/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.io.*;
import java.awt.*;
public static boolean internalCopy = false;
static int fileLoadingCount = 0;
-
+ class MyDesktopManager implements DesktopManager {
+
+ private DesktopManager delegate;
+
+ public MyDesktopManager(DesktopManager delegate) {
+ this.delegate = delegate;
+ }
+
+ public void activateFrame(JInternalFrame f) {
+ try {
+ delegate.activateFrame(f);
+ } catch (NullPointerException npe) {
+ Point p = getMousePosition();
+ instance.showPasteMenu(p.x,p.y);
+ }
+ }
+
+ public void beginDraggingFrame(JComponent f) {
+ delegate.beginDraggingFrame(f);
+ }
+
+ public void beginResizingFrame(JComponent f, int direction) {
+ delegate.beginResizingFrame(f, direction);
+ }
+
+ public void closeFrame(JInternalFrame f) {
+ delegate.closeFrame(f);
+ }
+
+ public void deactivateFrame(JInternalFrame f) {
+ delegate.deactivateFrame(f);
+ }
+
+ public void deiconifyFrame(JInternalFrame f) {
+ delegate.deiconifyFrame(f);
+ }
+
+ public void dragFrame(JComponent f, int newX, int newY) {
+ delegate.dragFrame(f, newX, newY);
+ }
+
+ public void endDraggingFrame(JComponent f) {
+ delegate.endDraggingFrame(f);
+ }
+
+ public void endResizingFrame(JComponent f) {
+ delegate.endResizingFrame(f);
+ }
+
+ public void iconifyFrame(JInternalFrame f) {
+ delegate.iconifyFrame(f);
+ }
+
+ public void maximizeFrame(JInternalFrame f) {
+ delegate.maximizeFrame(f);
+ }
+
+ public void minimizeFrame(JInternalFrame f) {
+ delegate.minimizeFrame(f);
+ }
+
+ public void openFrame(JInternalFrame f) {
+ delegate.openFrame(f);
+ }
+
+ public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
+ int newHeight) {
+ delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
+ }
+
+ public void setBoundsForFrame(JComponent f, int newX, int newY,
+ int newWidth, int newHeight) {
+ delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
+ }
+
+ // All other methods, simply delegate
+
+ }
/**
* Creates a new Desktop object.
*/
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
false);
+ boolean showjconsole = jalview.bin.Cache.getDefault(
+ "SHOW_JAVA_CONSOLE", false);
desktop = new MyDesktopPane(selmemusage);
showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
- desktop.setDesktopManager(new DefaultDesktopManager());
-
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- String x = jalview.bin.Cache.getProperty("SCREEN_X");
- String y = jalview.bin.Cache.getProperty("SCREEN_Y");
- String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
- String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
-
- if ((x != null) && (y != null) && (width != null) && (height != null))
+ desktop.setDesktopManager(new MyDesktopManager(new DefaultDesktopManager()));
+ Rectangle dims = getLastKnownDimensions("");
+ if (dims != null)
{
- setBounds(Integer.parseInt(x), Integer.parseInt(y), Integer
- .parseInt(width), Integer.parseInt(height));
+ setBounds(dims);
}
else
{
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
setBounds((int) (screenSize.width - 900) / 2,
(int) (screenSize.height - 650) / 2, 900, 650);
}
+ jconsole = new Console(this, showjconsole);
+ // add essential build information
+ jconsole.setHeader("Jalview Desktop "
+ + jalview.bin.Cache.getProperty("VERSION") + "\n"
+ + "Build Date: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
+ + "Java version: " + System.getProperty("java.version") + "\n"
+ + System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
+
+ showConsole(showjconsole);
this.addWindowListener(new WindowAdapter()
{
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
// Spawn a thread that shows the splashscreen
- new SplashScreen();
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ new SplashScreen();
+ }
+ });
discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is
// displayed.
+ // Thread off a new instance of the file chooser - this reduces the time it
+ // takes to open it later on.
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ Cache.log.debug("Filechooser init thread started.");
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
+ jalview.io.AppletFormatAdapter.READABLE_FNAMES,
+ jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+ Cache.log.debug("Filechooser init thread finished.");
+ }
+ }).start();
+ }
+
+ /**
+ * recover the last known dimensions for a jalview window
+ *
+ * @param windowName
+ * - empty string is desktop, all other windows have unique prefix
+ * @return null or last known dimensions scaled to current geometry (if last
+ * window geom was known)
+ */
+ Rectangle getLastKnownDimensions(String windowName)
+ {
+ // TODO: lock aspect ratio for scaling desktop Bug #0058199
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
+ String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
+ String width = jalview.bin.Cache.getProperty(windowName
+ + "SCREEN_WIDTH");
+ String height = jalview.bin.Cache.getProperty(windowName
+ + "SCREEN_HEIGHT");
+ if ((x != null) && (y != null) && (width != null) && (height != null))
+ {
+ int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer
+ .parseInt(width), ih = Integer.parseInt(height);
+ if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
+ {
+ // attempt #1 - try to cope with change in screen geometry - this
+ // version doesn't preserve original jv aspect ratio.
