/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Fred Hutchinson Cancer Research Center and Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.ui.panel;
import org.apache.log4j.Logger;
import org.broad.igv.feature.Range;
import org.broad.igv.feature.RegionOfInterest;
import org.broad.igv.feature.Strand;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.lists.GeneList;
import org.broad.igv.ui.IGV;
import org.broad.igv.event.IGVEventBus;
import org.broad.igv.event.IGVEventObserver;
import org.broad.igv.event.ViewChange;
import org.broad.igv.util.StringUtils;
import javax.swing.*;
import javax.swing.border.LineBorder;
import javax.swing.event.*;
import javax.swing.table.DefaultTableModel;
import javax.swing.table.TableColumnModel;
import javax.swing.table.TableModel;
import javax.swing.table.TableRowSorter;
import java.awt.*;
import java.awt.event.*;
import java.util.*;
import java.util.List;
/**
* @author Damon May
* <p/>
* This dialog displays a list of RegionOfInterest in a table and allows editing.
* Navigation to the start of a region is done by selecting the appropriate row.
* <p/>
* This dialog is not intended to be persistent. To view one of these, create it.
* <p/>
*/
public class RegionNavigatorDialog extends JDialog implements Observer, IGVEventObserver {
private static Logger log = Logger.getLogger(AttributePanel.class);
//Column indexes, in case table structure changes
private static final int TABLE_COLINDEX_CHR = 0;
private static final int TABLE_COLINDEX_START = 1;
private static final int TABLE_COLINDEX_END = 2;
private static final int TABLE_COLINDEX_DESC = 3;
//The active instance of RegionNavigatorDialog (only one at a time)
public static RegionNavigatorDialog activeInstance;
private DefaultTableModel regionTableModel;
// private List<RegionOfInterest> regions;
private TableRowSorter<TableModel> regionTableRowSorter;
//Indicates that we're in the process of synching the table with the regions list, so we shouldn't
//do anything about TableChanged events.
private boolean synchingRegions = false;
/**
* Return the active RegionNavigatorDialog. null if none
*
* @return
*/
public static RegionNavigatorDialog getOrCreateInstance(Frame owner) {
if (activeInstance == null) {
activeInstance = new RegionNavigatorDialog(owner);
}
return activeInstance;
}
/**
* Return the active RegionNavigatorDialog. null if none
*
* @return
*/
public static RegionNavigatorDialog getInstance() {
return activeInstance;
}
/**
* dispose the active instance and get rid of the pointer. Return whether or not there was an
* active instance
*/
public static boolean destroyInstance() {
if (activeInstance == null)
return false;
activeInstance.dispose();
activeInstance = null;
return true;
}
private RegionNavigatorDialog(Frame owner) {
super(owner);
initComponents();
postInit();
}
private RegionNavigatorDialog(Dialog owner) {
super(owner);
initComponents();
postInit();
}
public void update(Observable observable, Object object) {
synchRegions();
}
public void receiveEvent(Object e) {
synchRegions();
}
/**
* Synchronize the regions ArrayList with the passed-in regionsCollection, and update UI
*/
public void synchRegions() {
//Indicate that we're synching regions, so that we don't respond to tableChanged events
synchingRegions = true;
List<RegionOfInterest> regions = retrieveRegionsAsList();
regionTableModel = (DefaultTableModel) regionTable.getModel();
while (regionTableModel.getRowCount() > 0) {
regionTableModel.removeRow(0);
}
regionTableModel.setRowCount(regions.size());
for (int i = 0; i < regions.size(); i++) {
RegionOfInterest region = regions.get(i);
regionTableModel.setValueAt(region.getDescription(), i, TABLE_COLINDEX_DESC);
regionTableModel.setValueAt(region.getDisplayStart(), i, TABLE_COLINDEX_START);
