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TrackMenuUtils.java
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TrackMenuUtils.java
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/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.track;
import org.apache.commons.math.stat.StatUtils;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.PreferenceManager;
import org.broad.igv.blat.BlatClient;
import org.broad.igv.dev.api.api;
import org.broad.igv.feature.Exon;
import org.broad.igv.feature.IGVFeature;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.renderer.*;
import org.broad.igv.ui.DataRangeDialog;
import org.broad.igv.ui.HeatmapScaleDialog;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.UIConstants;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.panel.IGVPopupMenu;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.ui.util.UIUtilities;
import org.broad.igv.util.StringUtils;
import org.broad.igv.util.stats.KMPlotFrame;
import org.broad.tribble.Feature;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.*;
import java.util.List;
/**
* @author jrobinso
*/
public class TrackMenuUtils {
static Logger log = Logger.getLogger(TrackMenuUtils.class);
final static String LEADING_HEADING_SPACER = " ";
private static final WindowFunction[] ORDERED_WINDOW_FUNCTIONS = new WindowFunction[]{
WindowFunction.min,
WindowFunction.percentile2,
WindowFunction.percentile10,
WindowFunction.median,
WindowFunction.mean,
WindowFunction.percentile90,
WindowFunction.percentile98,
WindowFunction.max,
WindowFunction.none
};
private static List<TrackMenuItemBuilder> trackMenuItems = new ArrayList<TrackMenuItemBuilder>();
/**
* Called by plugins to add a listener, which is then called when TrackMenus are created
* to generate menu entries.
* @param builder
*/
@api
public static void addTrackMenuItemBuilder(TrackMenuItemBuilder builder){
trackMenuItems.add(builder);
}
/**
* Return a popup menu with items applicable to the collection of tracks.
*
* @param tracks
* @return
*/
public static IGVPopupMenu getPopupMenu(final Collection<Track> tracks, String title, TrackClickEvent te) {
if (log.isDebugEnabled()) {
log.debug("enter getPopupMenu");
}
IGVPopupMenu menu = new IGVPopupMenu();
JLabel popupTitle = new JLabel(LEADING_HEADING_SPACER + title, JLabel.CENTER);
popupTitle.setFont(UIConstants.boldFont);
if (popupTitle != null) {
menu.add(popupTitle);
menu.addSeparator();
}
addStandardItems(menu, tracks, te);
return menu;
}
/**
* Add menu items which have been added through the api, not known until runtime
* @param menu
* @param tracks
* @param te
*/
public static void addPluginItems(JPopupMenu menu, Collection<Track> tracks, TrackClickEvent te) {
List<JMenuItem> items = new ArrayList<JMenuItem>(0);
for(TrackMenuItemBuilder builder: trackMenuItems){
JMenuItem item = builder.build(tracks, te);
if(item != null){
items.add(item);
}
}
if(items.size() > 0){
menu.addSeparator();
for(JMenuItem item: items){
menu.add(item);
}
}
}
public static void addStandardItems(JPopupMenu menu, Collection<Track> tracks, TrackClickEvent te) {
boolean hasDataTracks = false;
boolean hasFeatureTracks = false;
boolean hasOtherTracks = false;
for (Track track : tracks) {
// TODO -- this is ugly, refactor to remove instanceof
if (track instanceof DataTrack) {
hasDataTracks = true;
} else if (track instanceof FeatureTrack) {
hasFeatureTracks = true;
} else {
hasOtherTracks = true;
}
if (hasDataTracks && hasFeatureTracks && hasOtherTracks) {
break;
}
}
boolean featureTracksOnly = hasFeatureTracks && !hasDataTracks && !hasOtherTracks;
boolean dataTracksOnly = !hasFeatureTracks && hasDataTracks && !hasOtherTracks;
addSharedItems(menu, tracks, hasFeatureTracks);
menu.addSeparator();
if (dataTracksOnly) {
addDataItems(menu, tracks);
} else if (featureTracksOnly) {
addFeatureItems(menu, tracks, te);
}
menu.addSeparator();
menu.add(getRemoveMenuItem(tracks));
}