+ // take ratio of current screen size vs original screen size.
+ double sw = ((1f * screenSize.width) / (1f * Integer
+ .parseInt(jalview.bin.Cache
+ .getProperty("SCREENGEOMETRY_WIDTH"))));
+ double sh = ((1f * screenSize.height) / (1f * Integer
+ .parseInt(jalview.bin.Cache
+ .getProperty("SCREENGEOMETRY_HEIGHT"))));
+ // rescale the bounds depending upon the current screen geometry.
+ ix = (int) (ix * sw);
+ iw = (int) (iw * sw);
+ iy = (int) (iy * sh);
+ ih = (int) (ih * sh);
+ jalview.bin.Cache.log.debug("Got last known dimensions for "
+ + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ + " height:" + ih);
+ }
+ // return dimensions for new instance
+ return new Rectangle(ix, iy, iw, ih);
+ }
+ return null;
}
private void doVamsasClientCheck()
}
/**
- * DOCUMENT ME!
+ * Adds and opens the given frame to the desktop
*
* @param frame
* DOCUMENT ME!
boolean resizable)
{
+ // TODO: allow callers to determine X and Y position of frame (eg. via
+ // bounds object).
// TODO: consider fixing method to update entries in the window submenu with
// the current window title
for (int i = 0; i < files.size(); i++)
{
String file = files.get(i).toString();
- String protocol = (protocols==null) ? FormatAdapter.FILE : (String) protocols.get(i);
+ String protocol = (protocols == null) ? FormatAdapter.FILE
+ : (String) protocols.get(i);
String format = null;
if (file.endsWith(".jar"))
*/
public void quit()
{
- jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
- jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
- jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
- jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
+ Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ jalview.bin.Cache
+ .setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+ jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height
+ + "");
+ storeLastKnownDimensions("", new Rectangle(getBounds().x,
+ getBounds().y, getWidth(), getHeight()));
+
+ if (jconsole != null)
+ {
+ storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
+ jconsole.stopConsole();
+ }
System.exit(0);
}
+ private void storeLastKnownDimensions(String string, Rectangle jc)
+ {
+ jalview.bin.Cache.log.debug("Storing last known dimensions for "
+ + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ + " height:" + jc.height);
+
+ jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
+ jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
+ jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
+ jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
+ }
+
/**
* DOCUMENT ME!
*
desktop.showMemoryUsage(showMemusage.isSelected());
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ protected void showConsole_actionPerformed(ActionEvent e)
+ {
+ showConsole(showConsole.isSelected());
+ }
+
+ Console jconsole = null;
+
+ /**
+ * control whether the java console is visible or not
+ *
+ * @param selected
+ */
+ void showConsole(boolean selected)
+ {
+ showConsole.setSelected(selected);
+ // TODO: decide if we should update properties file
+ Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected)
+ .toString());
+ jconsole.setVisible(selected);
+ }
+
void reorderAssociatedWindows(boolean minimize, boolean close)
{
JInternalFrame[] frames = desktop.getAllFrames();
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
- JProgressBar progpanel = addProgressPanel("Saving jalview project "+choice.getName());
+ JProgressBar progpanel = addProgressPanel("Saving jalview project "
+ + choice.getName());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
// TODO catch and handle errors for savestate
new Jalview2XML().SaveState(choice);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getAbsolutePath();
- setProgressBar("loading jalview project "+chooser.getSelectedFile().getName(),choice.hashCode());
+ setProgressBar("loading jalview project "
+ + chooser.getSelectedFile().getName(), choice.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
new Jalview2XML().LoadJalviewAlign(choice);
- setProgressBar(null,choice.hashCode());
+ setProgressBar(null, choice.hashCode());
}
}
public static AlignmentPanel[] getAlignmentPanels(String viewId)
{
int count = 0;
- if (Desktop.desktop==null)
+ if (Desktop.desktop == null)
{
// no frames created and in headless mode
// TODO: verify that frames are recoverable when in headless mode
}
/**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- * @param file
+ * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+ *
+ * @param file
* @return true if import was a success and a session was started.