regionTableModel.setValueAt(region.getDisplayEnd(), i, TABLE_COLINDEX_END);
regionTableModel.setValueAt(region.getChr(), i, TABLE_COLINDEX_CHR);
}
//Done synching regions, allow ourselves to respond to tableChanged events
synchingRegions = false;
regionTableModel.fireTableDataChanged();
}
private List<RegionOfInterest> retrieveRegionsAsList() {
return new ArrayList<RegionOfInterest>(IGV.getInstance().getSession().getAllRegionsOfInterest());
}
/**
* Populate the table with the loaded regions
*/
private void postInit() {
regionTableModel = (DefaultTableModel) regionTable.getModel();
regionTable.getSelectionModel().addListSelectionListener(new RegionTableSelectionListener());
regionTableModel.addTableModelListener(new RegionTableModelListener());
//custom row sorter required for displaying only a subset of rows
regionTableRowSorter = new TableRowSorter<TableModel>(regionTableModel);
regionTable.setRowSorter(regionTableRowSorter);
regionTableRowSorter.setRowFilter(new RegionRowFilter());
textFieldSearch.getDocument().addDocumentListener(new SearchFieldDocumentListener());
updateChromosomeDisplayed();
synchRegions();
ReferenceFrame defFrame = FrameManager.getDefaultFrame();
IGVEventBus.getInstance().subscribe(ViewChange.class, this);
IGV.getInstance().getSession().getRegionsOfInterestObservable().addObserver(this);
//resize window if small number of regions. By default, tables are initialized with 20
//rows, and that can look ungainly for empty windows or windows with a few rows.
//This correction is rather hacky. Minimum size of 5 rows set.
int newTableHeight = Math.min(regionTableModel.getRowCount() + 1, 5) * regionTable.getRowHeight();
//This is quite hacky -- need to find the size of the other components programmatically somehow, since
//it will vary on different platforms
int extraHeight = 225;
int newDialogHeight = newTableHeight + extraHeight;
if (newDialogHeight < getHeight()) {
regionTable.setPreferredScrollableViewportSize(new Dimension(regionTable.getPreferredSize().width,
newTableHeight));
setSize(getWidth(), newTableHeight + extraHeight);
update(getGraphics());
}
regionTable.addMouseListener(new RegionTablePopupHandler());
updateButtonsEnabled();
}
private class SearchFieldDocumentListener implements DocumentListener {
public void changedUpdate(DocumentEvent e) {
System.err.println("This should not happen");
}
public void insertUpdate(DocumentEvent e) {
regionTableModel.fireTableDataChanged();
}
public void removeUpdate(DocumentEvent e) {
regionTableModel.fireTableDataChanged();
}
}
/**
* When chromosome that's displayed is changed, need to update displayed regions. showSearchedRegions will do that
*/
public void updateChromosomeDisplayed() {
// regionTable.updateUI();
// showSearchedRegions();
regionTableModel.fireTableDataChanged();
}
/**
* Test whether we should display an entry
*
* @param regionChr
* @param regionDesc
* @return
*/
protected boolean shouldIncludeRegion(String regionChr, String regionDesc) {
//if table is empty, a non-region event is fed here. Test for it and don't display
if (regionChr == null)
return false;
String filterStringLowercase = null;
if (textFieldSearch.getText() != null)
filterStringLowercase = textFieldSearch.getText().toLowerCase();
String chr = FrameManager.getDefaultFrame().getChrName();
//show only regions matching the search string (if specified)
if ((filterStringLowercase != null && !filterStringLowercase.isEmpty() &&
(regionDesc == null || !regionDesc.toLowerCase().contains(filterStringLowercase))))
return false;
//if this checkbox is checked, show all chromosomes
if (checkBoxShowAllChrs.isSelected())
return true;
//show only regions in the current chromosome
if (chr != null && !chr.isEmpty() && !regionChr.equals(chr))
return false;
return true;
}
/**
