Version "
- + jalview.bin.Cache.getProperty("VERSION")
- + "; last updated: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
- }
+ StringBuilder message = new StringBuilder(1024);
+ message.append("Version: ")
+ .append(Cache.getProperty("VERSION")).append("
")
+ .append("Built: ")
+ .append(Cache.getDefault("BUILD_DATE", "unknown"))
+ .append(" from ").append(Cache.getBuildDetailsForSplash())
+ .append("");
- if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
- .equals("Checking"))
+ String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
+ if (latestVersion.equals("Checking"))
{
// JBP removed this message for 2.11: May be reinstated in future version
// message.append("
...Checking latest version...");
}
- else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
- .equals(jalview.bin.Cache.getProperty("VERSION")))
+ else if (!latestVersion.equals(Cache.getProperty("VERSION")))
{
boolean red = false;
- if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
+ if (Cache.getProperty("VERSION").toLowerCase()
.indexOf("automated build") == -1)
{
red = true;
@@ -1346,45 +1390,48 @@ public class Desktop extends jalview.jbgui.GDesktop
message.append("");
}
- message.append("
!! Version "
- + jalview.bin.Cache.getDefault("LATEST_VERSION",
- "..Checking..")
- + " is available for download from "
- + jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
- + " !!");
+ message.append("
!! Version ")
+ .append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
+ .append(" is available for download from ")
+ .append(Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org"))
+ .append(" !!");
if (red)
{
message.append("
");
}
}
- message.append("
Authors: " + jalview.bin.Cache.getDefault(
- "AUTHORFNAMES",
- "The Jalview Authors (See AUTHORS file for current list)")
- + "
Development managed by The Barton Group, University of Dundee, Scotland, UK.
"
- + "
For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list"
- + "
If you use Jalview, please cite:"
- + "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "
Bioinformatics doi: 10.1093/bioinformatics/btp033"
- + "");
- return message;
+ message.append("
Authors: ");
+ message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
+ message.append(CITATION);
+
+ return message.toString();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on requesting Help documentation
*/
@Override
- public void documentationMenuItem_actionPerformed(ActionEvent e)
+ public void documentationMenuItem_actionPerformed()
{
try
{
- Help.showHelpWindow();
+ if (Platform.isJS())
+ {
+ BrowserLauncher.openURL("http://www.jalview.org/help.html");
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ Help.showHelpWindow();
+ }
} catch (Exception ex)
{
+ System.err.println("Error opening help: " + ex.getMessage());
}
}
@@ -1444,9 +1491,9 @@ public class Desktop extends jalview.jbgui.GDesktop
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
- jalview.bin.Cache.log.debug("Collecting garbage...");
+ Cache.log.debug("Collecting garbage...");
System.gc();
- jalview.bin.Cache.log.debug("Finished garbage collection.");
+ Cache.log.debug("Finished garbage collection.");
}
/*
@@ -1484,11 +1531,14 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
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);
+ if (jconsole != null) // BH 2018
+ {
+ showConsole.setSelected(selected);
+ Cache.setProperty("SHOW_JAVA_CONSOLE",
+ Boolean.valueOf(selected).toString());
+ jconsole.setVisible(selected);
+ }
}
void reorderAssociatedWindows(boolean minimize, boolean close)
@@ -1577,12 +1627,12 @@ public class Desktop extends jalview.jbgui.GDesktop
@Override
protected void preferences_actionPerformed(ActionEvent e)
{
- new Preferences();
+ Preferences.openPreferences();
}
/**
- * Shows a file chooser dialog and writes out the current session as a Jalview
- * project file
+ * Prompts the user to choose a file and then saves the Jalview state as a
+ * Jalview project file
*/
@Override
public void saveState_actionPerformed()
@@ -1633,18 +1683,23 @@ public class Desktop extends jalview.jbgui.GDesktop
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
{ chosenFile.getName() }), chosenFile.hashCode());
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chosenFile.getParent());
+ Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- BackupFiles backupfiles = new BackupFiles(chosenFile);
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile)
+ : null;
- new Jalview2XML().saveState(backupfiles.getTempFile());
+ new Jalview2XML().saveState(
+ doBackup ? backupfiles.getTempFile() : chosenFile);
- backupfiles.setWriteSuccess(true);
- backupfiles.rollBackupsAndRenameTempFile();
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(true);
+ backupfiles.rollBackupsAndRenameTempFile();
+ }
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst saving current state to "
@@ -1695,49 +1750,51 @@ public class Desktop extends jalview.jbgui.GDesktop
"Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
- "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
- // allowBackupFiles
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two
+ // booleans:
+ // allFiles,
+ // allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- final File selectedFile = chooser.getSelectedFile();
- setProjectFile(selectedFile);
- final String choice = selectedFile.getAbsolutePath();
- Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
+ File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ String choice = selectedFile.getAbsolutePath();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+ new Thread(new Runnable()
