import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Component;
import java.awt.Dimension;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.geom.AffineTransform;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.List;
import java.util.ListIterator;
import java.util.Locale;
+import java.util.Map;
import java.util.Vector;
-import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Semaphore;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
import jalview.gui.ImageExporter.ImageWriterI;
import jalview.gui.QuitHandler.QResponse;
import jalview.io.BackupFiles;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.io.exceptions.ImageOutputException;
import jalview.jbgui.GSplitFrame;
import jalview.jbgui.GStructureViewer;
import jalview.project.Jalview2XML;
public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
+ private static int DRAG_MODE = JDesktopPane.OUTLINE_DRAG_MODE;
+
+ public static void setLiveDragMode(boolean b)
+ {
+ DRAG_MODE = b ? JDesktopPane.LIVE_DRAG_MODE
+ : JDesktopPane.OUTLINE_DRAG_MODE;
+ if (desktop != null)
+ desktop.setDragMode(DRAG_MODE);
+ }
+
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
public static boolean nosplash = false;
{
if (LaunchUtils.getJavaVersion() >= 11)
{
- jalview.bin.Console.info(
+ /*
+ * Send this message to stderr as the warning that follows (due to
+ * reflection) also goes to stderr.
+ */
+ jalview.bin.Console.errPrintln(
"Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that.");
}
+ final String awtAppClassName = "awtAppClassName";
try
{
Toolkit xToolkit = Toolkit.getDefaultToolkit();
Field awtAppClassNameField = null;
if (Arrays.stream(declaredFields)
- .anyMatch(f -> f.getName().equals("awtAppClassName")))
+ .anyMatch(f -> f.getName().equals(awtAppClassName)))
{
awtAppClassNameField = xToolkit.getClass()
- .getDeclaredField("awtAppClassName");
+ .getDeclaredField(awtAppClassName);
}
String title = ChannelProperties.getProperty("app_name");
}
else
{
- jalview.bin.Console.debug("XToolkit: awtAppClassName not found");
+ jalview.bin.Console
+ .debug("XToolkit: " + awtAppClassName + " not found");
}
} catch (Exception e)
{
- jalview.bin.Console.debug("Error setting awtAppClassName");
+ jalview.bin.Console.debug("Error setting " + awtAppClassName);
jalview.bin.Console.trace(Cache.getStackTraceString(e));
}
}
}
getContentPane().add(desktop, BorderLayout.CENTER);
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+ desktop.setDragMode(DRAG_MODE);
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
desktop.setDesktopManager(new MyDesktopManager(
- (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
- : Platform.isAMacAndNotJS()
- ? new AquaInternalFrameManager(
- desktop.getDesktopManager())
- : desktop.getDesktopManager())));
+ Platform.isJS() ? desktop.getDesktopManager()
+ : new DefaultDesktopManager()));
+ /*
+ (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+ : Platform.isAMacAndNotJS()
+ ? new AquaInternalFrameManager(
+ desktop.getDesktopManager())
+ : desktop.getDesktopManager())));
+ */
Rectangle dims = getLastKnownDimensions("");
if (dims != null)
setBounds(xPos, yPos, 900, 650);
}
+ // start dialogue queue for single dialogues
+ startDialogQueue();
+
if (!Platform.isJS())
/**
* Java only
}
// Thread off a new instance of the file chooser - this reduces the time
- // it
- // takes to open it later on.
+ // it takes to open it later on.
new Thread(new Runnable()
{
@Override
public void run()
{
jalview.bin.Console.debug("Filechooser init thread started.");
- String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ String fileFormat = FileLoader.getUseDefaultFileFormat()
+ ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+ : null;
JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
fileFormat);
jalview.bin.Console.debug("Filechooser init thread finished.");
}
});
desktop.addMouseListener(ma);
+
+ if (Platform.isJS())
+ {
+ // used for jalviewjsTest
+ jalview.bin.Console.info("JALVIEWJS: CREATED DESKTOP");
+ }
+
}
/**
public void paste()
{
- try
+ // quick patch for JAL-4150 - needs some more work and test coverage
+ // TODO - unify below and AlignFrame.paste()
+ // TODO - write tests and fix AlignFrame.paste() which doesn't track if
+ // clipboard has come from a different alignment window than the one where
+ // paste has been called! JAL-4151
+
+ if (Desktop.jalviewClipboard != null)
{
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- Transferable contents = c.getContents(this);
+ // The clipboard was filled from within Jalview, we must use the
+ // sequences
+ // And dataset from the copied alignment
+ SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
+ // be doubly sure that we create *new* sequence objects.
