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

Example 11 with TaxonList

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

the class BeastGenerator method writeDifferentTaxa.

public void writeDifferentTaxa(AbstractPartitionData dataPartition, XMLWriter writer) {
    TaxonList taxonList = dataPartition.getTaxonList();
    String name = dataPartition.getPartitionTreeModel().getName();
    writer.writeComment("gene name = " + name + ", ntax= " + taxonList.getTaxonCount());
    writer.writeOpenTag(TaxaParser.TAXA, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, name + "." + TaxaParser.TAXA) });
    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        if (!(dataPartition instanceof PartitionPattern && ((PartitionPattern) dataPartition).getPatterns().isMasked(i))) {
            final Taxon taxon = taxonList.getTaxon(i);
            writer.writeIDref(TaxonParser.TAXON, taxon.getId());
        }
    }
    writer.writeCloseTag(TaxaParser.TAXA);
}

Example 12 with TaxonList

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

the class TipDateSamplingComponentOptions method selectOperators.

public void selectOperators(final ModelOptions modelOptions, final List<Operator> ops) {
    if (tipDateSamplingType == TipDateSamplingType.SAMPLE_INDIVIDUALLY || tipDateSamplingType == TipDateSamplingType.SAMPLE_PRECISION) {
        TaxonList taxa = getTaxonSet();
        String description = "Random walk for the age of this tip";
        //OperatorType type = OperatorType.RANDOM_WALK_ABSORBING;
        OperatorType type = OperatorType.UNIFORM;
        if (tipDateSamplingType == TipDateSamplingType.SAMPLE_PRECISION) {
            description = "Uniform sample from precision of age of this tip";
        //type = OperatorType.UNIFORM;
        }
        for (int i = 0; i < taxa.getTaxonCount(); i++) {
            Taxon taxon = taxa.getTaxon(i);
            Operator operator = tipDateOperators.get(taxon);
            if (operator == null) {
                Parameter parameter = getTipDateParameter(taxon);
                //                    operator = new Operator("age(" + taxon.getId() + ")", "", parameter, OperatorType.SCALE, 0.75, 1.0);
                operator = new Operator.Builder("age(" + taxon.getId() + ")", description, parameter, type, 1.0, 1.0).build();
                if (tipDateSamplingType == TipDateSamplingType.SAMPLE_INDIVIDUALLY) {
                    operator.setWeight(2.0);
                }
                tipDateOperators.put(taxon, operator);
            }
            ops.add(operator);
        }
    } else if (tipDateSamplingType == TipDateSamplingType.SAMPLE_JOINT) {
        ops.add(modelOptions.getOperator("treeModel.tipDates"));
    }
}

Example 13 with TaxonList

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

the class UncertainAttributePatternsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String attributeName = xo.getStringAttribute(ATTRIBUTE);
    TaxonList taxa = (TaxonList) xo.getChild(TaxonList.class);
    DataType dataType = DataTypeUtils.getDataType(xo);
    if (dataType == null) {
        throw new XMLParseException("dataType expected for attributePatterns element");
    }
    // using a SimpleSiteList rather than Patterns to allow ancestral reconstruction
    UncertainSiteList patterns = new UncertainSiteList(dataType, taxa);
    boolean normalize = xo.getAttribute(NORMALIZE, true);
    if (dataType == null) {
        // TODO Is this necessary given XMLSyntaxRules?
        throw new XMLParseException("dataType expected for attributePatterns element");
    }
    double[][] uncertainPattern = new double[taxa.getTaxonCount()][];
    // Parse attributes
    boolean attributeFound = false;
    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Taxon taxon = taxa.getTaxon(i);
        Object value = taxon.getAttribute(attributeName);
        if (value != null) {
            attributeFound = true;
            List<StateProbability> stateProbabilities;
            try {
                stateProbabilities = parseStates(value.toString(), dataType);
            } catch (StateParseException e) {
                throw new XMLParseException("State or probability for attribute (" + attributeName + ") in taxon " + taxon.getId() + " is invalid; state = \"" + e.getState() + "\" and probability =\"" + e.getProbability() + "\"");
            }
            uncertainPattern[i] = convertToPartials(stateProbabilities, dataType, normalize);
        } else {
            throw new XMLParseException("State for attribute (" + attributeName + ") in taxon " + taxon.getId() + " is unknown.");
        }
    }
    if (!attributeFound) {
        throw new XMLParseException("The attribute (" + attributeName + ") was missing in all taxa. Check the name of the attribute.");
    }
    patterns.addPattern(uncertainPattern);
    Logger.getLogger("dr.evolution").info("\n ---------------------------------\nCreating an uncertain attribute model for attribute \"" + attributeName + "\"");
    Logger.getLogger("dr.evolution").info("\tIf you publish results using this model, please reference:");
    Logger.getLogger("dr.evolution").info("\t" + Citable.Utils.getCitationString(patterns));
    Logger.getLogger("dr.evolution").info("\n");
    return patterns;
}

Example 14 with TaxonList

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

the class SitePatternsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    TaxonList taxa = null;
    int from = 0;
    int to = -1;
    int every = xo.getAttribute(EVERY, 1);
    boolean strip = xo.getAttribute(STRIP, true);
    boolean unique = xo.getAttribute(UNIQUE, true);
    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 (every <= 0)
        throw new XMLParseException("illegal 'every' attribute in patterns element");
    if (xo.hasChildNamed(TAXON_LIST)) {
        taxa = (TaxonList) xo.getElementFirstChild(TAXON_LIST);
    }
    int[] constantPatternCounts = null;
    if (xo.hasChildNamed(CONSTANT_PATTERNS)) {
        Parameter param = (Parameter) xo.getElementFirstChild(CONSTANT_PATTERNS);
        if (param.getDimension() != alignment.getStateCount()) {
            throw new XMLParseException("The " + CONSTANT_PATTERNS + " parameter length should be equal to the number of states");
        }
        constantPatternCounts = new int[param.getDimension()];
        int i = 0;
        for (double value : param.getParameterValues()) {
            constantPatternCounts[i] = (int) value;
            i++;
        }
    }
    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");
    SitePatterns patterns = new SitePatterns(alignment, taxa, from, to, every, strip, unique, constantPatternCounts);
    int f = from + 1;
    // fixed a *display* error by adding + 1 for consistency with f = from + 1
    int t = to + 1;
    if (to == -1)
        t = alignment.getSiteCount();
    if (xo.hasAttribute(XMLParser.ID)) {
        final Logger logger = Logger.getLogger("dr.evoxml");
        logger.info("Site patterns '" + xo.getId() + "' created from positions " + Integer.toString(f) + "-" + Integer.toString(t) + " of alignment '" + alignment.getId() + "'");
        if (every > 1) {
            logger.info("  only using every " + every + " site");
        }
        logger.info("  " + (unique ? "unique " : "") + "pattern count = " + patterns.getPatternCount());
    }
    return patterns;
}

Example 15 with TaxonList

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

the class LinkedGroupParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TaxonList taxa = null;
    double linkageProbability = 0.9999999999;
    if (xo.hasAttribute("probability")) {
        linkageProbability = xo.getDoubleAttribute("probability");
    }
    taxa = (TaxonList) xo.getChild(TaxonList.class);
    LinkedGroup lg = new LinkedGroup(taxa, linkageProbability);
    return lg;
}