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

Example 21 with Date

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

the class AncestralTraitTreeModelParser method parseAncestor.

private static AncestralTaxonInTree parseAncestor(MutableTreeModel tree, XMLObject xo, final int index) throws XMLParseException {
    Taxon ancestor = (Taxon) xo.getChild(Taxon.class);
    Parameter pseudoBranchLength = (Parameter) xo.getChild(Parameter.class);
    AncestralTaxonInTree ancestorInTree;
    NodeRef node = new NodeRef() {

        @Override
        public int getNumber() {
            return index;
        }

        @Override
        public void setNumber(int n) {
            throw new RuntimeException("Do not set");
        }
    };
    if (xo.hasChildNamed(MonophylyStatisticParser.MRCA)) {
        TaxonList descendants = MonophylyStatisticParser.parseTaxonListOrTaxa(xo.getChild(MonophylyStatisticParser.MRCA));
        try {
            ancestorInTree = new AncestralTaxonInTree(ancestor, tree, descendants, pseudoBranchLength, null, node, index, 0.0);
        } catch (TreeUtils.MissingTaxonException e) {
            throw new XMLParseException("Unable to find taxa for " + ancestor.getId());
        }
    } else {
        XMLObject cxo = xo.getChild(ANCESTRAL_PATH);
        Taxon taxon = (Taxon) cxo.getChild(Taxon.class);
        Parameter time = (Parameter) cxo.getChild(Parameter.class);
        boolean relativeHeight = cxo.getAttribute(RELATIVE_HEIGHT, false);
        double offset = 0;
        if (relativeHeight) {
            Object date = taxon.getAttribute("date");
            if (date != null && date instanceof Date) {
                offset = taxon.getHeight();
            } else {
                throw new XMLParseException("Taxon '" + taxon.getId() + "' has no specified date");
            }
        } else {
            if (time.getParameterValue(0) <= taxon.getHeight()) {
                throw new XMLParseException("Ancestral path time must be > sampling time for taxon '" + taxon.getId() + "'");
            }
        }
        Taxa descendent = new Taxa();
        descendent.addTaxon(taxon);
        try {
            ancestorInTree = new AncestralTaxonInTree(ancestor, tree, descendent, pseudoBranchLength, time, node, index, // TODO Refactor into separate class from MRCA version
            offset);
        } catch (TreeUtils.MissingTaxonException e) {
            throw new XMLParseException("Unable to find taxa for " + ancestor.getId());
        }
    }
    return ancestorInTree;
}

Example 22 with Date

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

the class SimpleNodeParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    SimpleNode node = new SimpleNode();
    Taxon taxon = null;
    if (xo.hasAttribute(HEIGHT)) {
        node.setHeight(xo.getDoubleAttribute(HEIGHT));
    }
    if (xo.hasAttribute(RATE)) {
        node.setRate(xo.getDoubleAttribute(RATE));
    }
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object child = xo.getChild(i);
        if (child instanceof dr.evolution.tree.SimpleNode) {
            node.addChild((dr.evolution.tree.SimpleNode) child);
        } else if (child instanceof Taxon) {
            taxon = (Taxon) child;
        } else if (child instanceof Date) {
            node.setAttribute("date", child);
        } else if (child instanceof Attribute) {
            Attribute attr = (Attribute) child;
            String name = attr.getAttributeName();
            Object value = attr.getAttributeValue();
            node.setAttribute(name, value);
        } else if (child instanceof Attribute[]) {
            Attribute[] attrs = (Attribute[]) child;
            for (int j = 0; j < attrs.length; j++) {
                String name = attrs[j].getAttributeName();
                Object value = attrs[j].getAttributeValue();
                node.setAttribute(name, value);
            }
        } else if (child instanceof XMLObject) {
            XMLObject xoc = (XMLObject) child;
            if (xoc.getName().equals(Attributable.ATTRIBUTE)) {
                node.setAttribute(xoc.getStringAttribute(Attributable.NAME), xoc.getAttribute(Attributable.VALUE));
            } else {
                throw new XMLParseException("Unrecognized element" + xoc.getName() + " found in node element!");
            }
        } else {
            throw new XMLParseException("Unrecognized element found in node element!");
        }
    }
    if (taxon != null) {
        node.setTaxon(taxon);
    }
    return node;
}

