*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.io.*;
import java.awt.*;
import java.awt.datatransfer.*;
import java.awt.dnd.*;
import java.awt.event.*;
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
import java.io.File;
+import java.io.FileOutputStream;
+import java.io.InputStream;
import java.lang.reflect.Constructor;
+import java.net.URL;
+import java.net.URLConnection;
+import java.nio.channels.ReadableByteChannel;
import java.util.*;
import javax.swing.*;
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);
// 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))
- {
- setBounds(Integer.parseInt(x), Integer.parseInt(y), Integer
- .parseInt(width), Integer.parseInt(height));
+ Rectangle dims = getLastKnownDimensions("");
+ if (dims!=null)
+ {
+ 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);
+ 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.
}
+ /**
+ * 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)
+ {
+ 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()
{
if (jalview.bin.Cache.vamsasJarsPresent())
{
Transferable t = evt.getTransferable();
java.util.List files = null;
+ java.util.List protocols = null;
try
{
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
String data = (String) t.getTransferData(uriListFlavor);
files = new java.util.ArrayList(1);
+ protocols = new java.util.ArrayList(1);
for (java.util.StringTokenizer st = new java.util.StringTokenizer(
data, "\r\n"); st.hasMoreTokens();)
{
// the line is a comment (as per the RFC 2483)
continue;
}
-
java.net.URI uri = new java.net.URI(s);
- java.io.File file = new java.io.File(uri);
- files.add(file);
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ protocols.add(FormatAdapter.URL);
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ protocols.add(FormatAdapter.FILE);
+ files.add(file.toString());
+ }
}
}
} catch (Exception e)
for (int i = 0; i < files.size(); i++)
{
String file = files.get(i).toString();
- String protocol = FormatAdapter.FILE;
+ 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());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ // TODO catch and handle errors for savestate
new Jalview2XML().SaveState(choice);
+ removeProgressPanel(progpanel);
+
}
}
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getAbsolutePath();
+ 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());
}
}
public static AlignmentPanel[] getAlignmentPanels(String viewId)
{
int count = 0;
+ if (Desktop.desktop == null)
+ {
+ // no frames created and in headless mode
+ // TODO: verify that frames are recoverable when in headless mode
+ return null;
+ }
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
ArrayList aps = new ArrayList();
for (int t = 0; t < frames.length; t++)
}
/**
- * 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;
+ }
+
+ try
+ {
+ // copy the URL content to a temporary local file
+ // TODO: be a bit cleverer here with nio (?!)
+ File file = File.createTempFile("vdocfromurl", ".vdj");
+ FileOutputStream fos = new FileOutputStream(file);
+ BufferedInputStream bis = new BufferedInputStream(url.openStream());
+ byte[] buffer = new byte[2048];
+ int ln;
+ while ((ln = bis.read(buffer)) > -1)
+ {
+ 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();
+ }
+
+ /**
+ * 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());
try
{
- v_client = new jalview.gui.VamsasApplication(this, file);
+ v_client = new jalview.gui.VamsasApplication(this, file, null);
} catch (Exception ex)
{
+ 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());
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());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
+ choice, ex);
}
+ removeProgressPanel(progpanel);
if (warnmsg != null)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
{
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);
git://source.jalview.org / jalview.git / blobdiff