public static void addZoomItems(JPopupMenu menu, final ReferenceFrame frame) {
if (FrameManager.isGeneListMode()) {
JMenuItem item = new JMenuItem("Reset panel to '" + frame.getName() + "'");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
frame.reset();
// TODO -- paint only panels for this frame
}
});
menu.add(item);
}
JMenuItem zoomOutItem = new JMenuItem("Zoom out");
zoomOutItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
frame.doZoomIncrement(-1);
}
});
menu.add(zoomOutItem);
JMenuItem zoomInItem = new JMenuItem("Zoom in");
zoomInItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
frame.doZoomIncrement(1);
}
});
menu.add(zoomInItem);
}
/**
* Return popup menu with items applicable to data tracks
*
* @return
*/
public static void addDataItems(JPopupMenu menu, final Collection<Track> tracks) {
if (log.isDebugEnabled()) {
log.debug("enter getDataPopupMenu");
}
final String[] labels = {"Heatmap", "Bar Chart", "Points", "Line Plot"};
final Class[] renderers = {HeatmapRenderer.class, BarChartRenderer.class,
PointsRenderer.class, LineplotRenderer.class
};
//JLabel popupTitle = new JLabel(LEADING_HEADING_SPACER + title, JLabel.CENTER);
JLabel rendererHeading = new JLabel(LEADING_HEADING_SPACER + "Type of Graph", JLabel.LEFT);
rendererHeading.setFont(UIConstants.boldFont);
menu.add(rendererHeading);
// Get existing selections
Set<Class> currentRenderers = new HashSet<Class>();
for (Track track : tracks) {
if (track.getRenderer() != null) {
currentRenderers.add(track.getRenderer().getClass());
}
}
// Create and renderer menu items
for (int i = 0; i < labels.length; i++) {
JCheckBoxMenuItem item = new JCheckBoxMenuItem(labels[i]);
final Class rendererClass = renderers[i];
if (currentRenderers.contains(rendererClass)) {
item.setSelected(true);
}
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
changeRenderer(tracks, rendererClass);
}
});
menu.add(item);
}
menu.addSeparator();
// Get union of all valid window functions for selected tracks
Set<WindowFunction> avaibleWindowFunctions = new HashSet();
for (Track track : tracks) {
avaibleWindowFunctions.addAll(track.getAvailableWindowFunctions());
}
avaibleWindowFunctions.add(WindowFunction.none);
// dataPopupMenu.addSeparator();
// Collection all window functions for selected tracks
Set<WindowFunction> currentWindowFunctions = new HashSet<WindowFunction>();
for (Track track : tracks) {
if (track.getWindowFunction() != null) {
currentWindowFunctions.add(track.getWindowFunction());
}
}
if (avaibleWindowFunctions.size() > 1 || currentWindowFunctions.size() > 1) {
JLabel statisticsHeading = new JLabel(LEADING_HEADING_SPACER + "Windowing Function", JLabel.LEFT);
statisticsHeading.setFont(UIConstants.boldFont);
menu.add(statisticsHeading);
for (final WindowFunction wf : ORDERED_WINDOW_FUNCTIONS) {
JCheckBoxMenuItem item = new JCheckBoxMenuItem(wf.getValue());
if (avaibleWindowFunctions.contains(wf) || currentWindowFunctions.contains(wf)) {
if (currentWindowFunctions.contains(wf)) {
item.setSelected(true);
}
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
changeStatType(wf.toString(), tracks);
}
});
menu.add(item);
}
}
menu.addSeparator();
}
menu.add(getDataRangeItem(tracks));
menu.add(getHeatmapScaleItem(tracks));
if (tracks.size() > 0) {
menu.add(getLogScaleItem(tracks));
}
menu.add(getAutoscaleItem(tracks));
menu.add(getShowDataRangeItem(tracks));
menu.addSeparator();
menu.add(getChangeKMPlotItem(tracks));
}
/**
* Return popup menu with items applicable to feature tracks
*
* @return
*/
private static void addFeatureItems(JPopupMenu featurePopupMenu, final Collection<Track> tracks, TrackClickEvent te) {
addDisplayModeItems(tracks, featurePopupMenu);
if (tracks.size() == 1) {
Track t = tracks.iterator().next();
Feature f = t.getFeatureAtMousePosition(te);
if (f != null) {
featurePopupMenu.addSeparator();
// If we are over an exon, copy its sequence instead of the entire feature.