{
- setProgressBar(MessageManager.formatMessage(
- "label.loading_jalview_project", new Object[]
- { choice }), choice.hashCode());
- try
- {
- new Jalview2XML().loadJalviewAlign(choice);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
+ @Override
+ public void run()
{
- Cache.log.error(
- "Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager.getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
+ try
+ {
+ new Jalview2XML().loadJalviewAlign(selectedFile);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager
+ .getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
}
- setProgressBar(null, choice.hashCode());
- }
- }).start();
- }
+ }, "Project Loader").start();
+ }
+ });
+
+ chooser.showOpenDialog(this);
}
@Override
@@ -1750,7 +1807,7 @@ public class Desktop extends jalview.jbgui.GDesktop
ArrayList fileLoadingPanels = new ArrayList<>();
- public void startLoading(final String fileName)
+ public void startLoading(final Object fileName)
{
if (fileLoadingCount == 0)
{
@@ -1925,9 +1982,7 @@ public class Desktop extends jalview.jbgui.GDesktop
// FIXME: ideally should use UI interface API
FeatureSettings viewFeatureSettings = (af.featureSettings != null
- && af.featureSettings.isOpen())
- ? af.featureSettings
- : null;
+ && af.featureSettings.isOpen()) ? af.featureSettings : null;
Rectangle fsBounds = af.getFeatureSettingsGeometry();
for (int i = 0; i < size; i++)
{
@@ -1960,7 +2015,8 @@ public class Desktop extends jalview.jbgui.GDesktop
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- // and materialise a new feature settings dialog instance for the new alignframe
+ // and materialise a new feature settings dialog instance for the new
+ // alignframe
// (closes the old as if 'OK' was pressed)
if (ap == af.alignPanel && newaf.featureSettings != null
&& newaf.featureSettings.isOpen()
@@ -2030,13 +2086,12 @@ public class Desktop extends jalview.jbgui.GDesktop
}
}
}
+
// refresh the feature setting UI for the source frame if it exists
- if (source.featureSettings != null
- && source.featureSettings.isOpen())
+ if (source.featureSettings != null && source.featureSettings.isOpen())
{
source.showFeatureSettingsUI();
}
-
}
public JInternalFrame[] getAllFrames()
@@ -2145,7 +2200,6 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
public class MyDesktopPane extends JDesktopPane implements Runnable
{
-
private static final float ONE_MB = 1048576f;
boolean showMemoryUsage = false;
@@ -2231,6 +2285,9 @@ public class Desktop extends jalview.jbgui.GDesktop
10, getHeight() - fm.getHeight());
}
}
+
+ // output debug scale message. Important for jalview.bin.HiDPISettingTest2
+ Desktop.debugScaleMessage(Desktop.getDesktop().getGraphics());
}
}
@@ -2327,7 +2384,7 @@ public class Desktop extends jalview.jbgui.GDesktop
openGroovyConsole();
} catch (Exception ex)
{
- jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+ Cache.log.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
@@ -2386,9 +2443,12 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
protected void addQuitHandler()
{
- getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
- .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
+ getRootPane()
+ .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke
+ .getKeyStroke(KeyEvent.VK_Q,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx()),
"Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
@@ -2439,6 +2499,8 @@ public class Desktop extends jalview.jbgui.GDesktop
@Override
public void setProgressBar(String message, long id)
{
+ // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
+
if (progressBars == null)
{
progressBars = new Hashtable<>();
@@ -2833,7 +2895,6 @@ public class Desktop extends jalview.jbgui.GDesktop
} catch (InterruptedException x)
{
}
- ;
}
if (instance == null)
{
@@ -2858,28 +2919,39 @@ public class Desktop extends jalview.jbgui.GDesktop
block.release();
}
+ /**
+ * Outputs an image of the desktop to file in EPS format, after prompting the
+ * user for choice of Text or Lineart character rendering (unless a preference
+ * has been set). The file name is generated as
+ *
+ *
+ * Jalview_snapshot_nnnnn.eps where nnnnn is the current timestamp in milliseconds
+ *
+ */
@Override
protected void snapShotWindow_actionPerformed(ActionEvent e)
{
+ // currently the menu option to do this is not shown
invalidate();
- File of;
- ImageMaker im = new jalview.util.ImageMaker(
- this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(),
- getHeight(), of = new File("Jalview_snapshot"
- + System.currentTimeMillis() + ".eps"),
- "View of desktop", null, 0, false);
- try
- {
- paintAll(im.getGraphics());
- im.writeImage();
- } catch (Exception q)
+
+ int width = getWidth();
+ int height = getHeight();
+ File of = new File(
+ "Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
+ ImageWriterI writer = new ImageWriterI()
{
- Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
- q);
- return;
- }
- Cache.log.info("Successfully written snapshot to file "
- + of.getAbsolutePath());
+ @Override
+ public void exportImage(Graphics g) throws Exception
+ {
+ paintAll(g);
+ Cache.log.info("Successfully written snapshot to file "
+ + of.getAbsolutePath());
+ }
+ };
+ String title = "View of desktop";
+ ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
+ title);
+ exporter.doExport(of, this, width, height, title);
}
/**
@@ -3051,11 +3123,33 @@ public class Desktop extends jalview.jbgui.GDesktop
* - the payload from the drop event
* @throws Exception
*/
- public static void transferFromDropTarget(List files,
+ public static void transferFromDropTarget(List