Example 23 with Date

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

the class TaxonParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    if (dr.xml.XMLParser.ID.contains("\'") && dr.xml.XMLParser.ID.contains("\"")) {
        // as it won't be possible to wrap it in either.
        throw new XMLParseException("Illegal taxon name, " + dr.xml.XMLParser.ID + ", - contains both single and double quotes");
    }
    Taxon taxon = new Taxon(xo.getStringAttribute(dr.xml.XMLParser.ID));
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object child = xo.getChild(i);
        if (child instanceof Date) {
            taxon.setDate((Date) child);
        } else if (child instanceof Location) {
            taxon.setLocation((Location) child);
        } else if (child instanceof Attribute) {
            final Attribute attr = (Attribute) child;
            taxon.setAttribute(attr.getAttributeName(), attr.getAttributeValue());
        } else if (child instanceof Attribute[]) {
            Attribute[] attrs = (Attribute[]) child;
            for (Attribute attr : attrs) {
                taxon.setAttribute(attr.getAttributeName(), attr.getAttributeValue());
            }
        } else {
            throw new XMLParseException("Unrecognized element found in taxon element");
        }
    }
    return taxon;
}

Example 24 with Date

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

the class DateParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    java.text.DateFormat dateFormat = java.text.DateFormat.getDateInstance(java.text.DateFormat.SHORT, java.util.Locale.UK);
    dateFormat.setLenient(true);
    if (xo.getChildCount() > 0) {
        throw new XMLParseException("No child elements allowed in date element.");
    }
    double value = 0.0;
    java.util.Date dateValue = null;
    if (xo.hasAttribute(VALUE)) {
        try {
            value = xo.getDoubleAttribute(VALUE);
        } catch (XMLParseException e) {
            String dateString = xo.getStringAttribute(VALUE);
            try {
                dateValue = dateFormat.parse(dateString);
            } catch (Exception ex) {
                throw new XMLParseException("value=" + dateString + " not recognised as a date, use DD/MM/YYYY");
            }
        }
    } else {
        throw new XMLParseException("Value attribute missing from date element.");
    }
    boolean backwards = false;
    if (xo.hasAttribute(DIRECTION)) {
        String direction = (String) xo.getAttribute(DIRECTION);
        if (direction.equals(BACKWARDS)) {
            backwards = true;
        }
    }
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    Date date;
    if (xo.hasAttribute(ORIGIN)) {
        String originString = (String) xo.getAttribute(ORIGIN);
        java.util.Date origin;
        try {
            origin = dateFormat.parse(originString);
        } catch (Exception e) {
            throw new XMLParseException("origin=" + originString + " not recognised as a date, use DD/MM/YYYY");
        }
        if (dateValue != null) {
            date = new Date(dateValue, units, origin);
        } else {
            date = new Date(value, units, backwards, origin);
        }
    } else {
        // No origin specified so use default (1st Jan 1970)
        if (dateValue != null) {
            date = new Date(dateValue, units);
        } else {
            date = new Date(value, units, backwards);
        }
    }
    if (xo.hasAttribute(UNCERTAINTY)) {
        double uncertainty = xo.getDoubleAttribute(UNCERTAINTY);
        date.setUncertainty(uncertainty);
    } else if (xo.hasAttribute(PRECISION)) {
        // Precision was the old term for uncertainty which was confusing
        // because it was the reciprocal. Parse this term synonymously for
        // backwards compatibility.
        double uncertainty = xo.getDoubleAttribute(PRECISION);
        date.setUncertainty(uncertainty);
    }
    return date;
}

Example 25 with Date

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

the class SequenceLikelihoodTest method createAlignmentWithAllUniquePatterns.

protected void createAlignmentWithAllUniquePatterns(Object[][] taxa_sequence, DataType dataType) {
    alignment = new SimpleAlignment();
    alignment.setDataType(dataType);
    int nTaxa = taxa_sequence[0].length;
    String[] allUniquePatterns = createAllUniquePatterns(nTaxa, dataType);
    taxa_sequence[1] = allUniquePatterns;
    // 6, 17
    taxa = new Taxon[nTaxa];
    System.out.println("Taxon len = " + taxa_sequence[0].length);
    System.out.println("Alignment len = " + taxa_sequence[1].length);
    if (taxa_sequence.length > 2)
        System.out.println("Date len = " + taxa_sequence[2].length);
    for (int i = 0; i < taxa_sequence[0].length; i++) {
        taxa[i] = new Taxon(taxa_sequence[0][i].toString());
        if (taxa_sequence.length > 2) {
            Date date = new Date((Double) taxa_sequence[2][i], Units.Type.YEARS, (Boolean) taxa_sequence[3][0]);
            taxa[i].setDate(date);
        }
        // taxonList.addTaxon(taxon);
        Sequence sequence = new Sequence(taxa_sequence[1][i].toString());
        sequence.setTaxon(taxa[i]);
        sequence.setDataType(dataType);
        alignment.addSequence(sequence);
    }
    System.out.println("Sequence pattern count = " + alignment.getPatternCount());
}