/*
* 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 Mon Nov 26 16:20:15 EST 2012
*/
package org.broad.igv.plugin.mongovariant;
import com.mongodb.WriteResult;
import org.broad.igv.track.Track;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.variant.VariantTrack;
import htsjdk.tribble.util.ParsingUtils;
import org.broadinstitute.gatk.tools.walkers.na12878kb.core.MongoVariantContext;
import org.broadinstitute.gatk.tools.walkers.na12878kb.core.NA12878DBArgumentCollection;
import org.broadinstitute.gatk.tools.walkers.na12878kb.core.NA12878KnowledgeBase;
import org.broadinstitute.gatk.tools.walkers.na12878kb.core.TruthStatus;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.GenotypeType;
import htsjdk.variant.variantcontext.VariantContext;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.IOException;
import java.util.Collections;
/**
* Dialog for reviewing a variant from a VCF file.
* The users opinion is submitted to a MongoDB, specified by
* system property {@link VariantReviewPlugin#DB_PATH_KEY}. Path can be relative to either the local machine,
* or NA12878kb package or the GenomeAnalysisTK jar
*/
public class VariantReviewDialog extends JDialog {
private VariantContext variantContext;
private VariantContext sampleVC;
private String userName;
//Path to spec file describing database
private String dbSpecPath;
public VariantReviewDialog(Frame owner, VariantContext vc, String dbSpecPath) {
super(owner);
initComponents();
truthField.setModel(new DefaultComboBoxModel(TruthStatus.values()));
genotypeTypeField.setModel(new DefaultComboBoxModel(GenotypeType.values()));
this.variantContext = vc;
this.userName = System.getProperty("user.name", "unknown");
this.dbSpecPath = dbSpecPath;
initComponentData(vc);
}
private void initComponentData(VariantContext variant) {
callsetField.setText(userName);
chrField.setText(variant.getChr());
startField.setText("" + variant.getStart());
stopField.setText("" + variant.getEnd());
truthField.setSelectedItem(TruthStatus.UNKNOWN);
initGenotypeTypeField(variant);
validate();
}
private void cancelButtonActionPerformed(ActionEvent e) {
setVisible(false);
}
/**
* Save information to Mongo
*
* @param e
*/
private void okButtonActionPerformed(ActionEvent e) {
String callsetName = callsetField.getText();
TruthStatus truthStatus = (TruthStatus) truthField.getSelectedItem();
boolean isComplexEvent = isComplexEventCB.isSelected();
int allele0 = -1;
int allele1 = -1;
GenotypeType gtt = (GenotypeType) genotypeTypeField.getSelectedItem();
switch (gtt) {
case HOM_REF:
allele0 = allele1 = 0;
break;
case HOM_VAR:
allele0 = allele1 = 1;
break;
case HET:
allele0 = 0;
allele1 = 1;
break;
}
MongoVariantContext mvc = VariantReviewSource.createMVC(allele0, allele1, callsetName, sampleVC, truthStatus, isComplexEvent);
String errorMessage = addCall(this.dbSpecPath, mvc);
if (errorMessage != null) {
MessageUtils.showErrorMessage(errorMessage, new IOException(errorMessage));
} else {
setVisible(false);
//Find the track showing results, clear it to force a refresh
for (Track t : IGV.getInstance().getFeatureTracks()) {
if (t instanceof VariantTrack) {
((VariantTrack) t).clearPackedFeatures();
}
}
IGV.getInstance().revalidateTrackPanels();
}
}
/**
* Add the specified mvc to the specified database
*
* @param dbSpecPath
* @param mvc
* @return
*/
static String addCall(String dbSpecPath, MongoVariantContext mvc) {
NA12878DBArgumentCollection args = new NA12878DBArgumentCollection(dbSpecPath);
String errorMessage = null;
NA12878KnowledgeBase kb = null;
try {
kb = new NA12878KnowledgeBase(null, args);
WriteResult wr = kb.addCall(mvc);
errorMessage = wr.getError();
} catch (Exception ex) {
errorMessage = ex.getMessage();
if (errorMessage == null) errorMessage = "" + ex;
} finally {
if (kb != null) kb.close();
}
return errorMessage;
}
private void truthFieldItemStateChanged(ItemEvent e) {
if (truthField.getSelectedItem() == TruthStatus.FALSE_POSITIVE) {
genotypeTypeField.setSelectedItem(GenotypeType.NO_CALL);
genotypeTypeField.setEnabled(false);
} else {
genotypeTypeField.setEnabled(true);
initGenotypeTypeField(this.variantContext);
}
}
private void initGenotypeTypeField(VariantContext variant) {
String mutationString = null;
GenotypeType gtt = GenotypeType.NO_CALL;
String prefSampleName = VariantReviewPlugin.getPreferentialSampleName();
//If there is only one sample, or we find the preferential sample,
//use that data.
