@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));
*/
}
/** Creates a new Launcher object. */
public Launcher() {
// Initialize the SystemTray now (to avoid a bug!)
SystemTray tray = null;
try {
tray = SystemTray.getDefaultSystemTray();
} catch (Throwable e) {
// Log to System error instead of standard error log.
System.err.println("Error loading system tray library, system tray support disabled.");
}
// Use the native look and feel.
try {
UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
} catch (Exception e) {
e.printStackTrace();
}
if (System.getProperty("app.name") != null) {
appName = System.getProperty("app.name");
} else {
appName = "Openfire";
}
binDir = new File("").getAbsoluteFile();
// See if the appdir property is set. If so, use it to find the executable.
if (System.getProperty("appdir") != null) {
binDir = new File(System.getProperty("appdir"));
}
configFile = new File(new File(binDir.getParent(), "conf"), "openfire.xml");
frame =
new DroppableFrame() {
@Override
public void fileDropped(File file) {
String fileName = file.getName();
if (fileName.endsWith(".jar") || fileName.endsWith(".war")) {
installPlugin(file);
}
}
};
frame.setTitle(appName);
ImageIcon splash;
JPanel mainPanel = new JPanel();
JLabel splashLabel = null;
cardPanel.setLayout(cardLayout);
// Set the icon.
try {
splash = new ImageIcon(getClass().getClassLoader().getResource("splash.gif"));
splashLabel = new JLabel("", splash, JLabel.CENTER);
onIcon = new ImageIcon(getClass().getClassLoader().getResource("openfire_on-16x16.gif"));
offIcon = new ImageIcon(getClass().getClassLoader().getResource("openfire_off-16x16.gif"));
frame.setIconImage(offIcon.getImage());
} catch (Exception e) {
e.printStackTrace();
}
mainPanel.setLayout(new BorderLayout());
cardPanel.setBackground(Color.white);
// Add buttons
final JButton startButton = new JButton("Start");
startButton.setActionCommand("Start");
final JButton stopButton = new JButton("Stop");
stopButton.setActionCommand("Stop");
final JButton browserButton = new JButton("Launch Admin");
browserButton.setActionCommand("Launch Admin");
final JButton quitButton = new JButton("Quit");
quitButton.setActionCommand("Quit");
toolbar.setLayout(new GridBagLayout());
toolbar.add(
startButton,
new GridBagConstraints(
0,
0,
1,
1,
0.0,
0.0,
GridBagConstraints.WEST,
GridBagConstraints.NONE,
new Insets(5, 5, 5, 5),
0,
0));
toolbar.add(
stopButton,
new GridBagConstraints(
1,
0,
1,
1,
0.0,
0.0,
GridBagConstraints.WEST,
GridBagConstraints.NONE,
new Insets(5, 5, 5, 5),
0,
0));
toolbar.add(
browserButton,
new GridBagConstraints(
2,
0,
1,
1,
0.0,
0.0,
GridBagConstraints.WEST,
GridBagConstraints.NONE,
new Insets(5, 5, 5, 5),
0,
0));
toolbar.add(
quitButton,
new GridBagConstraints(
3,
0,
1,
1,
0.0,
0.0,
GridBagConstraints.WEST,
GridBagConstraints.NONE,
new Insets(5, 5, 5, 5),
0,
0));
mainPanel.add(cardPanel, BorderLayout.CENTER);
mainPanel.add(toolbar, BorderLayout.SOUTH);
// create the main menu of the system tray icon
JPopupMenu menu = new JPopupMenu(appName + " Menu");
final JMenuItem showMenuItem = new JMenuItem("Hide");
showMenuItem.setActionCommand("Hide/Show");
menu.add(showMenuItem);
final JMenuItem startMenuItem = new JMenuItem("Start");
startMenuItem.setActionCommand("Start");
menu.add(startMenuItem);
final JMenuItem stopMenuItem = new JMenuItem("Stop");
stopMenuItem.setActionCommand("Stop");
menu.add(stopMenuItem);
final JMenuItem browserMenuItem = new JMenuItem("Launch Admin");
browserMenuItem.setActionCommand("Launch Admin");
menu.add(browserMenuItem);
menu.addSeparator();
final JMenuItem quitMenuItem = new JMenuItem("Quit");
quitMenuItem.setActionCommand("Quit");
menu.add(quitMenuItem);
browserButton.setEnabled(false);
stopButton.setEnabled(false);
browserMenuItem.setEnabled(false);
stopMenuItem.setEnabled(false);
ActionListener actionListener =
new ActionListener() {
public void actionPerformed(ActionEvent e) {
if ("Start".equals(e.getActionCommand())) {
frame.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
// Adjust button and menu items.
startButton.setEnabled(false);
stopButton.setEnabled(true);
startMenuItem.setEnabled(false);
stopMenuItem.setEnabled(true);
// Startup Application
startApplication();
// Change to the "on" icon.
frame.setIconImage(onIcon.getImage());
trayIcon.setIcon(onIcon);
// Start a thread to enable the admin button after 8 seconds.
