private static boolean checkSize(ResourceLocator locator) {
if (!PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SHOW_SIZE_WARNING)) {
return true;
}
final String path = locator.getPath();
long size = FileUtils.getLength(path);
int maxSize = 50000000; // 50 mb
if (path.endsWith(".gz") || path.endsWith(".bgz")) {
maxSize /= 4;
}
if (size > maxSize) {
String message =
"The file "
+ path
+ " is large ("
+ (size / 1000000)
+ " mb). It is recommended "
+ "that large files be converted to the binary <i>.tdf</i> format using the IGVTools "
+ "<b>tile</b> command. Loading unconverted ascii fies of this size can lead to poor "
+ "performance or unresponsiveness (freezing). "
+ "<br><br>IGVTools can be launched from the <b>Tools</b> menu or separately as a "
+ "command line program. See the user guide for more details.<br><br>Click <b>Continue</b> "
+ "to continue loading, or <b>Cancel</b> to skip this file.";
return ConfirmDialog.optionallyShowConfirmDialog(
message, PreferenceManager.SHOW_SIZE_WARNING, true);
}
return true;
}
private JMenu createGenomeSpaceMenu() {
JMenu menu = new JMenu("GenomeSpace");
MenuAction menuAction = null;
menuAction = new LoadFromGSMenuAction("Load File from GenomeSpace...", KeyEvent.VK_U, igv);
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menu.addSeparator();
menuAction =
new LoadGenomeFromGSMenuAction("Load Genome from GenomeSpace...", KeyEvent.VK_Z, igv);
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menu.addSeparator();
menuAction = new GSSaveSessionMenuAction("Save Session to GenomeSpace...", igv);
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction = new GSOpenSessionMenuAction("Load Session from GenomeSpace...", igv);
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menu.add(new JSeparator());
menuAction =
new MenuAction("Logout") {
@Override
public void actionPerformed(ActionEvent e) {
GSUtils.logout();
if (MessageUtils.confirm(
"You must shutdown IGV to complete the GenomeSpace logout. Shutdown now?")) {
doExitApplication();
}
}
};
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menu.add(new JSeparator());
menuAction =
new MenuAction("Register... ") {
@Override
public void actionPerformed(ActionEvent e) {
try {
BrowserLauncher.openURL(GENOMESPACE_REG_PAGE);
} catch (IOException ex) {
log.error("Error opening browser", ex);
}
}
};
menuAction.setToolTipText(GENOMESPACE_REG_TOOLTIP);
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menu.setVisible(
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.GENOME_SPACE_ENABLE));
return menu;
}
private static synchronized String getDMHost() {
try {
return (new URL(
PreferenceManager.getInstance().get(PreferenceManager.GENOME_SPACE_DM_SERVER)))
.getHost();
} catch (MalformedURLException e) {
log.error(e);
return null;
}
}
private static ConnectionWrapper createConnection() {
String driver = "com.mysql.jdbc.Driver";
try {
Class.forName(driver).newInstance();
} catch (Exception e) {
e.printStackTrace();
}
final PreferenceManager preferenceManager = PreferenceManager.getInstance();
String host = preferenceManager.get(PreferenceManager.DB_HOST);
String db = preferenceManager.get(PreferenceManager.DB_NAME);
String port = preferenceManager.get(PreferenceManager.DB_PORT);
String url = "jdbc:mysql://" + host;
if (!port.equals("-1")) {
url += ":" + port;
}
url += "/" + db;
return connect(url);
}
/**
* Method description
*
* @param g
*/
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
if (PreferenceManager.getInstance().getAsBoolean(PreferenceManager.ENABLE_ANTIALISING)) {
((Graphics2D) g)
.setRenderingHint(
RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
}
paintLegend(g);
((Graphics2D) g)
.setRenderingHint(
RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_DEFAULT);
}
/** Test if the file type can be "tiled". */
private static void validateIsTilable(String typeString) {