* A row filter that shows only rows that contain filterString, case-insensitive
*/
private class RegionRowFilter extends RowFilter<TableModel, Object> {
public RegionRowFilter() {
super();
}
public boolean include(RowFilter.Entry entry) {
return shouldIncludeRegion((String) entry.getValue(TABLE_COLINDEX_CHR),
(String) entry.getValue(TABLE_COLINDEX_DESC));
}
}
/**
* Listen for updates to the cells, save changes to the Regions
*/
private class RegionTableModelListener implements TableModelListener {
public void tableChanged(TableModelEvent e) {
//If we're in the middle of synching regions, do nothing
if (synchingRegions)
return;
List<RegionOfInterest> regions = retrieveRegionsAsList();
int firstRow = e.getFirstRow();
//range checking because this method gets called after a clear event, and we don't want to
//try to find an updated region then
if (firstRow > regions.size() - 1)
return;
//update all rows affected
for (int i = firstRow; i <= Math.max(firstRow, Math.min(regionTable.getRowCount(), e.getLastRow())); i++)
updateROIFromRegionTable(i);
}
}
/**
* Updates all ROIs with the values currently stored in the region table
*/
public void updateROIsFromRegionTable() {
for (int i = 0; i < regionTable.getRowSorter().getModelRowCount(); i++)
updateROIFromRegionTable(i);
}
/**
* Updates a single ROI with the values currently stored in the region table
*
* @param tableRow: the viewable index of the table row
*/
public void updateROIFromRegionTable(int tableRow) {
List<RegionOfInterest> regions = retrieveRegionsAsList();
if (tableRow > regionTable.getRowCount() - 1)
return;
//must convert row index from view to model, in case of sorting, filtering
int rowIdx = 0;
try {
rowIdx = regionTable.getRowSorter().convertRowIndexToModel(tableRow);
} catch (ArrayIndexOutOfBoundsException x) {
return;
}
RegionOfInterest region = regions.get(rowIdx);
//dhmay changing 20110505: just update region values from all columns, instead of checking the event
//to see which column is affected. This is in response to an intermittent bug.
Object descObject = regionTableModel.getValueAt(rowIdx, TABLE_COLINDEX_DESC);
if (descObject != null)
region.setDescription(descObject.toString());
//stored values are 0-based end-exclusive, viewed values are 1-based end-inclusive. Check for negative number just in case
int storeStartValue =
Math.max(0, (Integer) regionTableModel.getValueAt(rowIdx, TABLE_COLINDEX_START) - 1);
region.setStart(storeStartValue);
int storeEndValue =
Math.max(0, (Integer) regionTableModel.getValueAt(rowIdx, TABLE_COLINDEX_END));
region.setEnd(storeEndValue);
}
/**
* Listen for selection change events, navigate UI to start of selected region
*/
private class RegionTableSelectionListener implements ListSelectionListener {
public void valueChanged(ListSelectionEvent e) {
if (!e.getValueIsAdjusting()) {
List<RegionOfInterest> regions = retrieveRegionsAsList();
int[] selectedRows = regionTable.getSelectedRows();
if (selectedRows != null && selectedRows.length > 0
&& regions.size() >= selectedRows.length) //dhmay: this is hacky. Bad things can happen with clear regions
{
RegionOfInterest firstStartRegion = null;
RegionOfInterest lastEndRegion = null;
Set<String> selectedChrs = new HashSet<String>();
//Figure out which region has the first start and which has the last end
for (int selectedRowIndex : selectedRows) {
int selectedModelRow = regionTableRowSorter.convertRowIndexToModel(selectedRowIndex);
RegionOfInterest region = regions.get(selectedModelRow);
selectedChrs.add(region.getChr());
if (firstStartRegion == null || region.getStart() < firstStartRegion.getStart())
firstStartRegion = region;
if (lastEndRegion == null || region.getEnd() > lastEndRegion.getEnd())
lastEndRegion = region;
}
//If there are multiple chromosomes represented in the selection, do nothing.
