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.ExecutorService;
import java.util.concurrent.Executors;
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;
* Send this message to stderr as the warning that follows (due to
* reflection) also goes to stderr.
*/
- System.err.println(
+ 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";
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");
+ }
}
/**
}
} catch (Exception ex)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"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());
}
} 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
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"));
/**
* 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);
+ }
+
}