if (f instanceof IGVFeature) {
double position = te.getChromosomePosition();
Collection<Exon> exons = ((IGVFeature) f).getExons();
if (exons != null) {
for (Exon exon : exons) {
if (position > exon.getStart() && position < exon.getEnd()) {
f = exon;
break;
}
}
}
}
featurePopupMenu.add(getCopyDetailsItem(f, te));
featurePopupMenu.add(getCopySequenceItem(f));
// featurePopupMenu.add(getBlatItem(f));
}
}
featurePopupMenu.addSeparator();
featurePopupMenu.add(getChangeFeatureWindow(tracks));
//---------------------//
//Track analysis
if (Globals.toolsMenuEnabled && tracks.size() >= 2) {
JMenuItem item = new JMenuItem("Create Overlap Track");
item.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
String newName = JOptionPane.showInputDialog(IGV.getMainFrame(), "Enter overlap track name: ", "Overlaps");
if (newName == null || newName.trim() == "") {
return;
}
CombinedFeatureSource source = new CombinedFeatureSource(tracks, CombinedFeatureSource.Operation.MULTIINTER);
Track newTrack = new FeatureTrack("", newName, source);
IGV.getInstance().getTrackPanel(IGV.FEATURE_PANEL_NAME).addTrack(newTrack);
IGV.getInstance().repaint();
}
});
item.setEnabled(CombinedFeatureSource.checkBEDToolsPathValid());
featurePopupMenu.add(item);
}
//--------------------//
}
/**
* Popup menu with items applicable to both feature and data tracks
*
* @return
*/
public static void addSharedItems(JPopupMenu menu, final Collection<Track> tracks, boolean hasFeatureTracks) {
//JLabel trackSettingsHeading = new JLabel(LEADING_HEADING_SPACER + "Track Settings", JLabel.LEFT);
//trackSettingsHeading.setFont(boldFont);
//menu.add(trackSettingsHeading);
menu.add(getTrackRenameItem(tracks));
String colorLabel = hasFeatureTracks
? "Change Track Color..." : "Change Track Color (Positive Values)...";
JMenuItem item = new JMenuItem(colorLabel);
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
changeTrackColor(tracks);
}
});
menu.add(item);
if (!hasFeatureTracks) {
// Change track color by attribute
item = new JMenuItem("Change Track Color (Negative Values)...");
item.setToolTipText(
"Change the alternate track color. This color is used when graphing negative values");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
changeAltTrackColor(tracks);
}
});
menu.add(item);
}
menu.add(getChangeTrackHeightItem(tracks));
menu.add(getChangeFontSizeItem(tracks));
}
private static void changeStatType(String statType, Collection<Track> selectedTracks) {
for (Track track : selectedTracks) {
track.setWindowFunction(WindowFunction.valueOf(statType));
}
refresh();
}
public static JMenuItem getTrackRenameItem(final Collection<Track> selectedTracks) {
// Change track height by attribute
JMenuItem item = new JMenuItem("Rename Track...");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
UIUtilities.invokeOnEventThread(new Runnable() {
public void run() {
renameTrack(selectedTracks);
}
});
}
});
if (selectedTracks.size() > 1) {
item.setEnabled(false);
}
return item;
}
private static JMenuItem getHeatmapScaleItem(final Collection<Track> selectedTracks) {
JMenuItem item = new JMenuItem("Set Heatmap Scale...");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
if (selectedTracks.size() > 0) {
ContinuousColorScale colorScale = selectedTracks.iterator().next().getColorScale();
HeatmapScaleDialog dlg = new HeatmapScaleDialog(IGV.getMainFrame(), colorScale);
dlg.setVisible(true);
if (!dlg.isCanceled()) {
colorScale = dlg.getColorScale();
// dlg.isFlipAxis());
for (Track track : selectedTracks) {
track.setColorScale(colorScale);
}
IGV.getInstance().repaint();
}
}
}
});
return item;
}
public static JMenuItem getDataRangeItem(final Collection<Track> selectedTracks) {
JMenuItem item = new JMenuItem("Set Data Range...");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
if (selectedTracks.size() > 0) {
// Create a datarange that spans the extent of prev tracks range
float mid = 0;
float min = Float.MAX_VALUE;
float max = Float.MIN_VALUE;
