/*
* SamplesPanel.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.app.tempest;
import dr.app.beauti.options.DateGuesser;
import dr.app.beauti.tipdatepanel.GuessDatesDialog;
import dr.app.beauti.util.PanelUtils;
import dr.evolution.util.Date;
import dr.evolution.util.TimeScale;
import dr.evolution.util.Units;
import dr.evolution.util.TaxonList;
import dr.app.gui.table.*;
import jam.framework.Exportable;
import jam.table.HeaderRenderer;
import dr.app.gui.table.TableEditorStopper;
import jam.table.TableRenderer;
import javax.swing.*;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
import javax.swing.plaf.BorderUIResource;
import javax.swing.table.AbstractTableModel;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
/**
* @author Andrew Rambaut
* @version $Id: DataPanel.java,v 1.17 2006/09/05 13:29:34 rambaut Exp $
*/
public class SamplesPanel extends JPanel implements Exportable {
/**
*
*/
private static final long serialVersionUID = 5283922195494563924L;
JScrollPane scrollPane = new JScrollPane();
JTable dataTable = null;
DataTableModel dataTableModel = null;
ClearDatesAction clearDatesAction = new ClearDatesAction();
GuessDatesAction guessDatesAction = new GuessDatesAction();
JComboBox unitsCombo = new JComboBox(new String[]{"Years", "Months", "Days"});
JComboBox directionCombo = new JComboBox(new String[]{"Since some time in the past", "Before the present"});
TempestFrame frame = null;
TaxonList taxonList = null;
int datesUnits;
int datesDirection;
double maximumTipHeight = 0.0;
DateGuesser guesser = new DateGuesser();
double[] heights = null;
GuessDatesDialog guessDatesDialog = null;
public SamplesPanel(TempestFrame parent, TaxonList taxonList) {
this.frame = parent;
dataTableModel = new DataTableModel();
TableSorter sorter = new TableSorter(dataTableModel);
dataTable = new JTable(sorter);
sorter.setTableHeader(dataTable.getTableHeader());
dataTable.getTableHeader().setReorderingAllowed(false);
dataTable.getTableHeader().setDefaultRenderer(
new HeaderRenderer(SwingConstants.LEFT, new Insets(0, 4, 0, 4)));
dataTable.getColumnModel().getColumn(0).setCellRenderer(
new TableRenderer(SwingConstants.LEFT, new Insets(0, 4, 0, 4)));
dataTable.getColumnModel().getColumn(0).setPreferredWidth(80);
dataTable.getColumnModel().getColumn(1).setCellRenderer(
new TableRenderer(SwingConstants.LEFT, new Insets(0, 4, 0, 4)));
dataTable.getColumnModel().getColumn(1).setPreferredWidth(80);
dataTable.getColumnModel().getColumn(1).setCellEditor(
new DateCellEditor());
dataTable.getColumnModel().getColumn(2).setCellRenderer(
new TableRenderer(SwingConstants.LEFT, new Insets(0, 4, 0, 4)));
dataTable.getColumnModel().getColumn(2).setPreferredWidth(80);
dataTable.getColumnModel().getColumn(2).setCellEditor(
new DateCellEditor());
dataTable.getColumnModel().getColumn(3).setCellRenderer(
new TableRenderer(SwingConstants.LEFT, new Insets(0, 4, 0, 4)));
dataTable.getColumnModel().getColumn(3).setPreferredWidth(80);
TableEditorStopper.ensureEditingStopWhenTableLosesFocus(dataTable);
dataTable.getSelectionModel().addListSelectionListener(new ListSelectionListener() {
public void valueChanged(ListSelectionEvent evt) {
selectionChanged();
}
});
scrollPane = new JScrollPane(dataTable,
JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
scrollPane.setOpaque(false);
PanelUtils.setupComponent(unitsCombo);
PanelUtils.setupComponent(directionCombo);
JToolBar toolBar1 = new JToolBar();
toolBar1.setFloatable(false);
toolBar1.setOpaque(false);
toolBar1.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
JButton button = new JButton(clearDatesAction);
PanelUtils.setupComponent(button);
toolBar1.add(button);
button = new JButton(guessDatesAction);
PanelUtils.setupComponent(button);
toolBar1.add(button);
toolBar1.add(new JToolBar.Separator(new Dimension(12, 12)));
final JLabel unitsLabel = new JLabel("Dates specified as ");
toolBar1.add(unitsLabel);
toolBar1.add(unitsCombo);
toolBar1.add(directionCombo);
setOpaque(false);
setBorder(new BorderUIResource.EmptyBorderUIResource(new Insets(12, 12, 12, 12)));
setLayout(new BorderLayout(0, 0));
add(toolBar1, "North");
add(scrollPane, "Center");
ItemListener listener = new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
timeScaleChanged();
}
};
unitsCombo.addItemListener(listener);
directionCombo.addItemListener(listener);
setTaxonList(taxonList);
}
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.setPrecision(date.getPrecision());
taxonList.getTaxon(i).setDate(newDate);