boolean affective =
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.AFFECTIVE_ENABLE);
if (!(typeString.endsWith("cn")
|| typeString.endsWith("igv")
|| typeString.endsWith("wig")
||
// ifile.toLowerCase().endsWith("cpg.txt") ||
typeString.endsWith("ewig")
|| typeString.endsWith("cn")
|| typeString.endsWith("snp")
|| typeString.endsWith("xcn")
|| typeString.endsWith("gct")
|| typeString.endsWith("tab")
|| typeString.endsWith("mage-tab")
|| typeString.endsWith("bedgraph")
|| Preprocessor.isAlignmentFile(typeString)
|| affective)) {
throw new PreprocessingException(
"Tile command not supported for files of type: " + typeString);
}
}
private static ConnectionWrapper connect(String url) {
try {
return new ConnectionWrapper(DriverManager.getConnection(url, username, password));
} catch (SQLException e) {
int errorCode = e.getErrorCode();
if (errorCode == 1044 || errorCode == 1045) {
String host = PreferenceManager.getInstance().get(PreferenceManager.DB_HOST);
Frame parent = Globals.isHeadless() ? null : IGV.getMainFrame();
LoginDialog dlg = new LoginDialog(parent, false, host, false);
dlg.setVisible(true);
if (dlg.isCanceled()) {
throw new RuntimeException("Must login to access" + host);
}
username = dlg.getUsername();
password = new String(dlg.getPassword());
return connect(url);
} else {
MessageUtils.showMessage("<html>Error connecting to database: <br>" + e.getMessage());
return null;
}
}
}
private JMenu createViewMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>();
MenuAction menuAction = null;
// Preferences
menuAction =
new MenuAction("Preferences...", null, KeyEvent.VK_P) {
@Override
public void actionPerformed(ActionEvent e) {
UIUtilities.invokeOnEventThread(
new Runnable() {
public void run() {
IGV.getInstance().doViewPreferences();
}
});
}
};
menuAction.setToolTipText(PREFERENCE_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction =
new MenuAction("Color Legends ...", null, KeyEvent.VK_H) {
@Override
public void actionPerformed(ActionEvent e) {
(new LegendDialog(IGV.getMainFrame())).setVisible(true);
}
};
menuAction.setToolTipText(SHOW_HEATMAP_LEGEND_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuItems.add(new JSeparator());
menuAction =
new MenuAction("Show Name Panel", null, KeyEvent.VK_A) {
@Override
public void actionPerformed(ActionEvent e) {
JCheckBoxMenuItem menuItem = (JCheckBoxMenuItem) e.getSource();
if (menuItem.isSelected()) {
IGV.getInstance().getMainPanel().expandNamePanel();
} else {
IGV.getInstance().getMainPanel().collapseNamePanel();
}
IGV.getInstance().doRefresh();
}
};
boolean isShowing = IGV.getInstance().getMainPanel().isExpanded();
JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem();
menuItem.setSelected(isShowing);
menuItem.setAction(menuAction);
menuItems.add(menuItem);
JMenuItem panelWidthmenuItem = new JMenuItem();
menuAction =
new MenuAction("Set Name Panel Width...", null, KeyEvent.VK_A) {
@Override
public void actionPerformed(ActionEvent e) {
MainPanel mainPanel = IGV.getInstance().getMainPanel();
String currentValue = String.valueOf(mainPanel.getNamePanelWidth());
String newValue =
MessageUtils.showInputDialog("Enter track name panel width: ", currentValue);
if (newValue != null) {
try {
Integer w = Integer.parseInt(newValue);
if (w <= 0 || w == 1000) throw new NumberFormatException();
PreferenceManager.getInstance().put(PreferenceManager.NAME_PANEL_WIDTH, newValue);
mainPanel.setNamePanelWidth(w);
} catch (NumberFormatException ex) {
MessageUtils.showErrorMessage(
"Error: value must be a positive integer < 1000.", ex);
}
}
}
};
panelWidthmenuItem.setAction(menuAction);
menuItems.add(panelWidthmenuItem);
// Hide or Show the attribute panels
boolean isShow =
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SHOW_ATTRIBUTE_VIEWS_KEY);
IGV.getInstance().doShowAttributeDisplay(isShow); // <= WEIRD doing IGV.getInstance() here!