for (String sampleName : variant.getSampleNamesOrderedByName()) {
boolean isPref = sampleName.equalsIgnoreCase(prefSampleName);
if (isPref || mutationString == null) {
if(!variantContext.isBiallelic())
sampleVC = variantContext.subContextFromSamples(Collections.singleton(sampleName), true);
else
sampleVC = variantContext;
mutationString = ParsingUtils.join(",", ParsingUtils.sortList(sampleVC.getAlleles()));
Genotype genotype = sampleVC.getGenotype(sampleName);
gtt = genotype.getType();
if (isPref) break;
} else {
//If we have several samples with different mutations, don't know which
//to pick. Make that obvious to the user
if (gtt != sampleVC.getGenotype(sampleName).getType()) {
mutationString = "./.";
gtt = GenotypeType.UNAVAILABLE;
}
}
}
genotypeTypeField.setSelectedItem(gtt);
mutField.setText(mutationString);
mutField.setToolTipText(mutationString);
}
private void initComponents() {
// JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
dialogPane = new JPanel();
contentPanel = new JPanel();
panel1 = new JPanel();
label4 = new JLabel();
callsetField = new JTextField();
hSpacer1 = new JPanel(null);
panel2 = new JPanel();
label5 = new JLabel();
truthField = new JComboBox();
panel3 = new JPanel();
label6 = new JLabel();
genotypeTypeField = new JComboBox();
hSpacer2 = new JPanel(null);
panel7 = new JPanel();
label10 = new JLabel();
mutField = new JLabel();
hSpacer5 = new JPanel(null);
panel4 = new JPanel();
label7 = new JLabel();
chrField = new JLabel();
hSpacer3 = new JPanel(null);
panel5 = new JPanel();
label8 = new JLabel();
startField = new JLabel();
hSpacer4 = new JPanel(null);
panel6 = new JPanel();
label9 = new JLabel();
stopField = new JLabel();
panel8 = new JPanel();
hSpacer6 = new JPanel(null);
isComplexEventCB = new JCheckBox();
hSpacer7 = new JPanel(null);
buttonBar = new JPanel();
okButton = new JButton();
cancelButton = new JButton();
//======== this ========
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());
//======== dialogPane ========
{
dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
dialogPane.setPreferredSize(new Dimension(600, 150));
dialogPane.setLayout(new BorderLayout());
//======== contentPanel ========
{
contentPanel.setLayout(new BoxLayout(contentPanel, BoxLayout.X_AXIS));
//======== panel1 ========
{
panel1.setLayout(new BoxLayout(panel1, BoxLayout.PAGE_AXIS));
//---- label4 ----
label4.setText("Callset");
label4.setHorizontalAlignment(SwingConstants.CENTER);
label4.setMaximumSize(new Dimension(80, 16));
label4.setAlignmentX(0.5F);
panel1.add(label4);
//---- callsetField ----
callsetField.setMaximumSize(new Dimension(200, 1000));
callsetField.setMinimumSize(new Dimension(100, 28));
callsetField.setPreferredSize(new Dimension(100, 28));
panel1.add(callsetField);
}
contentPanel.add(panel1);
contentPanel.add(hSpacer1);
//======== panel2 ========
{
panel2.setLayout(new BoxLayout(panel2, BoxLayout.Y_AXIS));
//---- label5 ----
label5.setText("Truth");
label5.setHorizontalAlignment(SwingConstants.CENTER);
label5.setLabelFor(truthField);
label5.setHorizontalTextPosition(SwingConstants.CENTER);
label5.setAlignmentX(0.5F);
panel2.add(label5);
//---- truthField ----
truthField.addItemListener(new ItemListener() {
@Override
public void itemStateChanged(ItemEvent e) {
truthFieldItemStateChanged(e);
}
});
panel2.add(truthField);
}
contentPanel.add(panel2);
//======== panel3 ========
{
panel3.setLayout(new BoxLayout(panel3, BoxLayout.Y_AXIS));
//---- label6 ----
label6.setText("Genotype");
label6.setHorizontalAlignment(SwingConstants.CENTER);
label6.setAlignmentX(0.5F);
panel3.add(label6);
panel3.add(genotypeTypeField);
}
contentPanel.add(panel3);
//---- hSpacer2 ----
hSpacer2.setMinimumSize(new Dimension(20, 12));
hSpacer2.setPreferredSize(new Dimension(20, 10));
contentPanel.add(hSpacer2);
//======== panel7 ========
{
panel7.setMaximumSize(new Dimension(200, 1000));
panel7.setLayout(new BoxLayout(panel7, BoxLayout.Y_AXIS));
//---- label10 ----
label10.setText("Alleles");
label10.setHorizontalAlignment(SwingConstants.LEFT);
label10.setMaximumSize(new Dimension(200, 16));
panel7.add(label10);
//---- mutField ----
mutField.setText("A/G");