*/
public boolean vamsasImport(URL url)
// TODO: create progress bar
if (v_client != null)
{
-
+
jalview.bin.Cache.log
- .error("Implementation error - load session from a running session is not supported.");
- return false;
+ .error("Implementation error - load session from a running session is not supported.");
+ return false;
}
-
+
try
- {
+ {
// copy the URL content to a temporary local file
// TODO: be a bit cleverer here with nio (?!)
File file = File.createTempFile("vdocfromurl", ".vdj");
BufferedInputStream bis = new BufferedInputStream(url.openStream());
byte[] buffer = new byte[2048];
int ln;
- while ((ln = bis.read(buffer))>-1)
+ while ((ln = bis.read(buffer)) > -1)
{
- fos.write(buffer,0,ln);
+ fos.write(buffer, 0, ln);
}
bis.close();
fos.close();
- v_client = new jalview.gui.VamsasApplication(this, file, url.toExternalForm());
- } catch (Exception ex)
- {
- jalview.bin.Cache.log.error(
- "Failed to create new vamsas session from contents of URL "+url,ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- return v_client.inSession();
+ v_client = new jalview.gui.VamsasApplication(this, file, url
+ .toExternalForm());
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log.error(
+ "Failed to create new vamsas session from contents of URL "
+ + url, ex);
+ return false;
}
+ setupVamsasConnectedGui();
+ v_client.initial_update(); // TODO: thread ?
+ return v_client.inSession();
+ }
/**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- * @param file
+ * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+ *
+ * @param file
* @return true if import was a success and a session was started.
*/
public boolean vamsasImport(File file)
return false;
}
- setProgressBar("Importing VAMSAS session from "+file.getName(),file.hashCode());
+ setProgressBar("Importing VAMSAS session from " + file.getName(), file
+ .hashCode());
try
{
- v_client = new jalview.gui.VamsasApplication(this, file,null);
+ v_client = new jalview.gui.VamsasApplication(this, file, null);
} catch (Exception ex)
{
- setProgressBar("Importing VAMSAS session from "+file.getName(),file.hashCode());
+ setProgressBar("Importing VAMSAS session from " + file.getName(),
+ file.hashCode());
jalview.bin.Cache.log.error(
"New vamsas session from existing session file failed:", ex);
return false;
}
setupVamsasConnectedGui();
v_client.initial_update(); // TODO: thread ?
- setProgressBar("Importing VAMSAS session from "+file.getName(),file.hashCode());
+ setProgressBar("Importing VAMSAS session from " + file.getName(), file
+ .hashCode());
return v_client.inSession();
}
- public boolean joinVamsasSession(String mysesid) {
- if (v_client!=null)
+
+ public boolean joinVamsasSession(String mysesid)
+ {
+ if (v_client != null)
{
- throw new Error("Trying to join a vamsas session when another is already connected.");
+ throw new Error(
+ "Trying to join a vamsas session when another is already connected.");
}
- if (mysesid==null)
+ if (mysesid == null)
{
throw new Error("Invalid vamsas session id.");
}
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
- JProgressBar progpanel = addProgressPanel("Saving VAMSAS Document to "+choice.getName());
+ JProgressBar progpanel = addProgressPanel("Saving VAMSAS Document to "
+ + choice.getName());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
{
try
{
- Thread.sleep(3000);
maxMemory = runtime.maxMemory() / 1048576f;
allocatedMemory = runtime.totalMemory() / 1048576f;
freeMemory = runtime.freeMemory() / 1048576f;
// instance.set.setBorder(border1);
}
repaint();
-
+ // sleep after showing usage
+ Thread.sleep(3000);
} catch (Exception ex)
{
ex.printStackTrace();
public void paintComponent(Graphics g)
{
- if (showMemoryUsage)
+ if (showMemoryUsage && g != null)
{
if (percentUsage < 20)
g.setColor(Color.red);
-
- g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
- + "MB; Max Memory: " + df.format(maxMemory) + "MB; "
- + df.format(percentUsage) + "%", 10, getHeight()
- - g.getFontMetrics().getHeight());
+ FontMetrics fm = g.getFontMetrics();
+ if (fm != null)
+ {
+ g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
+ + "MB; Max Memory: " + df.format(maxMemory) + "MB; "
+ + df.format(percentUsage) + "%", 10, getHeight()
+ - fm.getHeight());
+ }
}
}
return v_client;
}
+
+ public void startServiceDiscovery()
+ {
+ discoverer.start();
+
+ try {
+ new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance()).start();
+ } catch (Exception e)
+ {
+ Cache.log.info("Exception when trying to launch Envision2 workflow discovery.",e);
+ Cache.log.info(e.getStackTrace());
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff