Examples with CodonLabeling dr.evomodel.substmodel.CodonLabeling used on opensource projects

Example 1 with CodonLabeling

use of dr.evomodel.substmodel.CodonLabeling in project beast-mcmc by beast-dev.

the class CodonPartitionedRobustCountingParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    AncestralStateBeagleTreeLikelihood[] partition = new AncestralStateBeagleTreeLikelihood[3];
    String[] labels = new String[] { FIRST, SECOND, THIRD };
    int patternCount = -1;
    BranchRateModel testBranchRateModel = null;
    for (int i = 0; i < 3; i++) {
        partition[i] = (AncestralStateBeagleTreeLikelihood) xo.getChild(labels[i]).getChild(AncestralStateBeagleTreeLikelihood.class);
        if (i == 0) {
            patternCount = partition[i].getPatternCount();
        } else {
            if (partition[i].getPatternCount() != patternCount) {
                throw new XMLParseException("Codon-partitioned robust counting requires all partitions to have the same length." + " Make sure that partitions include all unique sites and do not strip gaps.");
            }
        }
        // Ensure that siteRateModel has one category
        if (partition[i].getSiteRateModel().getCategoryCount() > 1) {
            throw new XMLParseException("Robust counting currently only implemented for single category models");
        }
        // Ensure that branchRateModel is the same across all partitions
        if (testBranchRateModel == null) {
            testBranchRateModel = partition[i].getBranchRateModel();
        } else if (testBranchRateModel != partition[i].getBranchRateModel()) {
            throw new XMLParseException("Robust counting currently requires the same branch rate model for all partitions");
        }
    }
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    Codons codons = Codons.UNIVERSAL;
    if (xo.hasAttribute(GeneticCode.GENETIC_CODE)) {
        String codeStr = xo.getStringAttribute(GeneticCode.GENETIC_CODE);
        codons = Codons.findByName(codeStr);
    }
    String labelingString = (String) xo.getAttribute(LABELING);
    CodonLabeling codonLabeling = CodonLabeling.parseFromString(labelingString);
    if (codonLabeling == null) {
        throw new XMLParseException("Unrecognized codon labeling '" + labelingString + "'");
    }
    String branchFormatString = xo.getAttribute(BRANCH_FORMAT, StratifiedTraitOutputFormat.SUM_OVER_SITES.getText());
    StratifiedTraitOutputFormat branchFormat = StratifiedTraitOutputFormat.parseFromString(branchFormatString);
    if (branchFormat == null) {
        throw new XMLParseException("Unrecognized branch output format '" + branchFormat + "'");
    }
    String logFormatString = xo.getAttribute(LOG_FORMAT, StratifiedTraitOutputFormat.SUM_OVER_SITES.getText());
    StratifiedTraitOutputFormat logFormat = StratifiedTraitOutputFormat.parseFromString(logFormatString);
    if (logFormat == null) {
        throw new XMLParseException("Unrecognized log output format '" + branchFormat + "'");
    }
    boolean useUniformization = xo.getAttribute(USE_UNIFORMIZATION, false);
    boolean includeExternalBranches = xo.getAttribute(INCLUDE_EXTERNAL, true);
    boolean includeInternalBranches = xo.getAttribute(INCLUDE_INTERNAL, true);
    boolean doUnconditionedPerBranch = xo.getAttribute(DO_UNCONDITIONED_PER_BRANCH, false);
    boolean averageRates = xo.getAttribute(AVERAGE_RATES, true);
    boolean saveCompleteHistory = xo.getAttribute(SAVE_HISTORY, false);
    boolean useNewNeutralModel = xo.getAttribute(USE_NEW_NEUTRAL_MODEL, false);
    String prefix = xo.hasAttribute(PREFIX) ? xo.getStringAttribute(PREFIX) : null;
    return new CodonPartitionedRobustCounting(xo.getId(), tree, partition, codons, codonLabeling, useUniformization, includeExternalBranches, includeInternalBranches, doUnconditionedPerBranch, saveCompleteHistory, averageRates, useNewNeutralModel, branchFormat, logFormat, prefix);
}