/*
* 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.
*/
/*
* GenomeSelectionDialog.java
*
* Created on November 8, 2007, 3:51 PM
*/
package org.broad.igv.ui;
import org.broad.igv.DirectoryManager;
import org.broad.igv.feature.genome.GenomeListItem;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.ui.util.UIUtilities;
import org.broad.igv.util.LongRunningTask;
import org.broad.igv.util.RunnableResult;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
import java.awt.*;
import java.awt.event.*;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
/**
* Dialog box for selecting genomes. User can choose from a list,
* which is filtered according to text box input
*/
public class GenomeSelectionDialog extends javax.swing.JDialog {
private boolean isCanceled = true;
private List<GenomeListItem> selectedValuesList = null;
private List<GenomeListItem> allListItems;
private DefaultListModel genomeListModel;
/**
* @param parent
* @param listSelectionMode Selection mode for genome list
*/
public GenomeSelectionDialog(java.awt.Frame parent, Collection<GenomeListItem> inputListItems, final int listSelectionMode) {
super(parent);
initComponents();
UIUtilities.invokeOnEventThread(new Runnable() {
@Override
public void run() {
genomeList.setSelectionMode(listSelectionMode);
}
});
initData(inputListItems);
downloadSequenceCB.setVisible(listSelectionMode == ListSelectionModel.SINGLE_SELECTION);
}
private void initData(Collection<GenomeListItem> inputListItems) {
this.allListItems = new ArrayList<GenomeListItem>(inputListItems);
//We don't show those currently in the box
//We only check by id, as some local genomes might be the same except for path
for(GenomeListItem gli: GenomeManager.getInstance().getGenomeListItems()){
removeById(gli.getId());
}
this.allListItems.removeAll(GenomeManager.getInstance().getGenomeListItems());
rebuildGenomeList();
}
private void removeById(String id){
int ci = 0;
for(; ci < this.allListItems.size(); ci++){
GenomeListItem gli = this.allListItems.get(ci);
if(gli.getId().equals(id)){
break;
}
}
if(ci < this.allListItems.size()) this.allListItems.remove(ci);
}
private void rebuildGenomeList() {
String filterText = genomeFilter.getText().trim().toLowerCase();
rebuildGenomeList(filterText);
}
/**
* Filter the list of displayed genomes so we only show this
* with the text the user entered.
*/
private void rebuildGenomeList(String filterText) {
if (genomeListModel == null) {
genomeListModel = new DefaultListModel();
UIUtilities.invokeOnEventThread(new Runnable() {
@Override
public void run() {
genomeList.setModel(genomeListModel);
}
});
}
genomeListModel.clear();
filterText = filterText.toLowerCase().trim();
for (GenomeListItem listItem : allListItems) {
if (listItem.getDisplayableName().toLowerCase().contains(filterText)) {
genomeListModel.addElement(listItem);
}
}
}
/**
* If a genome is single clicked, we just store the selection.
* When a genome is double clicked, we treat that as the user
* wanting to load the genome.
*
* @param e
*/
private void genomeListMouseClicked(MouseEvent e) {
switch (e.getClickCount()) {
case 1:
List<GenomeListItem> selValues = genomeList.getSelectedValuesList();
downloadSequenceCB.setEnabled(selValues != null && selValues.size() == 1);
break;
case 2:
okButtonActionPerformed(null);
break;
}
}
private void genomeEntryKeyReleased(KeyEvent e) {
rebuildGenomeList(genomeFilter.getText());
}
public List<GenomeListItem> getSelectedValuesList() {
return selectedValuesList;
}
public boolean downloadSequence(){
return !isCanceled() && downloadSequenceCB.isEnabled() && downloadSequenceCB.isSelected();
}
static void downloadGenome(final Frame dialogsParent, final GenomeListItem genomeListItem) {
final File targetDir = DirectoryManager.getGenomeCacheDirectory();
if(!targetDir.exists()){
targetDir.mkdirs();
}
Runnable runnable = new Runnable() {
@Override
public void run() {
try {
RunnableResult result = GenomeManager.getInstance().downloadWholeGenome(genomeListItem.getLocation(), targetDir, dialogsParent);
if(result == RunnableResult.FAILURE){
throw new IOException("Unknown Failure");
}
} catch (IOException e) {
String msg = String.format("Error downloading genome %s from %s: %s", genomeListItem.getId(), genomeListItem.getLocation(), e.getMessage());
MessageUtils.showErrorMessage(msg, e);
}
}
};
LongRunningTask.submit(runnable);
}
public boolean isCanceled() {
return isCanceled;
}
/**
* This method is called from within the constructor to
* initialize the form.
* WARNING: Do NOT modify this code. The content of this method is
* always regenerated by the Form Editor.