//Because what would we do? Maybe a status message should be displayed somehow, but a
//dialog would get annoying.
if (selectedChrs.size() > 1)
return;
// if (checkBoxZoomWhenNav.isSelected()) {
// // Option (1), zoom and center on group of selected regions, with an interval equal to
// // 20% of the length of the end regions on either side for context (dhmay reduced from 100%)
// int start = firstStartRegion.getStart() - (int) (0.2 * firstStartRegion.getLength());
// int end = lastEndRegion.getEnd() + (int) (0.2 * lastEndRegion.getLength());
// FrameManager.getDefaultFrame().jumpTo(selectedChrs.iterator().next(), start, end);
// } else {
// // Option (2), center on the FIRST selected region without changing resolution
// FrameManager.getDefaultFrame().centerOnLocation(firstStartRegion.getCenter());
// }
}
}
}
}
/**
* Return the selected regions in the table view.
*
* @param selectedRows
* @return
*/
private List<RegionOfInterest> getSelectedRegions(int[] selectedRows) {
List<RegionOfInterest> selectedRegions = new ArrayList<RegionOfInterest>();
List<RegionOfInterest> regions = retrieveRegionsAsList();
for (int selectedRowIndex : selectedRows) {
int selectedModelRow = regionTableRowSorter.convertRowIndexToModel(selectedRowIndex);
selectedRegions.add(regions.get(selectedModelRow));
}
return selectedRegions;
}
private void regionTableMouseClicked(MouseEvent e) {
//We update the state of associated buttons
//whenever the user clicks a mouse button
updateButtonsEnabled();
}
private void updateButtonsEnabled() {
boolean enableMutStates = regionTable.getSelectedRowCount() >= 1;
boolean enableZoomToRegion = regionTable.getSelectedRowCount() == 1;
removeButton.setEnabled(enableMutStates);
viewButton.setEnabled(enableMutStates);
checkBoxZoomWhenNav.setEnabled(enableZoomToRegion);
}
private void thisWindowActivated(WindowEvent e) {
synchRegions();
}
private void thisWindowDeactivated(WindowEvent e) {
updateROIsFromRegionTable();
}
private void thisWindowClosed(WindowEvent e) {
IGV.getInstance().getSession().getRegionsOfInterestObservable().deleteObserver(this);
destroyInstance();
}
private void initComponents() {
// JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
dialogPane = new JPanel();
contentPanel = new JPanel();
panel3 = new JPanel();
checkBoxShowAllChrs = new JCheckBox();
addButton = new JButton();
removeButton = new JButton();
scrollPane1 = new JScrollPane();
regionTable = new JTable();
panel1 = new JPanel();
panel2 = new JPanel();
viewButton = new JButton();
checkBoxZoomWhenNav = new JCheckBox();
panel4 = new JPanel();
label1 = new JLabel();
textFieldSearch = new JTextField();
clearSearchButton = new JButton();
cancelAction = new CancelAction();
addAction = new AddRegionAction();
actionRemoveRegions = new RemoveSelectedRegionsAction();
showAllChromosomesCheckboxAction = new ShowAllChromosomesCheckboxAction();
viewAction = new ViewSelectedAction();
//======== this ========
setTitle("Regions of Interest");
setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
addWindowListener(new WindowAdapter() {
@Override
public void windowActivated(WindowEvent e) {
thisWindowActivated(e);
}
@Override
public void windowClosed(WindowEvent e) {
thisWindowClosed(e);
}
@Override
public void windowDeactivated(WindowEvent e) {
thisWindowDeactivated(e);
}
});
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());
//======== dialogPane ========
{
dialogPane.setBorder(null);