Thread thread =
new Thread() {
@Override
public void run() {
try {
sleep(8000);
} catch (InterruptedException ie) {
// Ignore.
}
// Enable the Launch Admin button/menu item only if the
// server has started.
if (stopButton.isEnabled()) {
browserButton.setEnabled(true);
browserMenuItem.setEnabled(true);
frame.setCursor(Cursor.getDefaultCursor());
}
}
};
thread.start();
} else if ("Stop".equals(e.getActionCommand())) {
stopApplication();
// Change to the "off" button.
frame.setIconImage(offIcon.getImage());
trayIcon.setIcon(offIcon);
// Adjust buttons and menu items.
frame.setCursor(Cursor.getDefaultCursor());
browserButton.setEnabled(false);
startButton.setEnabled(true);
stopButton.setEnabled(false);
browserMenuItem.setEnabled(false);
startMenuItem.setEnabled(true);
stopMenuItem.setEnabled(false);
} else if ("Launch Admin".equals(e.getActionCommand())) {
launchBrowser();
} else if ("Quit".equals(e.getActionCommand())) {
stopApplication();
System.exit(0);
} else if ("Hide/Show".equals(e.getActionCommand())
|| "PressAction".equals(e.getActionCommand())) {
// Hide/Unhide the window if the user clicked in the system tray icon or
// selected the menu option
if (frame.isVisible()) {
frame.setVisible(false);
frame.setState(Frame.ICONIFIED);
showMenuItem.setText("Show");
} else {
frame.setVisible(true);
frame.setState(Frame.NORMAL);
showMenuItem.setText("Hide");
}
}
}
};
// Register a listener for the radio buttons.
startButton.addActionListener(actionListener);
stopButton.addActionListener(actionListener);
browserButton.addActionListener(actionListener);
quitButton.addActionListener(actionListener);
// Register a listener for the menu items.
quitMenuItem.addActionListener(actionListener);
browserMenuItem.addActionListener(actionListener);
stopMenuItem.addActionListener(actionListener);
startMenuItem.addActionListener(actionListener);
showMenuItem.addActionListener(actionListener);
// Set the system tray icon with the menu
trayIcon = new TrayIcon(offIcon, appName, menu);
trayIcon.setIconAutoSize(true);
trayIcon.addActionListener(actionListener);
if (tray != null) {
tray.addTrayIcon(trayIcon);
}
frame.addWindowListener(
new WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
stopApplication();
System.exit(0);
}
@Override
public void windowIconified(WindowEvent e) {
// Make the window disappear when minimized
frame.setVisible(false);
showMenuItem.setText("Show");
}
});
cardPanel.add("main", splashLabel);
frame.getContentPane().add(mainPanel, BorderLayout.CENTER);
frame.pack();
frame.setSize(400, 300);
frame.setResizable(true);
GraphicUtils.centerWindowOnScreen(frame);
frame.setVisible(true);
// Setup command area
final ImageIcon icon = new ImageIcon(getClass().getClassLoader().getResource("splash2.gif"));
pane =
new DroppableTextPane() {
@Override
public void paintComponent(Graphics g) {
final Dimension size = pane.getSize();
int x = (size.width - icon.getIconWidth()) / 2;
int y = (size.height - icon.getIconHeight()) / 2;
// Approach 1: Dispaly image at at full size
g.setColor(Color.white);
g.fillRect(0, 0, size.width, size.height);
g.drawImage(icon.getImage(), x, y, null);
setOpaque(false);
super.paintComponent(g);
}
@Override
public void fileDropped(File file) {
String fileName = file.getName();
if (fileName.endsWith(".jar") || fileName.endsWith(".war")) {
installPlugin(file);
}
}
};
pane.setEditable(false);
final JPanel bevelPanel = new JPanel();
bevelPanel.setBackground(Color.white);
bevelPanel.setLayout(new BorderLayout());
bevelPanel.setBorder(BorderFactory.createLoweredBevelBorder());
bevelPanel.add(new JScrollPane(pane), BorderLayout.CENTER);
cardPanel.add("running", bevelPanel);
// Start the app.
startButton.doClick();
}
/**
* 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);
}
}