boolean drawBaseline = true;
boolean isLog = true;
for (Track t : selectedTracks) {
DataRange dr = t.getDataRange();
min = Math.min(min, dr.getMinimum());
max = Math.max(max, dr.getMaximum());
mid += dr.getBaseline();
drawBaseline &= dr.isDrawBaseline();
isLog &= dr.isLog();
}
mid /= selectedTracks.size();
if (mid < min) {
mid = min;
} else if (mid > max) {
min = max;
}
DataRange prevAxisDefinition = new DataRange(min, mid, max, drawBaseline, isLog);
DataRangeDialog dlg = new DataRangeDialog(IGV.getMainFrame(), prevAxisDefinition);
dlg.setVisible(true);
if (!dlg.isCanceled()) {
min = Math.min(dlg.getMax(), dlg.getMin());
max = Math.max(dlg.getMin(), dlg.getMax());
mid = dlg.getBase();
mid = Math.max(min, Math.min(mid, max));
DataRange axisDefinition = new DataRange(dlg.getMin(), mid, dlg.getMax(),
drawBaseline, dlg.isLog());
for (Track track : selectedTracks) {
track.setDataRange(axisDefinition);
if (track instanceof DataTrack) {
((DataTrack) track).setAutoScale(false);
}
}
IGV.getInstance().repaint();
}
}
}
});
return item;
}
private static JMenuItem getDrawBorderItem() {
// Change track height by attribute
final JCheckBoxMenuItem drawBorderItem = new JCheckBoxMenuItem("Draw borders");
drawBorderItem.setSelected(FeatureTrack.isDrawBorder());
drawBorderItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
FeatureTrack.setDrawBorder(drawBorderItem.isSelected());
IGV.getInstance().repaintDataPanels();
}
});
return drawBorderItem;
}
public static JMenuItem getLogScaleItem(final Collection<Track> selectedTracks) {
// Change track height by attribute
final JCheckBoxMenuItem logScaleItem = new JCheckBoxMenuItem("Log scale");
final boolean logScale = selectedTracks.iterator().next().getDataRange().isLog();
logScaleItem.setSelected(logScale);
logScaleItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
DataRange.Type scaleType = logScaleItem.isSelected() ?
DataRange.Type.LOG :
DataRange.Type.LINEAR;
for (Track t : selectedTracks) {
t.getDataRange().setType(scaleType);
}
IGV.getInstance().repaintDataPanels();
}
});
return logScaleItem;
}
private static JMenuItem getAutoscaleItem(final Collection<Track> selectedTracks) {
final JCheckBoxMenuItem autoscaleItem = new JCheckBoxMenuItem("Autoscale");
if (selectedTracks.size() == 0) {
autoscaleItem.setEnabled(false);
} else {
boolean autoScale = checkAutoscale(selectedTracks);
autoscaleItem.setSelected(autoScale);
autoscaleItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
boolean autoScale = autoscaleItem.isSelected();
for (Track t : selectedTracks) {
if (t instanceof DataTrack) {
((DataTrack) t).setAutoScale(autoScale);
}
}
IGV.getInstance().repaintDataPanels();
}
});
}
return autoscaleItem;
}
private static boolean checkAutoscale(Collection<Track> selectedTracks) {
boolean autoScale = false;
for (Track t : selectedTracks) {
if (t instanceof DataTrack && ((DataTrack) t).isAutoScale()) {
autoScale = true;
break;
}
}
return autoScale;
}
public static JMenuItem getShowDataRangeItem(final Collection<Track> selectedTracks) {
final JCheckBoxMenuItem item = new JCheckBoxMenuItem("Show Data Range");
if (selectedTracks.size() == 0) {
item.setEnabled(false);
} else {
boolean showDataRange = true;
for (Track t : selectedTracks) {
if (!t.isShowDataRange()) {
showDataRange = false;
break;
}
}
item.setSelected(showDataRange);
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
boolean showDataRange = item.isSelected();
for (Track t : selectedTracks) {
if (t instanceof DataTrack) {
((DataTrack) t).setShowDataRange(showDataRange);
}
}
IGV.getInstance().repaintDataPanels();
}
});
}
return item;
}
public static void addDisplayModeItems(final Collection<Track> tracks, JPopupMenu menu) {
// Find "most representative" state from track collection
Map<Track.DisplayMode, Integer> counts = new HashMap<Track.DisplayMode, Integer>(Track.DisplayMode.values().length);
Track.DisplayMode currentMode = null;
for (Track t : tracks) {