dialogPane.setLayout(new BorderLayout());
//======== contentPanel ========
{
contentPanel.setLayout(new BorderLayout());
//======== panel3 ========
{
panel3.setComponentOrientation(ComponentOrientation.LEFT_TO_RIGHT);
panel3.setBorder(LineBorder.createBlackLineBorder());
panel3.setLayout(new FlowLayout(FlowLayout.LEFT));
//---- checkBoxShowAllChrs ----
checkBoxShowAllChrs.setAction(showAllChromosomesCheckboxAction);
checkBoxShowAllChrs.setToolTipText("View regions from all chromosomes (otherwise, current chromosome only)");
checkBoxShowAllChrs.setSelected(true);
panel3.add(checkBoxShowAllChrs);
//---- addButton ----
addButton.setAction(addAction);
addButton.setText("Add");
addButton.setActionCommand("Add");
panel3.add(addButton);
//---- removeButton ----
removeButton.setAction(actionRemoveRegions);
removeButton.setText("Remove");
panel3.add(removeButton);
}
contentPanel.add(panel3, BorderLayout.NORTH);
//======== scrollPane1 ========
{
//---- regionTable ----
regionTable.setModel(new DefaultTableModel(
new Object[][]{
{null, null, null, null},
},
new String[]{
"Chr", "Start", "End", "Description"
}
) {
Class<?>[] columnTypes = new Class<?>[]{
String.class, Integer.class, Integer.class, Object.class
};
boolean[] columnEditable = new boolean[]{
false, true, true, true
};
@Override
public Class<?> getColumnClass(int columnIndex) {
return columnTypes[columnIndex];
}
@Override
public boolean isCellEditable(int rowIndex, int columnIndex) {
return columnEditable[columnIndex];
}
});
{
TableColumnModel cm = regionTable.getColumnModel();
cm.getColumn(0).setPreferredWidth(50);
cm.getColumn(1).setPreferredWidth(100);
cm.getColumn(2).setPreferredWidth(100);
cm.getColumn(3).setPreferredWidth(200);
}
regionTable.setAutoCreateRowSorter(true);
regionTable.addMouseListener(new MouseAdapter() {
@Override
public void mouseClicked(MouseEvent e) {
regionTableMouseClicked(e);
}
});
scrollPane1.setViewportView(regionTable);
}
contentPanel.add(scrollPane1, BorderLayout.CENTER);
//======== panel1 ========
{
panel1.setLayout(new BoxLayout(panel1, BoxLayout.Y_AXIS));
//======== panel2 ========
{
panel2.setBorder(LineBorder.createBlackLineBorder());
panel2.setLayout(new FlowLayout(FlowLayout.LEFT));
//---- viewButton ----
viewButton.setText("View");
viewButton.setAction(viewAction);
viewButton.setActionCommand("View");
panel2.add(viewButton);
//---- checkBoxZoomWhenNav ----
checkBoxZoomWhenNav.setText("Zoom to Region");
checkBoxZoomWhenNav.setToolTipText("When navigating to a region, change zoom level?");
checkBoxZoomWhenNav.setSelected(true);
panel2.add(checkBoxZoomWhenNav);
}
panel1.add(panel2);
//======== panel4 ========
{
panel4.setBorder(LineBorder.createBlackLineBorder());
panel4.setLayout(new FlowLayout(FlowLayout.LEFT));
//---- label1 ----
label1.setText("Search");
panel4.add(label1);
//---- textFieldSearch ----
textFieldSearch.setToolTipText("Search for regions containing the specified description text.");
textFieldSearch.setPreferredSize(new Dimension(200, 28));
panel4.add(textFieldSearch);
//---- clearSearchButton ----
clearSearchButton.setAction(cancelAction);
clearSearchButton.setText("Clear Search");
panel4.add(clearSearchButton);
}
panel1.add(panel4);
}
contentPanel.add(panel1, BorderLayout.SOUTH);
}
dialogPane.add(contentPanel, BorderLayout.CENTER);
}
contentPane.add(dialogPane, BorderLayout.CENTER);
pack();
setLocationRelativeTo(getOwner());
// JFormDesigner - End of component initialization //GEN-END:initComponents