mutField.setMaximumSize(new Dimension(200, 1000));
panel7.add(mutField);
}
contentPanel.add(panel7);
//---- hSpacer5 ----
hSpacer5.setMinimumSize(new Dimension(20, 12));
hSpacer5.setPreferredSize(new Dimension(20, 10));
contentPanel.add(hSpacer5);
//======== panel4 ========
{
panel4.setMaximumSize(new Dimension(46, 1000));
panel4.setLayout(new BoxLayout(panel4, BoxLayout.Y_AXIS));
//---- label7 ----
label7.setText("Chr");
label7.setHorizontalAlignment(SwingConstants.LEFT);
label7.setVerticalAlignment(SwingConstants.TOP);
panel4.add(label7);
//---- chrField ----
chrField.setText("testChr");
chrField.setAlignmentY(0.0F);
chrField.setMaximumSize(new Dimension(46, 1000));
panel4.add(chrField);
}
contentPanel.add(panel4);
//---- hSpacer3 ----
hSpacer3.setMinimumSize(new Dimension(20, 12));
hSpacer3.setPreferredSize(new Dimension(20, 10));
contentPanel.add(hSpacer3);
//======== panel5 ========
{
panel5.setMaximumSize(new Dimension(500, 1000));
panel5.setMinimumSize(new Dimension(80, 32));
panel5.setPreferredSize(new Dimension(80, 32));
panel5.setLayout(new BoxLayout(panel5, BoxLayout.Y_AXIS));
//---- label8 ----
label8.setText("Start");
label8.setHorizontalAlignment(SwingConstants.LEFT);
label8.setMaximumSize(new Dimension(100, 16));
panel5.add(label8);
//---- startField ----
startField.setText("54321");
startField.setMaximumSize(new Dimension(500, 1000));
startField.setMinimumSize(new Dimension(400, 16));
startField.setPreferredSize(new Dimension(400, 16));
startField.setHorizontalTextPosition(SwingConstants.LEFT);
startField.setHorizontalAlignment(SwingConstants.LEFT);
panel5.add(startField);
}
contentPanel.add(panel5);
//---- hSpacer4 ----
hSpacer4.setMinimumSize(new Dimension(20, 12));
hSpacer4.setPreferredSize(new Dimension(20, 10));
contentPanel.add(hSpacer4);
//======== panel6 ========
{
panel6.setMaximumSize(new Dimension(500, 1000));
panel6.setMinimumSize(new Dimension(100, 32));
panel6.setPreferredSize(new Dimension(100, 32));
panel6.setLayout(new BoxLayout(panel6, BoxLayout.Y_AXIS));
//---- label9 ----
label9.setText("Stop");
label9.setHorizontalAlignment(SwingConstants.LEFT);
label9.setMaximumSize(new Dimension(100, 16));
panel6.add(label9);
//---- stopField ----
stopField.setText("12345");
stopField.setMaximumSize(new Dimension(500, 1000));
stopField.setHorizontalTextPosition(SwingConstants.LEADING);
stopField.setHorizontalAlignment(SwingConstants.LEFT);
stopField.setMinimumSize(new Dimension(400, 16));
stopField.setPreferredSize(new Dimension(400, 16));
panel6.add(stopField);
}
contentPanel.add(panel6);
}
dialogPane.add(contentPanel, BorderLayout.NORTH);
//======== panel8 ========
{
panel8.setLayout(new BoxLayout(panel8, BoxLayout.X_AXIS));
//---- hSpacer6 ----
hSpacer6.setMaximumSize(new Dimension(300, 32767));
hSpacer6.setPreferredSize(new Dimension(115, 10));
panel8.add(hSpacer6);
//---- isComplexEventCB ----
isComplexEventCB.setText("Complex Event");
panel8.add(isComplexEventCB);
panel8.add(hSpacer7);
}
dialogPane.add(panel8, 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("Save");
okButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
okButtonActionPerformed(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(800, 160);
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 panel1;
private JLabel label4;
private JTextField callsetField;
private JPanel hSpacer1;
private JPanel panel2;
private JLabel label5;
private JComboBox truthField;
private JPanel panel3;
private JLabel label6;
private JComboBox genotypeTypeField;
private JPanel hSpacer2;
private JPanel panel7;
private JLabel label10;
private JLabel mutField;
private JPanel hSpacer5;
private JPanel panel4;
private JLabel label7;
private JLabel chrField;
private JPanel hSpacer3;
private JPanel panel5;
private JLabel label8;
private JLabel startField;
private JPanel hSpacer4;
private JPanel panel6;
private JLabel label9;
private JLabel stopField;
private JPanel panel8;
private JPanel hSpacer6;
private JCheckBox isComplexEventCB;
private JPanel hSpacer7;
private JPanel buttonBar;
private JButton okButton;
private JButton cancelButton;
// JFormDesigner - End of variables declaration //GEN-END:variables
}