Track.DisplayMode mode = t.getDisplayMode();
if (counts.containsKey(mode)) {
counts.put(mode, counts.get(mode) + 1);
} else {
counts.put(mode, 1);
}
}
int maxCount = -1;
for (Map.Entry<Track.DisplayMode, Integer> count : counts.entrySet()) {
if (count.getValue() > maxCount) {
currentMode = count.getKey();
maxCount = count.getValue();
}
}
ButtonGroup group = new ButtonGroup();
Map<String, Track.DisplayMode> modes = new LinkedHashMap<String, Track.DisplayMode>(4);
modes.put("Collapsed", Track.DisplayMode.COLLAPSED);
modes.put("Expanded", Track.DisplayMode.EXPANDED);
modes.put("Squished", Track.DisplayMode.SQUISHED);
boolean showAS = Boolean.parseBoolean(System.getProperty("showAS", "false"));
if (showAS) {
modes.put("Alternative Splice", Track.DisplayMode.ALTERNATIVE_SPLICE);
}
for (final Map.Entry<String, Track.DisplayMode> entry : modes.entrySet()) {
JRadioButtonMenuItem mm = new JRadioButtonMenuItem(entry.getKey());
mm.setSelected(currentMode == entry.getValue());
mm.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
setTrackDisplayMode(tracks, entry.getValue());
refresh();
}
});
group.add(mm);
menu.add(mm);
}
}
private static void setTrackDisplayMode(Collection<Track> tracks, Track.DisplayMode mode) {
for (Track t : tracks) {
t.setDisplayMode(mode);
}
}
public static JMenuItem getRemoveMenuItem(final Collection<Track> selectedTracks) {
boolean multiple = selectedTracks.size() > 1;
JMenuItem item = new JMenuItem("Remove Track" + (multiple ? "s" : ""));
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
if (selectedTracks.isEmpty()) {
return;
}
StringBuffer buffer = new StringBuffer();
for (Track track : selectedTracks) {
buffer.append("\n\t");
buffer.append(track.getName());
}
String deleteItems = buffer.toString();
JTextArea textArea = new JTextArea();
textArea.setEditable(false);
JScrollPane scrollPane = new JScrollPane(textArea);
textArea.setText(deleteItems);
JOptionPane optionPane = new JOptionPane(scrollPane,
JOptionPane.PLAIN_MESSAGE,
JOptionPane.YES_NO_OPTION);
optionPane.setPreferredSize(new Dimension(550, 500));
JDialog dialog = optionPane.createDialog(IGV.getMainFrame(), "Remove The Following Tracks");
dialog.setVisible(true);
Object choice = optionPane.getValue();
if ((choice == null) || (JOptionPane.YES_OPTION != ((Integer) choice).intValue())) {
return;
}
IGV.getInstance().removeTracks(selectedTracks);
IGV.getInstance().doRefresh();
}
});
return item;
}
public static void changeRenderer(final Collection<Track> selectedTracks, Class rendererClass) {
for (Track track : selectedTracks) {
// TODO -- a temporary hack to facilitate RNAi development
if (track.getTrackType() == TrackType.RNAI) {
if (rendererClass == BarChartRenderer.class) {
rendererClass = RNAiBarChartRenderer.class;
}
}
track.setRendererClass(rendererClass);
}
refresh();
}
public static void renameTrack(final Collection<Track> selectedTracks) {
if (selectedTracks.isEmpty()) {
return;
}
Track t = selectedTracks.iterator().next();
String newName = JOptionPane.showInputDialog(IGV.getMainFrame(), "Enter new name: ", t.getName());
if (newName == null || newName.trim() == "") {
return;
}
t.setName(newName);
refresh();
}
public static void changeTrackHeight(final Collection<Track> selectedTracks) {
if (selectedTracks.isEmpty()) {
return;
}
final String parameter = "Track height";
int value = getIntValue(parameter, getRepresentativeTrackHeight(selectedTracks));
if (value == Integer.MIN_VALUE) {
return;
}
value = Math.max(0, value);
for (Track track : selectedTracks) {
track.setHeight(value);
}
refresh();
}
public static void changeFeatureVisibilityWindow(final Collection<Track> selectedTracks) {
Collection<Track> featureTracks = new ArrayList(selectedTracks.size());
for (Track t : selectedTracks) {
if (t instanceof FeatureTrack) {
featureTracks.add(t);
}
}
if (featureTracks.isEmpty()) {
return;
}
int origValue = featureTracks.iterator().next().getVisibilityWindow();
double origValueKB = (origValue / 1000.0);