}
// JFormDesigner - Variables declaration - DO NOT MODIFY //GEN-BEGIN:variables
// Generated using JFormDesigner non-commercial license
private JPanel dialogPane;
private JPanel contentPanel;
private JPanel panel3;
private JCheckBox checkBoxShowAllChrs;
private JButton addButton;
private JButton removeButton;
private JScrollPane scrollPane1;
private JTable regionTable;
private JPanel panel1;
private JPanel panel2;
private JButton viewButton;
private JCheckBox checkBoxZoomWhenNav;
private JPanel panel4;
private JLabel label1;
private JTextField textFieldSearch;
private JButton clearSearchButton;
private CancelAction cancelAction;
private AddRegionAction addAction;
private RemoveSelectedRegionsAction actionRemoveRegions;
private ShowAllChromosomesCheckboxAction showAllChromosomesCheckboxAction;
private ViewSelectedAction viewAction;
// JFormDesigner - End of variables declaration //GEN-END:variables
private class CancelAction extends AbstractAction {
private CancelAction() {
// JFormDesigner - Action initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
putValue(NAME, "Cancel");
putValue(SHORT_DESCRIPTION, "Clear search box");
// JFormDesigner - End of action initialization //GEN-END:initComponents
}
public void actionPerformed(ActionEvent e) {
textFieldSearch.setText("");
}
}
/**
* Add a new RegionOfInterest for the current chromosome, with 0 start and end
*/
private class AddRegionAction extends AbstractAction {
private AddRegionAction() {
// JFormDesigner - Action initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
putValue(NAME, "Add");
putValue(SHORT_DESCRIPTION, "Add a new region");
// JFormDesigner - End of action initialization //GEN-END:initComponents
}
public void actionPerformed(ActionEvent e) {
String chr = FrameManager.getDefaultFrame().getChrName();
if (FrameManager.isGeneListMode()) {
JOptionPane.showMessageDialog(IGV.getMainFrame(),
"Regions cannot be created in gene list or split-screen views.",
"Error", JOptionPane.INFORMATION_MESSAGE);
} else if (chr == null || chr.isEmpty()) {
JOptionPane.showMessageDialog(IGV.getMainFrame(),
"No chromosome is specified. Can't create a region without a chromosome.",
"Error", JOptionPane.INFORMATION_MESSAGE);
} else if (chr.equalsIgnoreCase("All")) {
JOptionPane.showMessageDialog(IGV.getMainFrame(),
"Regions cannot be created in the All Chromosomes view.",
"Error", JOptionPane.INFORMATION_MESSAGE);
} else {
Range r = FrameManager.getDefaultFrame().getCurrentRange();
RegionOfInterest newRegion = new RegionOfInterest(r.getChr(), r.getStart(), r.getEnd(), "");
IGV.getInstance().getSession().addRegionOfInterestWithNoListeners(newRegion);
}
updateButtonsEnabled();
}
}
private class RemoveSelectedRegionsAction extends AbstractAction {
private RemoveSelectedRegionsAction() {
// JFormDesigner - Action initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
putValue(NAME, "Remove");
putValue(SHORT_DESCRIPTION, "Remove all selected regions");
// JFormDesigner - End of action initialization //GEN-END:initComponents
}
public void actionPerformed(ActionEvent e) {
int[] selectedRows = regionTable.getSelectedRows();
if (selectedRows != null && selectedRows.length > 0) {
List<RegionOfInterest> selectedRegions = getSelectedRegions(selectedRows);
IGV.getInstance().getSession().removeRegionsOfInterest(selectedRegions);
synchRegions();
} else {
//todo dhmay -- I don't fully understand this call. Clean this up.
