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

Example 26 with Date

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

the class TraceCorrelationAssert method createAlignment.

protected void createAlignment(Object[][] taxa_sequence, DataType dataType) {
    alignment = new SimpleAlignment();
    alignment.setDataType(dataType);
    // alignment.setDataType(Nucleotides.INSTANCE);
    // 6, 17
    taxa = new Taxon[taxa_sequence[0].length];
    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);
    }
}

Example 27 with Date

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

the class DateGuesser method guessDates.

public void guessDates(List<Taxon> taxonList, Map<Taxon, String> taxonDateMap) {
    dateFormat = new SimpleDateFormat(calendarDateFormat);
    dateFormat.setTimeZone(TimeZone.getTimeZone("GMT"));
    for (int i = 0; i < taxonList.size(); i++) {
        Taxon taxon = taxonList.get(i);
        // Allocates a Date object and initializes it to represent the specified number of milliseconds since the
        // standard base time known as "the epoch", namely January 1, 1970, 00:00:00 GMT
        java.util.Date origin = new java.util.Date(0);
        double[] values = new double[2];
        try {
            if (taxonDateMap != null) {
                String dateString = taxonDateMap.get(taxon);
                if (dateString == null) {
                    continue;
                }
                parseDate(taxon.getId(), dateString, values);
            } else {
                switch(guessType) {
                    case ORDER:
                        guessDateFromOrder(taxonList.get(i).getId(), order, fromLast, values);
                        break;
                    case PREFIX:
                        guessDateFromPrefix(taxonList.get(i).getId(), prefix, order, fromLast, values);
                        break;
                    case REGEX:
                        guessDateFromRegex(taxonList.get(i).getId(), regex, values);
                        break;
                    default:
                        throw new IllegalArgumentException("unknown GuessType");
                }
            }
        } catch (GuessDatesException gfe) {
        // @todo catch errors and give to user
        }
        double d = values[0];
        if (!parseCalendarDates && !parseCalendarDatesAndPrecision) {
            if (offset > 0) {
                if (unlessLessThan > 0) {
                    if (d < unlessLessThan) {
                        d += offset2;
                    } else {
                        d += offset;
                    }
                } else {
                    d += offset;
                }
            }
        }
        // @todo if any taxa aren't set then return warning
        Date date = Date.createTimeSinceOrigin(d, Units.Type.YEARS, origin);
        date.setUncertainty(values[1]);
        taxon.setAttribute("date", date);
    }
}

Example 28 with Date

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

the class DateGuesser method parseDate.

private void parseDate(String label, String value, double[] values) throws GuessDatesException {
    double d;
    double p = 0.0;
    if (dateFormat1 == null) {
        // set the timezones to GMT so they match the origin date...
        dateFormat1 = new SimpleDateFormat("yyyy-MM-dd");
        dateFormat1.setTimeZone(TimeZone.getTimeZone("GMT"));
        dateFormat2 = new SimpleDateFormat("yyyy-MM");
        dateFormat2.setTimeZone(TimeZone.getTimeZone("GMT"));
        dateFormat3 = new SimpleDateFormat("yyyy");
        dateFormat3.setTimeZone(TimeZone.getTimeZone("GMT"));
    }
    if (parseCalendarDatesAndPrecision) {
        try {
            Date date = new Date(dateFormat1.parse(value));
            d = date.getTimeValue();
            p = 0.0;
        } catch (ParseException pe) {
            try {
                Date date = new Date(dateFormat2.parse(value));
                d = date.getTimeValue();
                p = 1.0 / 12.0;
            } catch (ParseException pe2) {
                try {
                    Date date = new Date(dateFormat3.parse(value));
                    d = date.getTimeValue();
                    p = 1.0;
                } catch (ParseException pe3) {
                    throw new GuessDatesException("Badly formatted date for taxon, " + label);
                }
            }
        }
    } else if (parseCalendarDates) {
        try {
            Date date = new Date(dateFormat.parse(value));
            d = date.getTimeValue();
        } catch (ParseException pe) {
            throw new GuessDatesException("Badly formatted date for taxon, " + label);
        }
    } else {
        try {
            d = Double.parseDouble(value);
        } catch (NumberFormatException nfe) {
            throw new GuessDatesException("Badly formatted date for taxon, " + label);
        }
    }
    values[0] = d;
    values[1] = p;
}

Example 29 with Date

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

the class TipDateSamplingComponentOptions method getTaxonSet.

public TaxonList getTaxonSet() {
    TaxonList taxa = options.taxonList;
    if (tipDateSamplingTaxonSet != null) {
        taxa = tipDateSamplingTaxonSet;
    }
    if (tipDateSamplingType == TipDateSamplingType.SAMPLE_PRECISION) {
        Taxa precisionTaxonList = new Taxa();
        for (int i = 0; i < taxa.getTaxonCount(); i++) {
            Taxon taxon = taxa.getTaxon(i);
            Date date = taxon.getDate();
            if (date.getUncertainty() > 0.0) {
                precisionTaxonList.addTaxon(taxon);
            }
        }
        taxa = precisionTaxonList;
    }
    return taxa;
}

Example 30 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());
    }
}