+ SequenceI[] sequences = new SequenceI[newseq.length];
+ for (int i = 0; i < newseq.length; i++)
+ {
+ sequences[i] = new Sequence(newseq[i]);
+ }
+ Alignment alignment = new Alignment(sequences);
+ // dataset is inherited
+ alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+ AlignFrame af = new AlignFrame(alignment, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ String newtitle = new String("Copied sequences");
+
+ if (Desktop.jalviewClipboard[2] != null)
+ {
+ HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ af.viewport.setHiddenColumns(hc);
+ }
+
+ Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
- if (contents != null)
+ }
+ else
+ {
+ try
{
- String file = (String) contents
- .getTransferData(DataFlavor.stringFlavor);
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable contents = c.getContents(this);
- FileFormatI format = new IdentifyFile().identify(file,
- DataSourceType.PASTE);
+ if (contents != null)
+ {
+ String file = (String) contents
+ .getTransferData(DataFlavor.stringFlavor);
- new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
+ FileFormatI format = new IdentifyFile().identify(file,
+ DataSourceType.PASTE);
+ new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
+
+ }
+ } catch (Exception ex)
+ {
+ jalview.bin.Console.outPrintln(
+ "Unable to paste alignment from system clipboard:\n" + ex);
}
- } catch (Exception ex)
- {
- System.out.println(
- "Unable to paste alignment from system clipboard:\n" + ex);
}
}
setKeyBindings(frame);
- desktop.add(frame);
+ // Since the latest FlatLaf patch, we occasionally have problems showing
+ // structureViewer frames...
+ int tries = 3;
+ boolean shown = false;
+ Exception last = null;
+ do
+ {
+ try
+ {
+ desktop.add(frame);
+ shown = true;
+ } catch (IllegalArgumentException iaex)
+ {
+ last = iaex;
+ tries--;
+ jalview.bin.Console.info("Squashed IllegalArgument Exception ("
+ + tries + " left) for " + frame.getTitle(), iaex);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException iex)
+ {
+ }
+ ;
+ }
+ } while (!shown && tries > 0);
+ if (!shown)
+ {
+ jalview.bin.Console.error(
+ "Serious Problem whilst showing window " + frame.getTitle(),
+ last);
+ }
windowMenu.add(menuItem);
@Override
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
- String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ String fileFormat = FileLoader.getUseDefaultFileFormat()
+ ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+ : null;
JalviewFileChooser chooser = JalviewFileChooser.forRead(
Cache.getProperty("LAST_DIRECTORY"), fileFormat,
BackupFiles.getEnabled());
new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE,
format);
- return null;
});
chooser.showOpenDialog(this);
}
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
- Callable<Void> action = () -> {
+ Runnable action = () -> {
@SuppressWarnings("unchecked")
String url = (history instanceof JTextField
? ((JTextField) history).getText()
JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
MessageManager.getString("label.url_not_found"),
JvOptionPane.WARNING_MESSAGE);
-
- return null; // Void
+ return;
}
if (viewport != null)
new FileLoader().LoadFile(url, DataSourceType.URL, format);
}
}
- return null; // Void
};
String dialogOption = MessageManager
.getString("label.input_alignment_from_url");
public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag)
{
- final Callable<Void> doDesktopQuit = () -> {
+ final Runnable doDesktopQuit = () -> {
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
if (jvnews != null)
{
storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+ }
+
+ // Frames should all close automatically. Keeping external
+ // viewers open should already be decided by user.
