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

Example 6 with Date

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

the class TipDatesPanel method setDates.

private void setDates() {
    if (options.taxonList == null) {
        // validation of check empty taxonList
        return;
    }
    int result;
    do {
        if (dateValueDialog == null) {
            dateValueDialog = new SetValueDialog(frame, "Set Date for Taxa");
        }
        int[] selRows = dataTable.getSelectedRows();
        if (selRows.length == 1) {
            precisionValueDialog.setDescription("Set date value for selected taxon");
        } else if (selRows.length > 1) {
            dateValueDialog.setDescription("Set date values for selected taxa");
        } else {
            dateValueDialog.setDescription("Set date values for all taxa");
        }
        result = dateValueDialog.showDialog();
        if (result == -1 || result == JOptionPane.CANCEL_OPTION) {
            return;
        }
        // currentTrait.guessTrait = true; // ?? no use?
        String value = dateValueDialog.getValue();
        java.util.Date origin = new java.util.Date(0);
        double d = Double.parseDouble(value);
        Date date = Date.createTimeSinceOrigin(d, Units.Type.YEARS, origin);
        if (selRows.length > 0) {
            for (int row : selRows) {
                options.taxonList.getTaxon(row).setAttribute("date", date);
            }
        } else {
            for (Taxon taxon : options.taxonList) {
                taxon.setAttribute("date", date);
            }
        }
        // adjust the dates to the current timescale...
        timeScaleChanged();
        dataTableModel.fireTableDataChanged();
    } while (result < 0);
}

Example 7 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;
    dr.evolution.util.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 8 with Date

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

the class SamplesPanel method timeScaleChanged.

public final void timeScaleChanged() {
    Units.Type units = Units.Type.YEARS;
    switch(unitsCombo.getSelectedIndex()) {
        case 0:
            units = Units.Type.YEARS;
            break;
        case 1:
            units = Units.Type.MONTHS;
            break;
        case 2:
            units = Units.Type.DAYS;
            break;
    }
    boolean backwards = directionCombo.getSelectedIndex() == 1;
    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        Date date = taxonList.getTaxon(i).getDate();
        double d = date.getTimeValue();
        Date newDate = createDate(d, units, backwards, 0.0);
        newDate.setUncertainty(date.getUncertainty());
        taxonList.getTaxon(i).setDate(newDate);
    }
    calculateHeights();
    dataTableModel.fireTableDataChanged();
    frame.timeScaleChanged();
}

Example 9 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 10 with Date

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

the class TreeUtils method getTipDates.

/**
 * Gets the tip dates from a tree.
 */
public static void getTipDates(Tree tree, Variate dates) {
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        Taxon taxon = tree.getNodeTaxon(tree.getExternalNode(i));
        Object date = taxon.getAttribute("date");
        if (date != null) {
            if (date instanceof Date) {
                dates.add(((Date) date).getTimeValue());
            } else {
                try {
                    dates.add(Double.parseDouble(date.toString()));
                } catch (NumberFormatException nfe) {
                    dates.add(0.0);
                }
            }
        } else {
            dates.add(0.0);
        }
    }
}