menuAction =
new MenuAction("Show Attribute Display", null, KeyEvent.VK_A) {
@Override
public void actionPerformed(ActionEvent e) {
JCheckBoxMenuItem menuItem = (JCheckBoxMenuItem) e.getSource();
PreferenceManager.getInstance().setShowAttributeView(menuItem.getState());
IGV.getInstance().getMainPanel().invalidate();
IGV.getInstance().doRefresh();
}
};
menuItem = MenuAndToolbarUtils.createMenuItem(menuAction, isShow);
menuItems.add(menuItem);
menuAction =
new MenuAction("Select Attributes to Show...", null, KeyEvent.VK_S) {
@Override
public void actionPerformed(ActionEvent e) {
IGV.getInstance().doSelectDisplayableAttribute();
}
};
menuAction.setToolTipText(SELECT_DISPLAYABLE_ATTRIBUTES_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction =
new MenuAction("Show Header Panel", null, KeyEvent.VK_A) {
@Override
public void actionPerformed(ActionEvent e) {
JCheckBoxMenuItem menuItem = (JCheckBoxMenuItem) e.getSource();
if (menuItem.isSelected()) {
IGV.getInstance().getMainPanel().restoreHeader();
} else {
IGV.getInstance().getMainPanel().removeHeader();
}
IGV.getInstance().doRefresh();
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction, true));
menuItems.add(new JSeparator());
menuAction =
new MenuAction("Reorder Panels...", null, KeyEvent.VK_S) {
@Override
public void actionPerformed(ActionEvent e) {
ReorderPanelsDialog dlg = new ReorderPanelsDialog(IGV.getMainFrame());
dlg.setVisible(true);
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuItems.add(new JSeparator());
menuItems.add(new HistoryMenu("Go to"));
// Add to IGVPanel menu
MenuAction dataMenuAction = new MenuAction("View", null, KeyEvent.VK_V);
viewMenu = MenuAndToolbarUtils.createMenu(menuItems, dataMenuAction);
return viewMenu;
}
void createFileMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>();
MenuAction menuAction = null;
// We disable certain load items when there is no genome.
boolean genomeLoaded = GenomeManager.getInstance().getCurrentGenome() != null;
menuItems.add(new JSeparator());
// Load menu items
menuAction = new LoadFilesMenuAction("Load from File...", KeyEvent.VK_L, igv);
menuAction.setToolTipText(UIConstants.LOAD_TRACKS_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction = new LoadFromURLMenuAction(LoadFromURLMenuAction.LOAD_FROM_URL, KeyEvent.VK_U, igv);
menuAction.setToolTipText(UIConstants.LOAD_TRACKS_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction = new LoadFromServerAction("Load from Server...", KeyEvent.VK_S, igv);
menuAction.setToolTipText(UIConstants.LOAD_SERVER_DATA_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction = new LoadFromURLMenuAction(LoadFromURLMenuAction.LOAD_FROM_DAS, KeyEvent.VK_D, igv);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
if (PreferenceManager.getInstance().getAsBoolean(PreferenceManager.DB_ENABLED)) {
menuAction = new LoadFromDatabaseAction("Load from Database...", 0, igv);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
}
String genomeId = IGV.getInstance().getGenomeManager().getGenomeId();
if (EncodeFileBrowser.genomeSupported(genomeId)) {
menuAction = new BrowseEncodeAction("Load from ENCODE...", KeyEvent.VK_E, igv);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
}
// Disable loading if no genome loaded. Something of an edge case
if (!genomeLoaded) {
for (JComponent menuItem : menuItems) {
menuItem.setEnabled(false);
}
}
menuItems.add(new JSeparator());
// Session menu items
menuAction = new NewSessionMenuAction("New Session...", KeyEvent.VK_N, igv);
menuAction.setToolTipText(UIConstants.NEW_SESSION_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction = new OpenSessionMenuAction("Open Session...", KeyEvent.VK_O, igv);
menuAction.setToolTipText(UIConstants.RESTORE_SESSION_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction = new SaveSessionMenuAction("Save Session...", KeyEvent.VK_V, igv);
menuAction.setToolTipText(UIConstants.SAVE_SESSION_TOOLTIP);
JMenuItem saveSessionItem = MenuAndToolbarUtils.createMenuItem(menuAction);
menuItems.add(saveSessionItem);
saveSessionItem.setEnabled(genomeLoaded);
menuItems.add(new JSeparator());
// ***** Snapshots
// Snapshot Application
menuAction =
new MenuAction("Save Image ...", null, KeyEvent.VK_A) {
@Override
public void actionPerformed(ActionEvent e) {
igv.saveImage(igv.getMainPanel());
}
};
menuAction.setToolTipText(SAVE_IMAGE_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// TODO -- change "Exit" to "Close" for BioClipse
menuItems.add(new JSeparator()); // Exit
menuAction =
new MenuAction("Exit", null, KeyEvent.VK_X) {
@Override
public void actionPerformed(ActionEvent e) {
doExitApplication();
}
};
menuAction.setToolTipText(EXIT_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// Empty the recent sessions list before we start to do
