/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 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.
*/
/*
* Created by JFormDesigner on Thu Oct 31 22:31:02 EDT 2013
*/
package org.broad.igv.util.encode;
import java.awt.*;
import java.awt.event.*;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.text.ParseException;
import java.util.*;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.swing.*;
import javax.swing.border.*;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
import javax.swing.text.NumberFormatter;
import com.jidesoft.swing.JideBoxLayout;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.ui.IGV;
import org.broad.igv.util.Pair;
import org.broad.igv.util.ResourceLocator;
/**
* @author Jim Robinson
*/
public class EncodeFileBrowser extends JDialog {
private static Logger log = Logger.getLogger(EncodeFileBrowser.class);
private static Map<String, EncodeFileBrowser> instanceMap = Collections.synchronizedMap(new HashMap<String, EncodeFileBrowser>());
private static NumberFormatter numberFormatter = new NumberFormatter();
private JButton cancelButton;
private JPanel dialogPane;
private JPanel contentPanel;
private JScrollPane scrollPane1;
private JTable table;
private JPanel filterPanel;
private JLabel filterLabel;
private JTextField filterTextField;
private JLabel rowCountLabel;
private JPanel buttonBar;
private JButton okButton;
EncodeTableModel model;
private boolean canceled;
public synchronized static EncodeFileBrowser getInstance(String genomeId) throws IOException {
String encodeGenomeId = getEncodeGenomeId(genomeId);
EncodeFileBrowser instance = instanceMap.get(encodeGenomeId);
if (instance == null) {
Pair<String [], List<EncodeFileRecord>> records = getEncodeFileRecords(encodeGenomeId);
if (records == null) {
return null;
}
Frame parent = IGV.hasInstance() ? IGV.getMainFrame() : null;
instance = new EncodeFileBrowser(parent, new EncodeTableModel(records.getFirst(), records.getSecond()));
instanceMap.put(encodeGenomeId, instance);
}
return instance;
}
static HashSet<String> supportedGenomes = new HashSet<String>(Arrays.asList("hg19", "mm9"));
public static boolean genomeSupported(String genomeId) {
return genomeId != null && supportedGenomes.contains(getEncodeGenomeId(genomeId));
}
private static String getEncodeGenomeId(String genomeId) {
if (genomeId.equals("b37") || genomeId.equals("1kg_v37")) return "hg19";
else return genomeId;
}
private static Pair<String [], List<EncodeFileRecord>> getEncodeFileRecords(String genomeId) throws IOException {
InputStream is = null;
try {
is = EncodeFileBrowser.class.getResourceAsStream("encode." + genomeId + ".txt");
if (is == null) {
return null;
}
BufferedReader reader = new BufferedReader(new InputStreamReader(is));
String[] headers = Globals.tabPattern.split(reader.readLine());
List<EncodeFileRecord> records = new ArrayList<EncodeFileRecord>(20000);
String nextLine;
while ((nextLine = reader.readLine()) != null) {
if (!nextLine.startsWith("#")) {
String[] tokens = Globals.tabPattern.split(nextLine, -1);
String path = tokens[0];
Map<String, String> attributes = new HashMap<String, String>();
for (int i = 0; i < headers.length; i++) {
String value = i < tokens.length ? tokens[i] : "";
if (value.length() > 0) {
attributes.put(headers[i], value);
}
}
final EncodeFileRecord record = new EncodeFileRecord(path, attributes);
if(record.hasMetaData()) records.add(record);
}
}
return new Pair(headers, records);
} finally {
if (is != null) is.close();
}
}
private EncodeFileBrowser(Frame owner, EncodeTableModel model) {
super(owner);
this.model = model;
setModal(true);
initComponents();
init(model);
}
private void init(final EncodeTableModel model) {
setModal(true);
setTitle("Encode Production Data");
table.setAutoCreateRowSorter(true);
table.setModel(model);
table.setRowSorter(model.getSorter());
try {
rowCountLabel.setText(numberFormatter.valueToString(table.getRowCount()) + " rows");
} catch (ParseException e) {
}
table.setRowSelectionAllowed(false);
table.setColumnSelectionAllowed(false);
filterTextField.getDocument().addDocumentListener(
new DocumentListener() {
public void changedUpdate(DocumentEvent e) {
updateFilter();
}
public void insertUpdate(DocumentEvent e) {
updateFilter();
}
public void removeUpdate(DocumentEvent e) {
updateFilter();
}
});
}
/**
* Update the row filter regular expression from the expression in
* the text box.
*/
private void updateFilter() {
RowFilter<EncodeTableModel, Object> rf = null;
//If current expression doesn't parse, don't update.