double value = getNumericValue("Visibility window (kb)", origValueKB);
if (value == Integer.MIN_VALUE) {
return;
}
for (Track track : featureTracks) {
track.setVisibilityWindow((int) (value * 1000));
}
refresh();
}
public static void changeFontSize(final Collection<Track> selectedTracks) {
if (selectedTracks.isEmpty()) {
return;
}
final String parameter = "Font size";
int defaultValue = selectedTracks.iterator().next().getFontSize();
int value = getIntValue(parameter, defaultValue);
if (value == Integer.MIN_VALUE) {
return;
}
for (Track track : selectedTracks) {
track.setFontSize(value);
}
refresh();
}
public static int getIntValue(String parameter, int value) {
while (true) {
String height = JOptionPane.showInputDialog(
IGV.getMainFrame(), parameter + ": ",
String.valueOf(value));
if ((height == null) || height.trim().equals("")) {
return Integer.MIN_VALUE; // <= the logical "null" value
}
try {
value = Integer.parseInt(height);
return value;
} catch (NumberFormatException numberFormatException) {
JOptionPane.showMessageDialog(IGV.getMainFrame(),
parameter + " must be an integer number.");
}
}
}
public static double getNumericValue(String parameter, double value) {
while (true) {
String height = JOptionPane.showInputDialog(
IGV.getMainFrame(), parameter + ": ",
String.valueOf(value));
if ((height == null) || height.trim().equals("")) {
return Double.MIN_VALUE; // <= the logical "null" value
}
try {
value = Double.parseDouble(height);
return value;
} catch (NumberFormatException numberFormatException) {
MessageUtils.showMessage(parameter + " must be a number.");
}
}
}
public static void changeTrackColor(final Collection<Track> selectedTracks) {
if (selectedTracks.isEmpty()) {
return;
}
Color currentSelection = selectedTracks.iterator().next().getColor();
Color color = UIUtilities.showColorChooserDialog(
"Select Track Color (Positive Values)",
currentSelection);
if (color != null) {
for (Track track : selectedTracks) {
track.setColor(color);
}
refresh();
}
}
public static void changeAltTrackColor(final Collection<Track> selectedTracks) {
if (selectedTracks.isEmpty()) {
return;
}
Color currentSelection = selectedTracks.iterator().next().getColor();
Color color = UIUtilities.showColorChooserDialog(
"Select Track Color (Negative Values)",
currentSelection);
if (color == null) {
return;
}
for (Track track : selectedTracks) {
track.setAltColor(color);
}
refresh();
}
public static JMenuItem getCopyDetailsItem(final Feature f, final TrackClickEvent evt) {
JMenuItem item = new JMenuItem("Copy Details to Clipboard");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
ReferenceFrame frame = evt.getFrame();
int mouseX = evt.getMouseEvent().getX();
double location = frame.getChromosomePosition(mouseX);
if (f instanceof IGVFeature) {
String details = ((IGVFeature) f).getValueString(location, null);
if (details != null) {
details = details.replace("<br>", System.getProperty("line.separator"));
details += System.getProperty("line.separator") +
f.getChr() + ":" + (f.getStart() + 1) + "-" + f.getEnd();
StringUtils.copyTextToClipboard(details);
}
}
}
});
return item;
}
public static JMenuItem getCopySequenceItem(final Feature f) {
JMenuItem item = new JMenuItem("Copy Sequence");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
Genome genome = GenomeManager.getInstance().getCurrentGenome();
IGV.copySequenceToClipboard(genome, f.getChr(), f.getStart(), f.getEnd());
}
});
return item;
}
public static JMenuItem getBlatItem(final Feature f) {
JMenuItem item = new JMenuItem("Blat Sequence");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
BlatClient.doBlatQuery(f.getChr(), f.getStart(), f.getEnd());
}
});
return item;
}
/**
* Return a representative track height to use as the default. For now
* using the median track height.
*
* @return
*/
public static int getRepresentativeTrackHeight(Collection<Track> tracks) {
double[] heights = new double[tracks.size()];
int i = 0;
for (Track track : tracks) {