// anything with it
igv.getRecentSessionList().clear();
// Retrieve the stored session paths
String recentSessions = PreferenceManager.getInstance().getRecentSessions();
if (recentSessions != null) {
String[] sessions = recentSessions.split(";");
for (String sessionPath : sessions) {
if (!igv.getRecentSessionList().contains(sessionPath)) {
igv.getRecentSessionList().add(sessionPath);
}
}
}
if (!IGV.getInstance().getRecentSessionList().isEmpty()) {
menuItems.add(new JSeparator());
// Now add menu items
for (final String session : IGV.getInstance().getRecentSessionList()) {
OpenSessionMenuAction osMenuAction =
new OpenSessionMenuAction(session, session, IGV.getInstance());
menuItems.add(MenuAndToolbarUtils.createMenuItem(osMenuAction));
}
}
MenuAction fileMenuAction = new MenuAction("File", null, KeyEvent.VK_F);
if (fileMenu == null) {
fileMenu = MenuAndToolbarUtils.createMenu(menuItems, fileMenuAction);
} else {
fileMenu.removeAll();
for (JComponent item : menuItems) {
fileMenu.add(item);
}
}
}
private void okButtonActionPerformed(ActionEvent e) {
PreferenceManager.getInstance().putToolPath(pluginId, toolName, pathInput.getText());
setVisible(false);
}
private void loadAlignmentsTrack(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
try {
String dsName = locator.getTrackName();
// If the user tried to load the index, look for the file (this is a common mistake)
if (locator.getTypeString().endsWith(".sai") || locator.getTypeString().endsWith(".bai")) {
MessageUtils.showMessage(
"<html><b>ERROR:</b> Loading SAM/BAM index files are not supported: "
+ locator.getPath()
+ "<br>Load the SAM or BAM file directly. ");
return;
}
AlignmentDataManager dataManager = new AlignmentDataManager(locator, genome);
// Check that alignments we loaded actually match some data. Many BAM files will contain some
// sequences
// not represented in the genome, buf if there are no matches warn the user.
List<String> seqNames = dataManager.getSequenceNames();
if (seqNames != null && seqNames.size() > 0) {
if (!checkSequenceNames(locator.getPath(), genome, seqNames)) {
return;
}
}
if (locator.getTypeString().endsWith("bam") || locator.getTypeString().endsWith("cram")) {
if (!dataManager.hasIndex()) {
MessageUtils.showMessage(
"<html>Could not load index file for: "
+ locator.getPath()
+ "<br> An index file is required for SAM & BAM files.");
return;
}
}
AlignmentTrack alignmentTrack =
new AlignmentTrack(locator, dataManager, genome); // parser.loadTrack(locator, dsName);
alignmentTrack.setName(dsName);
alignmentTrack.setVisible(
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_ALIGNMENT_TRACK));
// Create coverage track
CoverageTrack covTrack =
new CoverageTrack(locator, dsName + " Coverage", alignmentTrack, genome);
covTrack.setVisible(
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_COV_TRACK));
newTracks.add(covTrack);
covTrack.setDataManager(dataManager);
dataManager.setCoverageTrack(covTrack);
alignmentTrack.setCoverageTrack(covTrack);
// Search for precalculated coverage data
// Skip for GA4GH & SU2C resources
if (!(Ga4ghAPIHelper.RESOURCE_TYPE.equals(locator.getType())
|| locator.getPath().contains("dataformat=.bam")
|| OAuthUtils.isGoogleCloud(locator.getPath()))) {
String covPath = locator.getCoverage();
if (covPath == null) {
boolean bypassFileAutoDiscovery =
PreferenceManager.getInstance()
.getAsBoolean(PreferenceManager.BYPASS_FILE_AUTO_DISCOVERY);
String path = locator.getPath();
if (!bypassFileAutoDiscovery && !path.contains("/query.cgi?")) {
covPath = path + ".tdf";
}
}
if (covPath != null) {
if (FileUtils.resourceExists(covPath)) {
log.debug("Loading TDF for coverage: " + covPath);
try {
TDFReader reader = TDFReader.getReader(covPath);
TDFDataSource ds = new TDFDataSource(reader, 0, dsName + " coverage", genome);
covTrack.setDataSource(ds);
} catch (Exception e) {
log.error("Error loading coverage TDF file", e);
}
}
}
}
boolean showSpliceJunctionTrack =
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_JUNCTION_TRACK);
SpliceJunctionTrack spliceJunctionTrack =
new SpliceJunctionTrack(
locator,
dsName + " Junctions",
dataManager,
alignmentTrack,
SpliceJunctionTrack.StrandOption.BOTH);
spliceJunctionTrack.setHeight(60);
spliceJunctionTrack.setVisible(showSpliceJunctionTrack);
newTracks.add(spliceJunctionTrack);
alignmentTrack.setSpliceJunctionTrack(spliceJunctionTrack);
newTracks.add(alignmentTrack);
log.debug("Alignment track loaded");
} catch (IndexNotFoundException e) {
MessageUtils.showMessage(
"<html>Could not find the index file for <br><br> "
+ e.getSamFile()
+ "<br><br>Note: The index file can be created using igvtools and must be in the same directory as the .sam file.");
}
}
/**
* Render the track in the given rectangle.