+ closeAll_actionPerformed(null);
+ // check for aborted quit
+ if (QuitHandler.quitCancelled())
+ {
+ jalview.bin.Console.debug("Desktop aborting quit");
+ return;
}
if (dialogExecutor != null)
dialogExecutor.shutdownNow();
}
- closeAll_actionPerformed(null);
-
if (groovyConsole != null)
{
// suppress a possible repeat prompt to save script
// instance.dispose();
}
instance.quit();
-
- return null; // Void
};
return QuitHandler.getQuitResponse(ui, doDesktopQuit, doDesktopQuit,
// this will run the shutdownHook but QuitHandler.getQuitResponse() should
// not run a second time if gotQuitResponse flag has been set (i.e. user
// confirmed quit of some kind).
- System.exit(0);
+ Jalview.exit("Desktop exiting.", ExitCode.OK);
}
private void storeLastKnownDimensions(String string, Rectangle jc)
}
} catch (Exception ex)
{
- System.err.println("Error opening help: " + ex.getMessage());
+ jalview.bin.Console
+ .errPrintln("Error opening help: " + ex.getMessage());
}
}
}
}
Jalview.setCurrentAlignFrame(null);
- System.out.println("ALL CLOSED");
+ jalview.bin.Console.info("ALL CLOSED");
/*
* reset state of singleton objects as appropriate (clear down session state
}
}
+ public int structureViewersStillRunningCount()
+ {
+ int count = 0;
+ JInternalFrame[] frames = desktop.getAllFrames();
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] != null
+ && frames[i] instanceof JalviewStructureDisplayI)
+ {
+ if (((JalviewStructureDisplayI) frames[i]).stillRunning())
+ count++;
+ }
+ }
+ return count;
+ }
+
@Override
public void raiseRelated_actionPerformed(ActionEvent e)
{
boolean autoSave = projectFile != null && !saveAs
&& BackupFiles.getEnabled();
- // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+ // jalview.bin.Console.outPrintln("autoSave="+autoSave+",
+ // projectFile='"+projectFile+"',
// saveAs="+saveAs+", Backups
// "+(BackupFiles.getEnabled()?"enabled":"disabled"));
saveState_actionPerformed(true);
}
- private void setProjectFile(File choice)
+ protected void setProjectFile(File choice)
{
this.projectFile = choice;
}
}
}
}, "Project Loader").start();
- return null;
});
chooser.showOpenDialog(this);
/**
* single thread that handles display of dialogs to user.
*/
- ExecutorService dialogExecutor = Executors.newSingleThreadExecutor();
+ ExecutorService dialogExecutor = Executors.newFixedThreadPool(3);
/**
* flag indicating if dialogExecutor should try to acquire a permit
/**
* pause the queue
*/
- private java.util.concurrent.Semaphore block = new Semaphore(0);
+ private Semaphore block = new Semaphore(0);
private static groovy.ui.Console groovyConsole;
{
if (dialogPause)
{
- try
- {
- block.acquire();
- } catch (InterruptedException x)
- {
- }
+ acquireDialogQueue();
}
if (instance == null)
{
});
}
+ private boolean dialogQueueStarted = false;
+
public void startDialogQueue()
{
+ if (dialogQueueStarted)
+ {
+ return;
+ }
// set the flag so we don't pause waiting for another permit and semaphore
// the current task to begin
- dialogPause = false;
+ releaseDialogQueue();
+ dialogQueueStarted = true;
+ }
+
+ public void acquireDialogQueue()
+ {
+ try
+ {
+ block.acquire();
+ dialogPause = true;
+ } catch (InterruptedException e)
+ {
+ jalview.bin.Console.debug("Interruption when acquiring DialogueQueue",
+ e);
+ }
+ }
+
+ public void releaseDialogQueue()
+ {
+ if (!dialogPause)
+ {
+ return;
+ }
block.release();
+ dialogPause = false;
}
/**
String title = "View of desktop";
ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
title);
- exporter.doExport(of, this, width, height, title);
+ try
+ {
+ exporter.doExport(of, this, width, height, title);
+ } catch (ImageOutputException ioex)
+ {
+ jalview.bin.Console.error(
+ "Unexpected error whilst writing Jalview desktop snapshot as EPS",
+ ioex);
+ }
}
/**
{
if (Platform.isAMacAndNotJS())
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Please ignore plist error - occurs due to problem with java 8 on OSX");
}
}
jalview.bin.Console.debug(Cache.getStackTraceString(e));
}
}
+
+ /**
+ * closes the current instance window, disposes and forgets about it.