try {
rf = new RegexFilter(filterTextField.getText());
} catch (java.util.regex.PatternSyntaxException e) {
return;
}
model.getSorter().setRowFilter(rf);
try {
rowCountLabel.setText(numberFormatter.valueToString(table.getRowCount()) + " rows");
} catch (ParseException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
}
private void loadButtonActionPerformed(ActionEvent e) {
canceled = false;
setVisible(false);
}
private void cancelButtonActionPerformed(ActionEvent e) {
canceled = true;
setVisible(false);
}
public boolean isCanceled() {
return canceled;
}
private Set<String> getLoadedPaths() {
if (!IGV.hasInstance()) return new HashSet<String>();
Collection<ResourceLocator> locators = IGV.getInstance().getDataResourceLocators();
HashSet<String> loadedPaths = new HashSet<String>(locators.size());
for (ResourceLocator locator : locators) {
loadedPaths.add(locator.getPath());
}
return loadedPaths;
}
/**
* @return the list of VISIBLE selected records. Filtered records are not returned even if record.selected == true
* @throws IOException
*/
public List<EncodeFileRecord> getSelectedRecords() throws IOException {
List<EncodeFileRecord> selectedRecords = new ArrayList<EncodeFileRecord>();
List<EncodeFileRecord> allRecords = model.getRecords();
int rowCount = table.getRowCount();
for (int i = 0; i < rowCount; i++) {
int modelIdx = table.convertRowIndexToModel(i);
EncodeFileRecord record = allRecords.get(modelIdx);
if (record.isSelected()) {
selectedRecords.add(record);
record.setSelected(false); // Prevent loading twice
}
}
return selectedRecords;
}
private class RegexFilter extends RowFilter {
List<Pair <String, Matcher>> matchers;
RegexFilter(String text) {
if (text == null) {
throw new IllegalArgumentException("Pattern must be non-null");
}
matchers = new ArrayList<Pair <String, Matcher>>();
String[] tokens = Globals.whitespacePattern.split(text);
for (String t : tokens) {
// If token contains an = sign apply to specified column only
String column = "*";
String value = t.trim();
if (t.contains("=")) {
String[] kv = Globals.equalPattern.split(t);
if (kv.length > 1) {
column = kv[0].trim();
value = kv[1].trim();
} else {
value = kv[0]; // Value is column name until more input is entered
}
}
matchers.add(new Pair(column, Pattern.compile("(?i)" + value).matcher("")));
}
}
/**
* Include row if each matcher succeeds in at least one column. In other words all the conditions
* are combined with "and"
*
* @param value
* @return
*/
@Override
public boolean include(Entry value) {
for (Pair<String, Matcher> entry : matchers) {
String column = entry.getFirst();
Matcher matcher = entry.getSecond();
// Search for a match in at least one column. The first column is the checkbox.
boolean found = false; // Pessimistic
int nColumns = table.getColumnCount();
for (int index = 1; index < nColumns; index++) {
// Include column headings in search. This is to prevent premature filtering when entering a
// specific column condition (e.g. cataType=ChipSeq)
matcher.reset(table.getColumnName(index).toLowerCase());
if (matcher.find()) {
found = true;
break;
}
boolean wildcard = column.equals("*");
if (wildcard || column.equalsIgnoreCase(table.getColumnName(index))) {
matcher.reset(value.getStringValue(index));
if (matcher.find()) {
found = true;
break;
}
}
}
if (!found) return false;
}
return true; // If we get here we matched them all
}
}
private void initComponents() {
dialogPane = new JPanel();
contentPanel = new JPanel();
scrollPane1 = new JScrollPane();
table = new JTable();
filterPanel = new JPanel();
filterLabel = new JLabel();
filterTextField = new JTextField();
rowCountLabel = new JLabel();
buttonBar = new JPanel();
okButton = new JButton();
cancelButton = new JButton();
getRootPane().setDefaultButton(okButton);
final String filterToolTip = "Enter multiple filter strings separated by commas. e.g. GM12878, ChipSeq";
filterLabel.setToolTipText(filterToolTip);
filterTextField.setToolTipText(filterToolTip);
//======== this ========
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());
//======== dialogPane ========
dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
dialogPane.setLayout(new BorderLayout());
//======== contentPanel ========
contentPanel.setLayout(new BorderLayout(0, 10));
//======== scrollPane1 ========
scrollPane1.setViewportView(table);
contentPanel.add(scrollPane1, BorderLayout.CENTER);
//======== panel1 ========
filterPanel.setLayout(new JideBoxLayout(filterPanel, JideBoxLayout.X_AXIS, 5));
//---- label1 ----
filterLabel.setText("Filter:");
filterPanel.add(filterLabel, JideBoxLayout.FIX);
//---- filterTextField ----
filterPanel.add(filterTextField, JideBoxLayout.VARY);
rowCountLabel.setHorizontalAlignment(JLabel.RIGHT);
JPanel sillyPanel = new JPanel();
sillyPanel.setLayout(new JideBoxLayout(sillyPanel, JideBoxLayout.X_AXIS, 0));
sillyPanel.setPreferredSize(new Dimension(100, 28));
sillyPanel.add(rowCountLabel, JideBoxLayout.VARY);
filterPanel.add(sillyPanel, JideBoxLayout.FIX);
contentPanel.add(filterPanel, BorderLayout.NORTH);
dialogPane.add(contentPanel, BorderLayout.CENTER);
//======== buttonBar ========
buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0));
buttonBar.setLayout(new GridBagLayout());
((GridBagLayout) buttonBar.getLayout()).columnWidths = new int[]{0, 85, 80};
((GridBagLayout) buttonBar.getLayout()).columnWeights = new double[]{1.0, 0.0, 0.0};
//---- okButton ----
okButton.setText("Load");
okButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
loadButtonActionPerformed(e);
}
});
buttonBar.add(okButton, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 5), 0, 0));
//---- cancelButton ----
cancelButton.setText("Cancel");
cancelButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
cancelButtonActionPerformed(e);
}
});
buttonBar.add(cancelButton, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 0), 0, 0));
dialogPane.add(buttonBar, BorderLayout.SOUTH);
contentPane.add(dialogPane, BorderLayout.CENTER);
setSize(700, 620);
setLocationRelativeTo(getOwner());
}
public static void main(String[] args) throws IOException {
getInstance("hg19").setVisible(true);
}
}