*
* @param track
* @param locusScores
* @param context
* @param arect
*/
public synchronized void renderScores(
Track track, List<LocusScore> locusScores, RenderContext context, Rectangle arect) {
boolean showMissingData =
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SHOW_MISSING_DATA_KEY);
Graphics2D noDataGraphics = context.getGraphic2DForColor(UIConstants.NO_DATA_COLOR);
Graphics2D tickGraphics = context.getGraphic2DForColor(Color.BLACK);
Rectangle adjustedRect = calculateDrawingRect(arect);
double origin = context.getOrigin();
double locScale = context.getScale();
Color posColor = track.getColor();
Color negColor = track.getAltColor();
// Get the Y axis definition, consisting of minimum, maximum, and base value. Often
// the base value is == min value which is == 0.
DataRange dataRange = track.getDataRange();
float maxValue = dataRange.getMaximum();
float baseValue = dataRange.getBaseline();
float minValue = dataRange.getMinimum();
boolean isLog = dataRange.isLog();
if (isLog) {
minValue = (float) (minValue == 0 ? 0 : Math.log10(minValue));
maxValue = (float) Math.log10(maxValue);
}
// Calculate the Y scale factor.
double delta = (maxValue - minValue);
double yScaleFactor = adjustedRect.getHeight() / delta;
// Calculate the Y position in pixels of the base value. Clip to bounds of rectangle
double baseDelta = maxValue - baseValue;
int baseY = (int) (adjustedRect.getY() + baseDelta * yScaleFactor);
if (baseY < adjustedRect.y) {
baseY = adjustedRect.y;
} else if (baseY > adjustedRect.y + adjustedRect.height) {
baseY = adjustedRect.y + adjustedRect.height;
}
int lastPx = 0;
for (LocusScore score : locusScores) {
// Note -- don't cast these to an int until the range is checked.
// could get an overflow.
double pX = ((score.getStart() - origin) / locScale);
double dx = Math.ceil((Math.max(1, score.getEnd() - score.getStart())) / locScale) + 1;
if ((pX + dx < 0)) {
continue;
} else if (pX > adjustedRect.getMaxX()) {
break;
}
float dataY = score.getScore();
if (isLog && dataY <= 0) {
continue;
}
if (!Float.isNaN(dataY)) {
// Compute the pixel y location. Clip to bounds of rectangle.