+ */
+ public static void closeDesktop()
+ {
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.instance.setVisible(false);
+ Desktop us = Desktop.instance;
+ Desktop.instance = null;
+ // call dispose in a separate thread - try to avoid indirect deadlocks
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ ExecutorService dex = us.dialogExecutor;
+ if (dex != null)
+ {
+ dex.shutdownNow();
+ us.dialogExecutor = null;
+ us.block.drainPermits();
+ }
+ us.dispose();
+ }
+ }).start();
+ }
+ }
+
+ /**
+ * checks if any progress bars are being displayed in any of the windows
+ * managed by the desktop
+ *
+ * @return
+ */
+ public boolean operationsAreInProgress()
+ {
+ JInternalFrame[] frames = getAllFrames();
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof IProgressIndicator)
+ {
+ if (((IProgressIndicator) frame).operationInProgress())
+ {
+ return true;
+ }
+ }
+ }
+ return operationInProgress();
+ }
+
+ /**
+ * keep track of modal JvOptionPanes open as modal dialogs for AlignFrames.
+ * The way the modal JInternalFrame is made means it cannot be a child of an
+ * AlignFrame, so closing the AlignFrame might leave the modal open :(
+ */
+ private static Map<AlignFrame, JInternalFrame> alignFrameModalMap = new HashMap<>();
+
+ protected static void addModal(AlignFrame af, JInternalFrame jif)
+ {
+ alignFrameModalMap.put(af, jif);
+ }
+
+ protected static void closeModal(AlignFrame af)
+ {
+ if (!alignFrameModalMap.containsKey(af))
+ {
+ return;
+ }
+ JInternalFrame jif = alignFrameModalMap.get(af);
+ if (jif != null)
+ {
+ try
+ {
+ jif.setClosed(true);
+ } catch (PropertyVetoException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ alignFrameModalMap.remove(af);
+ }
+
+ public void nonBlockingDialog(String title, String message, String button,
+ int type, boolean scrollable, boolean modal)
+ {
+ nonBlockingDialog(32, 2, title, message, null, button, type, scrollable,
+ modal);
+ }
+
+ public void nonBlockingDialog(int width, int height, String title,
+ String message, String boxtext, String button, int type,
+ boolean scrollable, boolean modal)
+ {
+ if (type < 0)
+ {
+ type = JvOptionPane.WARNING_MESSAGE;
+ }
+ JLabel jl = new JLabel(message);
+
+ JTextArea jta = new JTextArea(height, width);
+ // jta.setLineWrap(true);
+ jta.setEditable(false);
+ jta.setWrapStyleWord(true);
+ jta.setAutoscrolls(true);
+ jta.setText(boxtext);
+
+ JScrollPane jsp = scrollable
+ ? new JScrollPane(jta, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
+ JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED)
+ : null;
+
+ JvOptionPane jvp = JvOptionPane.newOptionDialog(this);
+
+ JPanel jp = new JPanel();
+ jp.setLayout(new BoxLayout(jp, BoxLayout.Y_AXIS));
+
+ if (message != null)
+ {
+ jl.setAlignmentX(Component.LEFT_ALIGNMENT);
+ jp.add(jl);
+ }
+ if (boxtext != null)
+ {
+ if (scrollable)
+ {
+ jsp.setAlignmentX(Component.LEFT_ALIGNMENT);
+ jp.add(jsp);
+ }
+ else
+ {
+ jta.setAlignmentX(Component.LEFT_ALIGNMENT);
+ jp.add(jta);
+ }
+ }
+
+ jvp.setResponseHandler(JOptionPane.YES_OPTION, () -> {
+ });
+ jvp.showDialogOnTopAsync(this, jp, title, JOptionPane.YES_OPTION, type,
+ null, new Object[]
+ { button }, button, modal, null, false);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff