = createTreeLikelihood(subPatterns, treeModel, branchModel, siteRateModel, branchRateModel, null, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, xo);
            treeLikelihood.setId(xo.getId() + "_" + instanceCount);
            likelihoods.add(treeLikelihood);
        }
        //construct compoundLikelihood
        compound = new CompoundLikelihood(instanceCount, likelihoods);
        //test timings 
        System.err.println("\nTesting instanceCount == " + instanceCount);
        start = System.nanoTime();
        for (int i = 0; i < TEST_RUNS; i++) {
            compound.makeDirty();
            compound.getLogLikelihood();
        }
        end = System.nanoTime();
        double newResult = end - start;
        System.err.println("Evaluation took: " + newResult);
        if (baseResult / newResult > TEST_CUTOFF) {
            instanceCount++;
            baseResult = newResult;
        } else {
            optimal = true;
            instanceCount--;
            System.err.println("\nCreating final BeagleTreeLikelihood with instanceCount: " + instanceCount);
            likelihoods = new ArrayList<Likelihood>();
            for (int i = 0; i < instanceCount; i++) {
                Patterns subPatterns = new Patterns((SitePatterns) patternList, 0, 0, 1, i, instanceCount);
                AbstractTreeLikelihood treeLikelihood = createTreeLikelihood(subPatterns, treeModel, branchModel, siteRateModel, branchRateModel, null, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, xo);
                treeLikelihood.setId(xo.getId() + "_" + instanceCount);
                likelihoods.add(treeLikelihood);
            }
            //construct compoundLikelihood
            compound = new CompoundLikelihood(instanceCount, likelihoods);
        }
    }
    return compound;
/*for (int i = 0; i < instanceCount; i++) {

            Patterns subPatterns = new Patterns((SitePatterns)patternList, 0, 0, 1, i, instanceCount);

            AbstractTreeLikelihood treeLikelihood = createTreeLikelihood(
                    subPatterns,
                    treeModel,
                    branchModel,
                    siteRateModel,
                    branchRateModel,
                    null,
                    useAmbiguities,
                    scalingScheme,
                    partialsRestrictions,
                    xo);
            treeLikelihood.setId(xo.getId() + "_" + instanceCount);
            likelihoods.add(treeLikelihood);
        }

        return new CompoundLikelihood(likelihoods);*/
}

Example 7 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class BeagleTreeLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    boolean useAmbiguities = xo.getAttribute(USE_AMBIGUITIES, false);
    int instanceCount = xo.getAttribute(INSTANCE_COUNT, 1);
    if (instanceCount < 1) {
        instanceCount = 1;
    }
    String ic = System.getProperty(BEAGLE_INSTANCE_COUNT);
    if (ic != null && ic.length() > 0) {
        instanceCount = Integer.parseInt(ic);
    }
    PatternList patternList = (PatternList) xo.getChild(PatternList.class);
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    GammaSiteRateModel siteRateModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
    FrequencyModel rootFreqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
    BranchModel branchModel = (BranchModel) xo.getChild(BranchModel.class);
    if (branchModel == null) {
        SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
        if (substitutionModel == null) {
            substitutionModel = siteRateModel.getSubstitutionModel();
        }
        if (substitutionModel == null) {
            throw new XMLParseException("No substitution model available for TreeLikelihood: " + xo.getId());
        }
        branchModel = new HomogeneousBranchModel(substitutionModel, rootFreqModel);
    }
    BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    TipStatesModel tipStatesModel = (TipStatesModel) xo.getChild(TipStatesModel.class);
    //        if (xo.getChild(TipStatesModel.class) != null) {
    //            throw new XMLParseException("Sequence Error Models are not supported under BEAGLE yet. Please use Native BEAST Likelihood.");
    //        }
    PartialsRescalingScheme scalingScheme = PartialsRescalingScheme.DEFAULT;
    boolean delayScaling = true;
    if (xo.hasAttribute(SCALING_SCHEME)) {
        scalingScheme = PartialsRescalingScheme.parseFromString(xo.getStringAttribute(SCALING_SCHEME));
        if (scalingScheme == null)
            throw new XMLParseException("Unknown scaling scheme '" + xo.getStringAttribute(SCALING_SCHEME) + "' in " + "OldBeagleTreeLikelihood object '" + xo.getId());
    }
    if (xo.hasAttribute(DELAY_SCALING)) {
        delayScaling = xo.getBooleanAttribute(DELAY_SCALING);
    }
    Map<Set<String>, Parameter> partialsRestrictions = null;
    if (xo.hasChildNamed(PARTIALS_RESTRICTION)) {
        XMLObject cxo = xo.getChild(PARTIALS_RESTRICTION);
        TaxonList taxonList = (TaxonList) cxo.getChild(TaxonList.class);
        //            Parameter parameter = (Parameter) cxo.getChild(Parameter.class);
        try {
            TreeUtils.getLeavesForTaxa(treeModel, taxonList);
        } catch (TreeUtils.MissingTaxonException e) {
            throw new XMLParseException("Unable to parse taxon list: " + e.getMessage());
        }
        throw new XMLParseException("Restricting internal nodes is not yet implemented.  Contact Marc");
    }
    if (instanceCount == 1 || patternList.getPatternCount() < instanceCount) {
        return createTreeLikelihood(patternList, treeModel, branchModel, siteRateModel, branchRateModel, tipStatesModel, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, xo);
    }
    if (tipStatesModel != null) {
        throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with a TipStateModel (i.e., a sequence error model).");
    }
    List<Likelihood> likelihoods = new ArrayList<Likelihood>();
    for (int i = 0; i < instanceCount; i++) {
        Patterns subPatterns = new Patterns(patternList, i, instanceCount);
        AbstractTreeLikelihood treeLikelihood = createTreeLikelihood(subPatterns, treeModel, branchModel, siteRateModel, branchRateModel, null, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, xo);
        treeLikelihood.setId(xo.getId() + "_" + instanceCount);
        likelihoods.add(treeLikelihood);
    }
    return new CompoundLikelihood(likelihoods);
}