double dy = isLog ? Math.log10(dataY) - baseValue : (dataY - baseValue);
int pY = baseY - (int) (dy * yScaleFactor);
if (pY < adjustedRect.y) {
pY = adjustedRect.y;
} else if (pY > adjustedRect.y + adjustedRect.height) {
pY = adjustedRect.y + adjustedRect.height;
}
Color color = (dataY >= baseValue) ? posColor : negColor;
drawDataPoint(color, (int) dx, (int) pX, baseY, pY, context);
}
if (showMissingData) {
// Draw from lastPx + 1 to pX - 1;
int w = (int) pX - lastPx - 4;
if (w > 0) {
noDataGraphics.fillRect(lastPx + 2, (int) arect.getY(), w, (int) arect.getHeight());
}
}
if (!Float.isNaN(dataY)) {
lastPx = (int) pX + (int) dx;
}
}
if (showMissingData) {
int w = (int) arect.getMaxX() - lastPx - 4;
if (w > 0) {
noDataGraphics.fillRect(lastPx + 2, (int) arect.getY(), w, (int) arect.getHeight());
}
}
}
@Override
public void renderBorder(Track track, RenderContext context, Rectangle arect) {
Rectangle adjustedRect = calculateDrawingRect(arect);
// Draw boundaries if there is room
if (adjustedRect.getHeight() >= 10) {
/// TrackProperties pros = track.getProperties();
// midline
DataRange axisDefinition = track.getDataRange();
float maxValue = axisDefinition.getMaximum();
float baseValue = axisDefinition.getBaseline();
float minValue = axisDefinition.getMinimum();
double maxX = adjustedRect.getMaxX();
double x = adjustedRect.getX();
double y = adjustedRect.getY();
if ((baseValue > minValue) && (baseValue < maxValue)) {
int baseY = computeYPixelValue(adjustedRect, axisDefinition, baseValue);
getBaselineGraphics(context).drawLine((int) x, baseY, (int) maxX, baseY);
}
PreferenceManager prefs = PreferenceManager.getInstance();
Color altColor = track.getAltColor();
Color borderColor =
(prefs.getAsBoolean(PreferenceManager.CHART_COLOR_BORDERS)
&& altColor != null
&& altColor.equals(track.getColor()))
? track.getColor()
: Color.lightGray;
Graphics2D borderGraphics = context.getGraphic2DForColor(borderColor);
// Draw the baseline -- todo, this is a wig track option?
double zeroValue = axisDefinition.getBaseline();
int zeroY = computeYPixelValue(adjustedRect, axisDefinition, zeroValue);
borderGraphics.drawLine(adjustedRect.x, zeroY, adjustedRect.x + adjustedRect.width, zeroY);
// Optionally draw "Y" line (UCSC track line option)
if (track.isDrawYLine()) {
Graphics2D yLineGraphics = context.getGraphic2DForColor(Color.gray);
int yLine = computeYPixelValue(adjustedRect, axisDefinition, track.getYLine());
GraphicUtils.drawDashedLine(
borderGraphics, adjustedRect.x, yLine, adjustedRect.x + adjustedRect.width, yLine);
}
// If the chart has + and - numbers draw both borders or none. This
// needs documented somewhere.
boolean drawBorders = true;
if (minValue * maxValue < 0) {
drawBorders =
prefs.getAsBoolean(PreferenceManager.CHART_DRAW_BOTTOM_BORDER)
&& prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TOP_BORDER);
}
if (drawBorders && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TOP_BORDER)) {
borderGraphics.drawLine(
adjustedRect.x, adjustedRect.y, adjustedRect.x + adjustedRect.width, adjustedRect.y);
}
if (drawBorders && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_BOTTOM_BORDER)) {
borderGraphics.drawLine(
adjustedRect.x,
adjustedRect.y + adjustedRect.height,
adjustedRect.x + adjustedRect.width,
adjustedRect.y + adjustedRect.height);
}
}
/*
(CHART_DRAW_TOP_BORDER));
prefs.setDrawBottomBorder(getBooleanPreference(CHART_DRAW_BOTTOM_BORDER));
prefs.setColorBorders(getBooleanPreference(CHART_COLOR_BORDERS));
prefs.setDrawAxis(getBooleanPreference(CHART_DRAW_Y_AXIS));
prefs.setDrawTrackName(getBooleanPreference(CHART_DRAW_TRACK_NAME));
prefs.setColorTrackName(getBooleanPreference(CHART_COLOR_TRACK_NAME));
prefs.setAutoscale(getBooleanPreference(CHART_AUTOSCALE));
prefs.setShowDataRange(getBooleanPreference(CHART_SHOW_DATA_RANGE));
*/
}
/**
* Method description
*
* @param track
* @param context
* @param arect
*/
@Override