}
calculateHeights();
dataTableModel.fireTableDataChanged();
frame.timeScaleChanged();
}
private Date createDate(double timeValue, Units.Type units, boolean backwards, double origin) {
if (backwards) {
return Date.createTimeAgoFromOrigin(timeValue, units, origin);
} else {
return Date.createTimeSinceOrigin(timeValue, units, origin);
}
}
private void setTaxonList(TaxonList taxonList) {
this.taxonList = taxonList;
setupTable();
unitsCombo.setSelectedIndex(datesUnits);
directionCombo.setSelectedIndex(datesDirection);
calculateHeights();
dataTableModel.fireTableDataChanged();
}
private void setupTable() {
dataTableModel.fireTableDataChanged();
}
public void getOptions() {
datesUnits = unitsCombo.getSelectedIndex();
datesDirection = directionCombo.getSelectedIndex();
}
public JComponent getExportableComponent() {
return dataTable;
}
public void selectionChanged() {
// nothing to do
}
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();
}
public void guessDates() {
if (guessDatesDialog == null) {
guessDatesDialog = new GuessDatesDialog(frame);
}
int result = guessDatesDialog.showDialog();
if (result == -1 || result == JOptionPane.CANCEL_OPTION) {
return;
}
guesser.guessDates = true;
guessDatesDialog.setupGuesser(guesser);
String warningMessage = null;
guesser.guessDates(taxonList);
if (warningMessage != null) {
JOptionPane.showMessageDialog(this, "Warning: some dates may not be set correctly - \n" + warningMessage,
"Error guessing dates",
JOptionPane.WARNING_MESSAGE);
}
// adjust the dates to the current timescale...
timeScaleChanged();
dataTableModel.fireTableDataChanged();
}
public class ClearDatesAction extends AbstractAction {
/**
*
*/
private static final long serialVersionUID = -7281309694753868635L;
public ClearDatesAction() {
super("Clear Dates");
setToolTipText("Use this tool to remove sampling dates from each taxon");
}
public void actionPerformed(ActionEvent ae) {
clearDates();
}
}
public class GuessDatesAction extends AbstractAction {
/**
*
*/
private static final long serialVersionUID = 8514706149822252033L;
public GuessDatesAction() {
super("Guess Dates");
setToolTipText("Use this tool to guess the sampling dates from the taxon labels");
}
public void actionPerformed(ActionEvent ae) {
guessDates();
}
}
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];
}
}
}
}
class DataTableModel extends AbstractTableModel {
/**
*
*/
private static final long serialVersionUID = -6707994233020715574L;
String[] columnNames = {"Name", "Date", "Precision", "Height"};
public DataTableModel() {
}
public int getColumnCount() {
return columnNames.length;
}
public int getRowCount() {
if (taxonList == null) return 0;
return taxonList.getTaxonCount();
}
public Object getValueAt(int row, int col) {
Date date = taxonList.getTaxon(row).getDate();
switch (col) {
case 0:
return taxonList.getTaxonId(row);
case 1:
if (date != null) {
return date.getTimeValue();
} else {
return "-";
}
case 2:
if (date != null) {
return date.getPrecision();
} else {
return "-";
}
case 3:
if (heights != null) {
return heights[row];
} else {
return "0.0";
}
}
return null;
}
public void setValueAt(Object aValue, int row, int col) {
if (col == 0) {
taxonList.getTaxon(row).setId(aValue.toString());
} else if (col == 1) {
Date date = taxonList.getTaxon(row).getDate();
if (date != null) {
double d = (Double) aValue;
Date newDate = createDate(d, date.getUnits(), date.isBackwards(), date.getOrigin());
taxonList.getTaxon(row).setDate(newDate);
}
} else if (col == 2) {
Date date = taxonList.getTaxon(row).getDate();
if (date != null) {
double d = (Double) aValue;
if (d >= 0.0) {
date.setPrecision(d);
}
}
}
timeScaleChanged();
}
public boolean isCellEditable(int row, int col) {
if (col == 0) return true;
if (col == 1 || col == 2) {
Date date = taxonList.getTaxon(row).getDate();
return (date != null);
}
return false;
}
public String getColumnName(int column) {
return columnNames[column];
}
public Class getColumnClass(int c) {
return getValueAt(0, c).getClass();
}
public String toString() {
StringBuffer buffer = new StringBuffer();
buffer.append(getColumnName(0));
for (int j = 1; j < getColumnCount(); j++) {
buffer.append("\t");
buffer.append(getColumnName(j));
}
buffer.append("\n");
for (int i = 0; i < getRowCount(); i++) {
buffer.append(getValueAt(i, 0));
for (int j = 1; j < getColumnCount(); j++) {
buffer.append("\t");
buffer.append(getValueAt(i, j));
}
buffer.append("\n");
}
return buffer.toString();
}
}
}