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

Example 1 with Date

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

the class SamplesPanel method clearDates.

public void clearDates() {
    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        java.util.Date origin = new java.util.Date(0);
        double d = 0.0;
        Date date = Date.createTimeSinceOrigin(d, Units.Type.YEARS, origin);
        taxonList.getTaxon(i).setAttribute("date", date);
    }
    // adjust the dates to the current timescale...
    timeScaleChanged();
    dataTableModel.fireTableDataChanged();
}

Example 2 with Date

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

the class SamplesPanel method calculateHeights.

private void calculateHeights() {
    maximumTipHeight = 0.0;
    if (taxonList == null || taxonList.getTaxonCount() == 0)
        return;
    heights = null;
    Date mostRecent = null;
    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        Date date = taxonList.getTaxon(i).getDate();
        if ((date != null) && (mostRecent == null || date.after(mostRecent))) {
            mostRecent = date;
        }
    }
    if (mostRecent != null) {
        heights = new double[taxonList.getTaxonCount()];
        TimeScale timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
        double time0 = timeScale.convertTime(mostRecent.getTimeValue(), mostRecent);
        for (int i = 0; i < taxonList.getTaxonCount(); i++) {
            Date date = taxonList.getTaxon(i).getDate();
            if (date != null) {
                heights[i] = timeScale.convertTime(date.getTimeValue(), date) - time0;
                if (heights[i] > maximumTipHeight)
                    maximumTipHeight = heights[i];
            }
        }
    }
}

Example 3 with Date

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

the class TipDatesPanel method clearDates.

private void clearDates() {
    for (int i = 0; i < options.taxonList.getTaxonCount(); i++) {
        java.util.Date origin = new java.util.Date(0);
        double d = 0.0;
        Date date = Date.createTimeSinceOrigin(d, Units.Type.YEARS, origin);
        options.taxonList.getTaxon(i).setAttribute("date", date);
    }
    // adjust the dates to the current timescale...
    timeScaleChanged();
    dataTableModel.fireTableDataChanged();
}

Example 4 with Date

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

the class TipDatesPanel method timeScaleChanged.

public final void timeScaleChanged() {
    Units.Type units = Units.Type.YEARS;
    switch((DateUnitsType) unitsCombo.getSelectedItem()) {
        case YEARS:
            units = Units.Type.YEARS;
            break;
        case MONTHS:
            units = Units.Type.MONTHS;
            break;
        case DAYS:
            units = Units.Type.DAYS;
            break;
    }
    boolean backwards = directionCombo.getSelectedItem() == DateUnitsType.BACKWARDS;
    for (int i = 0; i < options.taxonList.getTaxonCount(); i++) {
        Date date = options.taxonList.getTaxon(i).getDate();
        double d = date.getTimeValue();
        Date newDate = createDate(d, units, backwards, 0.0);
        newDate.setUncertainty(date.getUncertainty());
        options.taxonList.getTaxon(i).setDate(newDate);
    }
    if (specifyOriginDate.isSelected()) {
        String text = originDateText.getText();
        DateGuesser guesser = options.dateGuesser;
        guessDatesDialog.setupGuesser(guesser);
        try {
            options.originDate = guesser.parseDate(text);
        } catch (GuessDatesException e) {
            options.originDate = null;
        }
    } else {
        options.originDate = null;
    }
    if (options.originDate != null) {
        originDateLabel.setText(" date value: " + Double.toString(options.originDate.getTimeValue()));
    } else {
        originDateLabel.setText(" unable to parse date");
    }
    calculateHeights();
    if (options.useTipDates) {
        for (PartitionTreeModel treeModel : options.getPartitionTreeModels()) {
            treeModel.setTipCalibrations(true);
        }
    }
    dataTableModel.fireTableDataChanged();
    frame.setDirty();
}

Example 5 with Date

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

the class TipDatesPanel method calculateHeights.

private void calculateHeights() {
    options.maximumTipHeight = 0.0;
    if (options.taxonList == null || options.taxonList.getTaxonCount() == 0)
        return;
    heights = null;
    dr.evolution.util.Date mostRecent = options.originDate;
    for (int i = 0; i < options.taxonList.getTaxonCount(); i++) {
        Date date = options.taxonList.getTaxon(i).getDate();
        if ((date != null) && (mostRecent == null || date.after(mostRecent))) {
            mostRecent = date;
        }
    }
    if (mostRecent != null) {
        heights = new double[options.taxonList.getTaxonCount()];
        TimeScale timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
        double time0 = timeScale.convertTime(mostRecent.getTimeValue(), mostRecent);
        for (int i = 0; i < options.taxonList.getTaxonCount(); i++) {
            Taxon taxon = options.taxonList.getTaxon(i);
            Date date = taxon.getDate();
            if (date != null) {
                heights[i] = timeScale.convertTime(date.getTimeValue(), date) - time0;
                taxon.setAttribute("height", heights[i]);
                if (heights[i] > options.maximumTipHeight)
                    options.maximumTipHeight = heights[i];
            }
        }
    }
    frame.setStatusMessage();
}