public void renderAxis(Track track, RenderContext context, Rectangle arect) {
// For now disable axes for all chromosome view
if (context.getChr().equals(Globals.CHR_ALL)) {
return;
}
super.renderAxis(track, context, arect);
Rectangle drawingRect = calculateDrawingRect(arect);
PreferenceManager prefs = PreferenceManager.getInstance();
Color labelColor =
prefs.getAsBoolean(PreferenceManager.CHART_COLOR_TRACK_NAME)
? track.getColor()
: Color.black;
Graphics2D labelGraphics = context.getGraphic2DForColor(labelColor);
labelGraphics.setFont(FontManager.getFont(8));
if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TRACK_NAME)) {
// Only attempt if track height is > 25 pixels
if (arect.getHeight() > 25) {
Rectangle labelRect = new Rectangle(arect.x, arect.y + 10, arect.width, 10);
labelGraphics.setFont(FontManager.getFont(10));
GraphicUtils.drawCenteredText(track.getName(), labelRect, labelGraphics);
}
}
if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_Y_AXIS)) {
Rectangle axisRect = new Rectangle(arect.x, arect.y + 1, AXIS_AREA_WIDTH, arect.height);
DataRange axisDefinition = track.getDataRange();
float maxValue = axisDefinition.getMaximum();
float baseValue = axisDefinition.getBaseline();
float minValue = axisDefinition.getMinimum();
// Bottom (minimum tick mark)
int pY = computeYPixelValue(drawingRect, axisDefinition, minValue);
labelGraphics.drawLine(
axisRect.x + AXIS_AREA_WIDTH - 10, pY, axisRect.x + AXIS_AREA_WIDTH - 5, pY);
GraphicUtils.drawRightJustifiedText(
formatter.format(minValue), axisRect.x + AXIS_AREA_WIDTH - 15, pY, labelGraphics);
// Top (maximum tick mark)
int topPY = computeYPixelValue(drawingRect, axisDefinition, maxValue);
labelGraphics.drawLine(
axisRect.x + AXIS_AREA_WIDTH - 10, topPY, axisRect.x + AXIS_AREA_WIDTH - 5, topPY);
GraphicUtils.drawRightJustifiedText(
formatter.format(maxValue), axisRect.x + AXIS_AREA_WIDTH - 15, topPY + 4, labelGraphics);
// Connect top and bottom
labelGraphics.drawLine(
axisRect.x + AXIS_AREA_WIDTH - 10, topPY, axisRect.x + AXIS_AREA_WIDTH - 10, pY);
// Middle tick mark. Draw only if room
int midPY = computeYPixelValue(drawingRect, axisDefinition, baseValue);
if ((midPY < pY - 15) && (midPY > topPY + 15)) {
labelGraphics.drawLine(
axisRect.x + AXIS_AREA_WIDTH - 10, midPY, axisRect.x + AXIS_AREA_WIDTH - 5, midPY);
GraphicUtils.drawRightJustifiedText(
formatter.format(baseValue),
axisRect.x + AXIS_AREA_WIDTH - 15,
midPY + 4,
labelGraphics);
}
} else if (track.isShowDataRange() && arect.height > 20) {
drawScale(track.getDataRange(), context, arect);
}
}
/**
* Construct alignment blocks from the Goby alignment entry. This method uses the convention that
* '=' denotes a match to the reference.
*
* <p>Conventions for storing sequence variations in Goby alignments are described <a
* href="http://tinyurl.com/goby-sequence-variations">here</a>
*
* @param alignmentEntry The Goby alignment entry to use
*/
public void buildBlocks(Alignments.AlignmentEntry alignmentEntry) {
ObjectArrayList<AlignmentBlock> blocks = new ObjectArrayList<AlignmentBlock>();
ObjectArrayList<AlignmentBlock> insertionBlocks = new ObjectArrayList<AlignmentBlock>();
int start = alignmentEntry.getPosition();
ByteArrayList bases = new ByteArrayList();
ByteArrayList scores = new ByteArrayList();
int readLength = alignmentEntry.getQueryLength();
byte[] readBases = new byte[readLength];
byte[] readQual = new byte[readLength];
Arrays.fill(readBases, (byte) '=');
if (alignmentEntry.hasReadQualityScores()) {
readQual = alignmentEntry.getReadQualityScores().toByteArray();
} else {
Arrays.fill(readQual, (byte) 40);
}
int j = 0;
int insertedBases = 0;
int deletedBases = 0;
final int leftPadding = alignmentEntry.getQueryPosition();
boolean showSoftClipped =
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_SOFT_CLIPPED);
if (showSoftClipped && entry.hasSoftClippedBasesLeft()) {
int clipLength = entry.getSoftClippedBasesLeft().length();
addSoftClipBlock(
