/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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.*;
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.*;
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.
+ // 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!
+ * DOCUMENT ME!
* @param title
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param w
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param h
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public static synchronized void addInternalFrame(
final JInternalFrame frame, String title, int w, int h)
* DOCUMENT ME!
*
* @param frame
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param title
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param w
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param h
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param resizable
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public static synchronized void addInternalFrame(
final JInternalFrame frame, String title, int w, int h,
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
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drop(DropTargetDropEvent evt)
{
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"))
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
{
*/
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!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
+ "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
+ "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
+ "\nIf you use Jalview, please cite:"
- + "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""
- + "\nBioinformatics, 2004 20;426-7.");
-
+ + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void documentationMenuItem_actionPerformed(ActionEvent e)
{
}
}
System.out.println("ALL CLOSED");
+ if (v_client != null)
+ {
+ // TODO clear binding to vamsas document objects on close_all
+ }
}
public void raiseRelated_actionPerformed(ActionEvent e)
/*
* (non-Javadoc)
*
- * @see jalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.ActionEvent)
+ * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
+ * ActionEvent)
*/
protected void garbageCollect_actionPerformed(ActionEvent e)
{
/*
* (non-Javadoc)
*
- * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent)
+ * @see
+ * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
+ * )
*/
protected void showMemusage_actionPerformed(ActionEvent e)
{
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();
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void preferences_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void saveState_actionPerformed(ActionEvent e)
{
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);
+
}
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void loadState_actionPerformed(ActionEvent e)
{
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 int getViewCount(String viewId)
{
+ AlignViewport[] aps = getViewports(viewId);
+ return (aps == null) ? 0 : aps.length;
+ }
+
+ /**
+ *
+ * @param viewId
+ * @return all AlignmentPanels concerning the viewId sequence set
+ */
+ 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++)
{
if (frames[t] instanceof AlignFrame)
.equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
.getSequenceSetId()))
{
- count++;
+ aps.add(af.alignPanels.elementAt(a));
}
}
}
}
+ if (aps.size() == 0)
+ {
+ return null;
+ }
+ AlignmentPanel[] vap = new AlignmentPanel[aps.size()];
+ for (int t = 0; t < vap.length; t++)
+ {
+ vap[t] = (AlignmentPanel) aps.get(t);
+ }
+ return vap;
+ }
- return count;
+ /**
+ * get all the viewports on an alignment.
+ *
+ * @param sequenceSetId
+ * unique alignment id
+ * @return all viewports on the alignment bound to sequenceSetId
+ */
+ public static AlignViewport[] getViewports(String sequenceSetId)
+ {
+ Vector viewp = new Vector();
+ if (desktop != null)
+ {
+ javax.swing.JInternalFrame[] frames = instance.getAllFrames();
+
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof AlignFrame)
+ {
+ AlignFrame afr = ((AlignFrame) frames[t]);
+ if (afr.getViewport().getSequenceSetId().equals(sequenceSetId))
+ {
+ if (afr.alignPanels != null)
+ {
+ for (int a = 0; a < afr.alignPanels.size(); a++)
+ {
+ if (sequenceSetId.equals(((AlignmentPanel) afr.alignPanels
+ .elementAt(a)).av.getSequenceSetId()))
+ {
+ viewp.addElement(((AlignmentPanel) afr.alignPanels
+ .elementAt(a)).av);
+ }
+ }
+ }
+ else
+ {
+ viewp.addElement(((AlignFrame) frames[t]).getViewport());
+ }
+ }
+ }
+ }
+ if (viewp.size() > 0)
+ {
+ AlignViewport[] vp = new AlignViewport[viewp.size()];
+ viewp.copyInto(vp);
+ return vp;
+ }
+ }
+ return null;
}
public void explodeViews(AlignFrame af)
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- try
+ String fle = chooser.getSelectedFile().toString();
+ if (!vamsasImport(chooser.getSelectedFile()))
{
- v_client = new jalview.gui.VamsasApplication(this, chooser
- .getSelectedFile());
- } catch (Exception ex)
- {
- jalview.bin.Cache.log.error(
- "New vamsas session from existing session file failed:",
- ex);
- return;
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Couldn't import '" + fle + "' as a new vamsas session.",
+ "Vamsas Document Import Failed",
+ JOptionPane.ERROR_MESSAGE);
}
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
}
}
else
}
}
+ /**
+ * 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)
+ {
+ if (v_client != null)
+ {
+
+ jalview.bin.Cache.log
+ .error("Implementation error - load session from a running session is not supported.");
+ return false;
+ }
+
+ setProgressBar("Importing VAMSAS session from " + file.getName(), file
+ .hashCode());
+ try
+ {
+ 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)
+ {
+ throw new Error(
+ "Trying to join a vamsas session when another is already connected.");
+ }
+ if (mysesid == null)
+ {
+ throw new Error("Invalid vamsas session id.");
+ }
+ v_client = new VamsasApplication(this, mysesid);
+ setupVamsasConnectedGui();
+ v_client.initial_update();
+ return (v_client.inSession());
+ }
+
public void vamsasStart_actionPerformed(ActionEvent e)
{
if (v_client == null)
*
* if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
* jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
- *
*/
v_client = new VamsasApplication(this);
setupVamsasConnectedGui();
vamsasSave.setVisible(true);
vamsasStop.setVisible(true);
vamsasImport.setVisible(false); // Document import to existing session is
- // not possible for vamsas-client-1.0.
+ // not possible for vamsas-client-1.0.
}
protected void setupVamsasDisconnectedGui()
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,
* hide vamsas user gui bits when a vamsas document event is being handled.
*
* @param b
- * true to hide gui, false to reveal gui
+ * true to hide gui, false to reveal gui
*/
public void setVamsasUpdate(boolean b)
{
{
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());
+ }
}
}
/**
* Progress bars managed by the IProgressIndicator method.
*/
- private Hashtable progressBars;
+ private Hashtable progressBars, progressBarHandlers;
/*
* (non-Javadoc)
if (progressBars == null)
{
progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
}
if (progressBars.get(new Long(id)) != null)
{
JProgressBar progressPanel = (JProgressBar) progressBars
.remove(new Long(id));
+ if (progressBarHandlers.contains(new Long(id)))
+ {
+ progressBarHandlers.remove(new Long(id));
+ }
removeProgressPanel(progressPanel);
}
else
progressBars.put(new Long(id), addProgressPanel(message));
}
}
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#registerHandler(long,
+ * jalview.gui.IProgressIndicatorHandler)
+ */
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ {
+ throw new Error(
+ "call setProgressBar before registering the progress bar's handler.");
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton("Cancel");
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar("Cancelled "
+ + ((JLabel) progressPanel.getComponent(0)).getText(), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+
+ /**
+ * This will return the first AlignFrame viewing AlignViewport av. It will
+ * break if there are more than one AlignFrames viewing a particular av. This
+ *
+ * @param av
+ * @return alignFrame for av
+ */
+ public static AlignFrame getAlignFrameFor(AlignViewport av)
+ {
+ if (desktop != null)
+ {
+ AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId());
+ for (int panel = 0; aps != null && panel < aps.length; panel++)
+ {
+ if (aps[panel] != null && aps[panel].av == av)
+ {
+ return aps[panel].alignFrame;
+ }
+ }
+ }
+ return null;
+ }
+
+ public VamsasApplication getVamsasApplication()
+ {
+ 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