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

Example 36 with Date

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

the class PartitionedTreeModelParser method setPrecisionBounds.

private void setPrecisionBounds(Parameter newParameter, Taxon taxon) {
    Date date = taxon.getDate();
    if (date != null) {
        double precision = date.getUncertainty();
        if (precision > 0.0) {
            // taxon date not specified to exact value so add appropriate bounds
            double upper = Taxon.getHeightFromDate(date);
            double lower = Taxon.getHeightFromDate(date);
            if (date.isBackwards()) {
                upper += precision;
            } else {
                lower -= precision;
            }
            // set the bounds for the given precision
            newParameter.addBounds(new Parameter.DefaultBounds(upper, lower, 1));
            // set the initial value to be mid-point
            newParameter.setParameterValue(0, (upper + lower) / 2);
        }
    }
}

Example 37 with Date

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

the class TemporalRooting method setHeightsFromDates.

private void setHeightsFromDates(FlexibleTree tree) {
    dr.evolution.util.Date mostRecent = null;
    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Date date = taxa.getTaxon(i).getDate();
        if ((date != null) && (mostRecent == null || date.after(mostRecent))) {
            mostRecent = date;
        }
    }
    if (mostRecent != null) {
        TimeScale timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
        double time0 = timeScale.convertTime(mostRecent.getTimeValue(), mostRecent);
        for (int i = 0; i < tree.getExternalNodeCount(); i++) {
            NodeRef tip = tree.getExternalNode(i);
            Date date = tree.getNodeTaxon(tip).getDate();
            if (date != null) {
                tree.setNodeHeight(tip, timeScale.convertTime(date.getTimeValue(), date) - time0);
            } else {
                tree.setNodeHeight(tip, 0.0);
            }
        }
    }
}

Example 38 with Date

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

the class TreeUtils method setHeightsFromDates.

/**
 * Sets the tip heights from the tip dates
 */
public static void setHeightsFromDates(MutableTree tree) {
    dr.evolution.util.Date mostRecent = null;
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        Taxon taxon = tree.getNodeTaxon(tree.getExternalNode(i));
        dr.evolution.util.Date date = (dr.evolution.util.Date) taxon.getAttribute("date");
        if (date != null) {
            if ((mostRecent == null) || date.after(mostRecent)) {
                mostRecent = date;
            }
        }
    }
    TimeScale timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        NodeRef node = tree.getExternalNode(i);
        Taxon taxon = tree.getNodeTaxon(node);
        dr.evolution.util.Date date = (dr.evolution.util.Date) taxon.getAttribute("date");
        if (date != null) {
            double height = timeScale.convertTime(date.getTimeValue(), date);
            tree.setNodeHeight(node, height);
        } else {
            tree.setNodeHeight(node, 0.0);
        }
    }
    adjustInternalHeights(tree, tree.getRoot());
    if (mostRecent != null) {
        tree.setUnits(mostRecent.getUnits());
    }
}

Example 39 with Date

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

the class TransmissionTreeToVirusTree method makeTreelet.

// events are only relevant if there is a sampling event somewhere further up the tree
private FlexibleTree makeTreelet(InfectedUnit unit, ArrayList<Event> relevantEvents) {
    if (relevantEvents.size() == 0) {
        return null;
    }
    ArrayList<SimpleNode> nodes = new ArrayList<SimpleNode>();
    unit.sortEvents();
    double lastRelevantEventTime = Double.NEGATIVE_INFINITY;
    for (Event event : relevantEvents) {
        if (event.time > lastRelevantEventTime) {
            lastRelevantEventTime = event.time;
        }
    }
    double activeTime = lastRelevantEventTime - unit.infectionEvent.time;
    for (Event event : relevantEvents) {
        Taxon taxon;
        if (event.type == EventType.INFECTION) {
            taxon = new Taxon(event.infectee.id + "_infected_by_" + event.infector.id + "_" + event.time);
        } else {
            taxon = new Taxon(unit.id + "_sampled_" + event.time);
        }
        taxon.setDate(new Date(event.time - unit.infectionEvent.time, Units.Type.YEARS, false));
        SimpleNode node = new SimpleNode();
        node.setTaxon(taxon);
        nodes.add(node);
        node.setHeight(unit.infectionEvent.time - event.time);
        node.setAttribute("Event", event);
    }
    FlexibleNode treeletRoot;
    if (nodes.size() > 1) {
        treeletRoot = simulateCoalescent(nodes, demFunct, activeTime);
    } else {
        treeletRoot = new FlexibleNode(new SimpleTree(nodes.get(0)), nodes.get(0), true);
        treeletRoot.setHeight(0);
    }
    // add the root branch length
    FlexibleNode infectionNode = new FlexibleNode();
    infectionNode.setHeight(activeTime);
    infectionNode.addChild(treeletRoot);
    treeletRoot.setLength(activeTime - treeletRoot.getHeight());
    infectionNode.setAttribute("Event", unit.infectionEvent);
    FlexibleTree outTree = new FlexibleTree(infectionNode);
    for (int i = 0; i < outTree.getNodeCount(); i++) {
        FlexibleNode node = (FlexibleNode) outTree.getNode(i);
        node.setAttribute("Unit", unit.id);
    }
    return outTree;
}