JOptionPane.showMessageDialog(IGV.getMainFrame(), "No regions have been selected for removal.",
"Error", JOptionPane.INFORMATION_MESSAGE);
}
updateButtonsEnabled();
}
}
private class ViewSelectedAction extends AbstractAction {
private ViewSelectedAction() {
// JFormDesigner - Action initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
putValue(NAME, "View");
// JFormDesigner - End of action initialization //GEN-END:initComponents
}
public void actionPerformed(ActionEvent e) {
int[] selectedRows = regionTable.getSelectedRows();
if (selectedRows != null && selectedRows.length > 0) {
List<RegionOfInterest> selectedRegions = getSelectedRegions(selectedRows);
// Create an "on-the-fly" gene list
// TODO -- this is inefficient (converting regions -> strings then back again)
List<String> loci = new ArrayList<String>(selectedRegions.size());
if (checkBoxZoomWhenNav.isSelected() || selectedRegions.size() >= 2 || FrameManager.isGeneListMode()) {
for (RegionOfInterest roi : selectedRegions) {
loci.add(roi.getLocusString());
}
} else {
//Need to preserve current zoom, iff checkbox not selected and only choosing 1
RegionOfInterest roi = selectedRegions.get(0);
Range range = FrameManager.getDefaultFrame().getCurrentRange();
int length = range.getLength();
int start = roi.getCenter() - length / 2;
int end = start + length;
//Shift so we don't go below 0
if (start < 0) {
end += Math.abs(start);
start = 0;
}
loci.add(new RegionOfInterest(roi.getChr(), start, end, roi.getDescription()).getLocusString());
}
GeneList geneList = new GeneList("Regions of Interest", loci, false);
IGV.getInstance().setGeneList(geneList);
IGV.getInstance().resetFrames();
}
updateButtonsEnabled();
}
}
private class ShowAllChromosomesCheckboxAction extends AbstractAction {
private ShowAllChromosomesCheckboxAction() {
// JFormDesigner - Action initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
putValue(NAME, "Show All Chrs");
// JFormDesigner - End of action initialization //GEN-END:initComponents
}
public void actionPerformed(ActionEvent e) {
// TODO add your code here
synchRegions();
updateButtonsEnabled();
}
}
/**
* Creates an appropriate popup for the row under the cursor, with Copy Sequence and Copy Details actions.
* This class doesn't go back to the RegionOfInterest model -- it relies on the values stored in the
* TableModel, since that's all we need. It could easily grab the Region, though, like in RegionTableModelListener
*/
private class RegionTablePopupHandler extends MouseAdapter {
// Maximum length for "copy sequence" action
private static final int MAX_SEQUENCE_LENGTH = 1000000;
public void mousePressed(MouseEvent e) {
if (SwingUtilities.isRightMouseButton(e)) {
Point p = e.getPoint();
//must convert row index from view to model, in case of sorting, filtering
int row = regionTable.getRowSorter().convertRowIndexToModel(regionTable.rowAtPoint(p));
int col = regionTable.columnAtPoint(p);
if (row >= 0 && col >= 0) {
final String chr = (String) regionTableModel.getValueAt(row, TABLE_COLINDEX_CHR);
//displayed values are 1-based, so subract 1
final int start = (Integer) regionTableModel.getValueAt(row, TABLE_COLINDEX_START) - 1;
final int end = (Integer) regionTableModel.getValueAt(row, TABLE_COLINDEX_END) - 1;
final String desc = (String) regionTableModel.getValueAt(row, TABLE_COLINDEX_DESC);
JPopupMenu popupMenu = new IGVPopupMenu();
JMenuItem copySequenceItem = new JMenuItem("Copy Sequence");
copySequenceItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
int length = end - start;
if (length > MAX_SEQUENCE_LENGTH) {
JOptionPane.showMessageDialog(RegionNavigatorDialog.this, "Region is to large to copy sequence data.");
} else {
IGV.copySequenceToClipboard(GenomeManager.getInstance().getCurrentGenome(),
chr, start, end, Strand.NONE);
}
}
});
popupMenu.add(copySequenceItem);
JMenuItem copyDetailsItem = new JMenuItem("Copy Details");
copyDetailsItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
String details = chr + ":" + start + "-" + end;
if (desc != null && !desc.isEmpty())
details = details + ", " + desc;
StringUtils.copyTextToClipboard(details);
}
});
popupMenu.add(copyDetailsItem);
popupMenu.show(regionTable, p.x, p.y);
}
}
}
}
}