blocks,
Math.max(0, entry.getPosition() - clipLength),
entry.getSoftClippedBasesLeft(),
readQual,
entry.hasSoftClippedQualityLeft(),
entry.getSoftClippedQualityLeft().toByteArray(),
0);
}
for (Alignments.SequenceVariation var : alignmentEntry.getSequenceVariationsList()) {
final String from = var.getFrom();
final int fromLength = from.length();
final String to = var.getTo();
final int toLength = from.length();
final int sequenceVariationLength = Math.max(fromLength, toLength);
final ByteString toQuality = var.getToQuality();
if (hasReadInsertion(from)) {
bases.clear();
scores.clear();
for (int i = 0; i < sequenceVariationLength; i++) {
final char toChar = i >= toLength ? '-' : to.charAt(i);
int size = toQuality.size();
final byte qual = size > 0 && i < size ? toQuality.byteAt(i) : 40;
bases.add((byte) toChar);
scores.add(qual);
deletedBases++;
}
addBlock(insertionBlocks, alignmentEntry.getPosition() + var.getPosition(), bases, scores);
bases.clear();
scores.clear();
} else if (!to.contains("-")) {
for (int i = 0; i < toLength; i++) {
final int offset = j + var.getPosition() + i - 1 + leftPadding - insertedBases;
if (offset > 0 && offset < readBases.length) {
readBases[offset] = (byte) to.charAt(i);
if (i < toQuality.size()) {
readQual[offset] = toQuality.byteAt(i);
}
}
}
} else {
// has read deletion:
insertedBases++;
}
}
int pos = start;
int matchLength = alignmentEntry.getQueryAlignedLength() - deletedBases;
int endAlignmentRefPosition = matchLength + start;
bases.clear();
scores.clear();
int maxIndex = Math.min(readBases.length, readQual.length);
while (pos < endAlignmentRefPosition) {
final int index = pos - start + leftPadding;
if (index < maxIndex) {
bases.add(readBases[index]);
scores.add(readQual[index]);
} else {
break;
}
++pos;
}
addBlock(blocks, start, bases, scores);
blocks = introduceDeletions(blocks, entry);
if (showSoftClipped && entry.hasSoftClippedBasesRight()) {
int targetAlignedLength = entry.getTargetAlignedLength();
addSoftClipBlock(
blocks,
entry.getPosition() + targetAlignedLength,
entry.getSoftClippedBasesRight(),
readQual,
entry.hasSoftClippedQualityRight(),
entry.getSoftClippedQualityRight().toByteArray(),
entry.getQueryAlignedLength() + entry.getSoftClippedBasesLeft().length());
}
block = blocks.toArray(new AlignmentBlock[blocks.size()]);
Arrays.sort(block, blockComparator);
insertionBlock = insertionBlocks.toArray(new AlignmentBlock[insertionBlocks.size()]);
Arrays.sort(insertionBlock, blockComparator);
ObjectArrayList<GobyAlignment> list = null;
if (alignmentEntry.hasSplicedForwardAlignmentLink()
|| alignmentEntry.hasSplicedBackwardAlignmentLink()) {
// if has a forward link, store a reference to this alignment in the reader (which represents
// the window scope)
list = iterator.cacheSpliceComponent(this);
if (list.size() > 1 && spliceListIsValid(list)) {
final GobyAlignment spliceHeadAlignment = list.get(0);
ObjectArrayList<AlignmentBlock> splicedBlocks = new ObjectArrayList<AlignmentBlock>();
splicedBlocks.addAll(ObjectArrayList.wrap(spliceHeadAlignment.block));
splicedBlocks.addAll(blocks);
spliceHeadAlignment.block = splicedBlocks.toArray(new AlignmentBlock[splicedBlocks.size()]);
ObjectArrayList<AlignmentBlock> splicedInsertionBlocks =
new ObjectArrayList<AlignmentBlock>();
splicedInsertionBlocks.addAll(ObjectArrayList.wrap(spliceHeadAlignment.insertionBlock));
splicedInsertionBlocks.addAll(insertionBlocks);
spliceHeadAlignment.insertionBlock =
splicedInsertionBlocks.toArray(new AlignmentBlock[splicedInsertionBlocks.size()]);
if (spliceHeadAlignment.gapTypes == null) {
spliceHeadAlignment.gapTypes = new CharArrayList(10);
}
spliceHeadAlignment.gapTypes.add(SamAlignment.SKIPPED_REGION);
// Since the previous alignment carries this information, we clear up block and
// insertionBlock
// in this alignment, but keep any softClips:
this.block = keepSoftClips(block);
this.insertionBlock = new AlignmentBlock[0];
}
}
}