*/
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
private void initComponents() {
dialogPane = new JPanel();
contentPanel = new JPanel();
textArea1 = new JTextArea();
filterPanel = new JPanel();
label1 = new JLabel();
genomeFilter = new JTextField();
scrollPane1 = new JScrollPane();
genomeList = new JList7<GenomeListItem>();
downloadSequenceCB = new JCheckBox();
buttonBar = new JPanel();
okButton = new JButton();
cancelButton = new JButton();
//======== this ========
setModal(true);
setTitle("Genomes to add to list");
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());
//======== dialogPane ========
{
dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
dialogPane.setPreferredSize(new Dimension(350, 500));
dialogPane.setLayout(new BorderLayout());
//======== contentPanel ========
{
contentPanel.setLayout(new BoxLayout(contentPanel, BoxLayout.Y_AXIS));
//---- textArea1 ----
textArea1.setText("Selected genomes will be added to the genome dropdown list.");
textArea1.setLineWrap(true);
textArea1.setWrapStyleWord(true);
textArea1.setBackground(UIManager.getColor("Button.background"));
textArea1.setRows(2);
textArea1.setMaximumSize(new Dimension(2147483647, 60));
textArea1.setRequestFocusEnabled(false);
textArea1.setEditable(false);
contentPanel.add(textArea1);
//======== filterPanel ========
{
filterPanel.setMaximumSize(new Dimension(2147483647, 28));
filterPanel.setLayout(new GridBagLayout());
((GridBagLayout)filterPanel.getLayout()).columnWidths = new int[] {0, 0, 0};
((GridBagLayout)filterPanel.getLayout()).rowHeights = new int[] {0, 0};
((GridBagLayout)filterPanel.getLayout()).columnWeights = new double[] {1.0, 1.0, 1.0E-4};
((GridBagLayout)filterPanel.getLayout()).rowWeights = new double[] {1.0, 1.0E-4};
//---- label1 ----
label1.setText("Filter:");
label1.setLabelFor(genomeFilter);
label1.setRequestFocusEnabled(false);
filterPanel.add(label1, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.WEST, GridBagConstraints.VERTICAL,
new Insets(0, 0, 0, 0), 0, 0));
//---- genomeFilter ----
genomeFilter.setToolTipText("Filter genome list");
genomeFilter.setPreferredSize(new Dimension(220, 28));
genomeFilter.setMinimumSize(new Dimension(180, 28));
genomeFilter.setAlignmentX(0.0F);
genomeFilter.addKeyListener(new KeyAdapter() {
@Override
public void keyReleased(KeyEvent e) {
genomeEntryKeyReleased(e);
}
});
filterPanel.add(genomeFilter, new GridBagConstraints(1, 0, 1, 1, 1.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 0), 0, 0));
}
contentPanel.add(filterPanel);
//======== scrollPane1 ========
{
//---- genomeList ----
genomeList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
genomeList.addMouseListener(new MouseAdapter() {
@Override
public void mouseClicked(MouseEvent e) {
genomeListMouseClicked(e);
}
});
scrollPane1.setViewportView(genomeList);
}
contentPanel.add(scrollPane1);
//---- downloadSequenceCB ----
downloadSequenceCB.setText("Download Sequence");
downloadSequenceCB.setAlignmentX(1.0F);
downloadSequenceCB.setToolTipText("Download the full sequence for this organism. Note that these files can be very large (human is about 3 gigabytes)");
downloadSequenceCB.setMaximumSize(new Dimension(1000, 23));
downloadSequenceCB.setPreferredSize(new Dimension(300, 23));
downloadSequenceCB.setMinimumSize(new Dimension(300, 23));
contentPanel.add(downloadSequenceCB);
}
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("OK");
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, 5, 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, 5, 0), 0, 0));
}
dialogPane.add(buttonBar, BorderLayout.SOUTH);
}
contentPane.add(dialogPane, BorderLayout.CENTER);
pack();
setLocationRelativeTo(getOwner());
}// </editor-fold>//GEN-END:initComponents
private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
isCanceled = true;
selectedValuesList = null;
setVisible(false);
dispose();
}//GEN-LAST:event_cancelButtonActionPerformed
private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
isCanceled = false;
selectedValuesList = genomeList.getSelectedValuesList();
setVisible(false);
dispose();
}//GEN-LAST:event_okButtonActionPerformed
// Variables declaration - do not modify//GEN-BEGIN:variables
// Generated using JFormDesigner non-commercial license
private JPanel dialogPane;
private JPanel contentPanel;
private JTextArea textArea1;
private JPanel filterPanel;
private JLabel label1;
private JTextField genomeFilter;
private JScrollPane scrollPane1;
private JList7<GenomeListItem> genomeList;
private JCheckBox downloadSequenceCB;
private JPanel buttonBar;
private JButton okButton;
private JButton cancelButton;
// End of variables declaration//GEN-END:variables
}