Example 8 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class MonophylyStatisticParser method parseTaxonListOrTaxa.

public static TaxonList parseTaxonListOrTaxa(XMLObject cxo) {
    TaxonList taxa = (TaxonList) cxo.getChild(TaxonList.class);
    if (taxa == null) {
        Taxa taxa1 = new Taxa();
        for (int i = 0; i < cxo.getChildCount(); i++) {
            Object ccxo = cxo.getChild(i);
            if (ccxo instanceof Taxon) {
                taxa1.addTaxon((Taxon) ccxo);
            }
        }
        taxa = taxa1;
    }
    return taxa;
}

Example 9 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class ParsimonyStateStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree = (Tree) xo.getChild(Tree.class);
    XMLObject cxo = xo.getChild(STATE);
    TaxonList stateTaxa = (TaxonList) cxo.getChild(TaxonList.class);
    cxo = xo.getChild(MRCA);
    TaxonList mrcaTaxa = (TaxonList) cxo.getChild(TaxonList.class);
    try {
        return new ParsimonyStateStatistic(name, tree, stateTaxa, mrcaTaxa);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}

Example 10 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class AscertainedSitePatternsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    XMLObject xoc;
    TaxonList taxa = null;
    int from = -1;
    int to = -1;
    int every = xo.getAttribute(EVERY, 1);
    if (every <= 0)
        throw new XMLParseException("illegal 'every' attribute in patterns element");
    int startInclude = -1;
    int stopInclude = -1;
    int startExclude = -1;
    int stopExclude = -1;
    if (xo.hasAttribute(FROM)) {
        from = xo.getIntegerAttribute(FROM) - 1;
        if (from < 0)
            throw new XMLParseException("illegal 'from' attribute in patterns element");
    }
    if (xo.hasAttribute(TO)) {
        to = xo.getIntegerAttribute(TO) - 1;
        if (to < 0 || to < from)
            throw new XMLParseException("illegal 'to' attribute in patterns element");
    }
    if (xo.hasChildNamed(TAXON_LIST)) {
        taxa = (TaxonList) xo.getElementFirstChild(TAXON_LIST);
    }
    if (from > alignment.getSiteCount())
        throw new XMLParseException("illegal 'from' attribute in patterns element");
    if (to > alignment.getSiteCount())
        throw new XMLParseException("illegal 'to' attribute in patterns element");
    if (from < 0)
        from = 0;
    if (to < 0)
        to = alignment.getSiteCount() - 1;
    //        if (xo.hasAttribute(XMLParser.ID)) {
    Logger.getLogger("dr.evoxml").info("Creating ascertained site patterns '" + xo.getId() + "' from positions " + Integer.toString(from + 1) + "-" + Integer.toString(to + 1) + " of alignment '" + alignment.getId() + "'");
    if (every > 1) {
        Logger.getLogger("dr.evoxml").info("  only using every " + every + " site");
    }
    if (xo.hasChildNamed(INCLUDE)) {
        xoc = xo.getChild(INCLUDE);
        if (xoc.hasAttribute(FROM) && xoc.hasAttribute(TO)) {
            startInclude = xoc.getIntegerAttribute(FROM) - 1;
            stopInclude = xoc.getIntegerAttribute(TO);
        } else {
            throw new XMLParseException("both from and to attributes are required for includePatterns");
        }
        if (startInclude < 0 || stopInclude < startInclude) {
            throw new XMLParseException("invalid 'from' and 'to' attributes in includePatterns");
        }
        Logger.getLogger("dr.evoxml").info("\tAscertainment: Patterns in columns " + (startInclude + 1) + " to " + (stopInclude) + " are only possible. ");
    }
    if (xo.hasChildNamed(EXCLUDE)) {
        xoc = xo.getChild(EXCLUDE);
        if (xoc.hasAttribute(FROM) && xoc.hasAttribute(TO)) {
            startExclude = xoc.getIntegerAttribute(FROM) - 1;
            stopExclude = xoc.getIntegerAttribute(TO);
        } else {
            throw new XMLParseException("both from and to attributes are required for excludePatterns");
        }
        if (startExclude < 0 || stopExclude < startExclude) {
            throw new XMLParseException("invalid 'from' and 'to' attributes in includePatterns");
        }
        Logger.getLogger("dr.evoxml").info("\tAscertainment: Patterns in columns " + (startExclude + 1) + " to " + (stopExclude) + " are not possible. ");
    }
    AscertainedSitePatterns patterns = new AscertainedSitePatterns(alignment, taxa, from, to, every, startInclude, stopInclude, startExclude, stopExclude);
    Logger.getLogger("dr.evoxml").info("\tThere are " + patterns.getPatternCount() + " patterns in total.");
    Logger.getLogger("dr.evoxml").info("\tPlease cite:\n" + Citable.Utils.getCitationString(patterns));
    return patterns;
}