/*
* 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.
*/
package org.broad.igv.ga4gh;
import org.broad.igv.feature.genome.GenomeListItem;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.util.LongRunningTask;
import org.broad.igv.util.ResourceLocator;
import java.awt.*;
import java.awt.event.*;
import java.io.IOException;
import java.util.Arrays;
import javax.swing.*;
import javax.swing.border.*;
import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.DefaultTreeModel;
import javax.swing.tree.TreeNode;
import javax.swing.tree.TreePath;
/**
* @author James Robinson
*/
public class Ga4ghLoadDialog extends JDialog {
private final DefaultTreeModel treeModel;
Ga4ghProvider[] providers;
String selectedId;
public Ga4ghLoadDialog(Frame owner, Ga4ghProvider[] providers) {
super(owner);
initComponents();
this.providers = providers;
treeModel = new DefaultTreeModel(createNodes(providers));
this.selectionTree.setModel(treeModel);
}
private DefaultMutableTreeNode createNodes(Ga4ghProvider[] providers) {
DefaultMutableTreeNode top = new DefaultMutableTreeNode("Ga4gh");
for (Ga4ghProvider provider : providers) {
DefaultMutableTreeNode providerNode = new DefaultMutableTreeNode(provider.getName());
top.add(providerNode);
for (Ga4ghDataset dataset : provider.getDatasets()) {
DefaultMutableTreeNode datasetNode = new DefaultMutableTreeNode(dataset.getName());
providerNode.add(datasetNode);
for (Ga4ghReadset readset : dataset.getReadsets()) {
DefaultMutableTreeNode readsetNode = new DefaultMutableTreeNode(new LeafNode(provider, readset));
datasetNode.add(readsetNode);
}
}
}
return top;
}
private void loadButtonActionPerformed(ActionEvent e) {
setVisible(false);
LongRunningTask.submit(new Runnable() {
public void run() {
TreePath[] paths = selectionTree.getSelectionPaths();
for (TreePath path : paths) {
DefaultMutableTreeNode obj = (DefaultMutableTreeNode) path.getLastPathComponent();
Object userObject = obj.getUserObject();
if (userObject instanceof LeafNode) {
Ga4ghProvider provider = ((LeafNode) userObject).provider;
Ga4ghReadset readSet = ((LeafNode) userObject).readset;
setGenome(readSet.getGenomeId());
loadTrack(readSet.getId(), provider, readSet.getName());
}
}
}
});
}
private void cancelButtonActionPerformed(ActionEvent e) {
selectedId = null;
setVisible(false);
}
class LeafNode {
Ga4ghProvider provider;
Ga4ghReadset readset;
LeafNode(Ga4ghProvider provider, Ga4ghReadset readset) {
this.provider = provider;
this.readset = readset;
}
public String toString() {
return readset.getName();
}
}
private void loadTrack(String readsetId, Ga4ghProvider provider, String name) {
ResourceLocator locator = new ResourceLocator(readsetId);
locator.setName(name);
locator.setType(Ga4ghAPIHelper.RESOURCE_TYPE);
locator.setAttribute("provider", provider);
IGV.getInstance().loadTracks(Arrays.asList(locator));
}
private void setGenome(String genomeId) {
if (genomeId != null && !genomeId.equals(GenomeManager.getInstance().getGenomeId())) {
GenomeListItem item = GenomeManager.getInstance().findGenomeListItemById(genomeId);
if (item != null) {
GenomeManager.getInstance().loadGenomeById(genomeId);
}
}
}
private void initComponents() {
// JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
dialogPane = new JPanel();
contentPanel = new JPanel();
scrollPane1 = new JScrollPane();
selectionTree = new JTree();
buttonBar = new JPanel();
loadButton = new JButton();
cancelButton = new JButton();
label1 = new JLabel();
//======== this ========
setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
setTitle("GA4GH Prototype");
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());
//======== dialogPane ========
{
dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
dialogPane.setLayout(new BorderLayout());
//======== contentPanel ========
{
contentPanel.setLayout(new BoxLayout(contentPanel, BoxLayout.X_AXIS));
//======== scrollPane1 ========
{
scrollPane1.setViewportView(selectionTree);
}
contentPanel.add(scrollPane1);
}
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};
//---- loadButton ----
loadButton.setText("Load");
loadButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
loadButtonActionPerformed(e);
}
});
buttonBar.add(loadButton, 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);
//---- label1 ----
label1.setText("Select a readset to load");
dialogPane.add(label1, BorderLayout.NORTH);
}
contentPane.add(dialogPane, BorderLayout.CENTER);
setSize(795, 690);
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 JScrollPane scrollPane1;
private JTree selectionTree;
private JPanel buttonBar;
private JButton loadButton;
private JButton cancelButton;
private JLabel label1;
// JFormDesigner - End of variables declaration //GEN-END:variables
}