Version "
- + jalview.bin.Cache.getProperty("VERSION")
- + "; last updated: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
- }
-
- 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 +1388,48 @@ 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 +1489,9 @@ 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 +1529,14 @@ 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)
@@ -1581,8 +1629,8 @@ public class Desktop extends jalview.jbgui.GDesktop
}
/**
- * 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 +1681,22 @@ 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",
+ 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 "
@@ -1664,7 +1716,7 @@ public class Desktop extends jalview.jbgui.GDesktop
setProgressBar(null, chosenFile.hashCode());
}
}).start();
- }
+ }
}
@Override
@@ -1699,45 +1751,44 @@ public class Desktop extends jalview.jbgui.GDesktop
// 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(choice);
+ } 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();
- }
+ }).start();
+ }
+ });
+
+ chooser.showOpenDialog(this);
}
@Override
@@ -1750,7 +1801,7 @@ 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)
{
@@ -1952,9 +2003,9 @@ public class Desktop extends jalview.jbgui.GDesktop
/**
* Gather expanded views (separate AlignFrame's) with the same sequence set
- * identifier back in to this frame as additional views, and close the
- * expanded views. Note the expanded frames may themselves have multiple
- * views. We take the lot.
+ * identifier back in to this frame as additional views, and close the expanded
+ * views. Note the expanded frames may themselves have multiple views. We take
+ * the lot.
*
* @param source
*/
@@ -1990,7 +2041,6 @@ public class Desktop extends jalview.jbgui.GDesktop
}
}
}
-
}
public JInternalFrame[] getAllFrames()
@@ -2092,14 +2142,13 @@ public class Desktop extends jalview.jbgui.GDesktop
/**
* Proxy class for JDesktopPane which optionally displays the current memory
- * usage and highlights the desktop area with a red bar if free memory runs
- * low.
+ * usage and highlights the desktop area with a red bar if free memory runs low.
*
* @author AMW
*/
- public class MyDesktopPane extends JDesktopPane implements Runnable
+ public class MyDesktopPane extends JDesktopPane
+ implements Runnable
{
-
private static final float ONE_MB = 1048576f;
boolean showMemoryUsage = false;
@@ -2281,7 +2330,7 @@ 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"),
@@ -2335,8 +2384,8 @@ public class Desktop extends jalview.jbgui.GDesktop
}
/**
- * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
- * binding when opened
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding
+ * when opened
*/
protected void addQuitHandler()
{
@@ -2393,6 +2442,8 @@ 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<>();
@@ -2469,9 +2520,8 @@ public class Desktop extends jalview.jbgui.GDesktop
}
/**
- * This will return the first AlignFrame holding the given viewport instance.
- * It will break if there are more than one AlignFrames viewing a particular
- * av.
+ * This will return the first AlignFrame holding the given viewport instance. It
+ * will break if there are more than one AlignFrames viewing a particular av.
*
* @param viewport
* @return alignFrame for viewport
@@ -2787,7 +2837,6 @@ public class Desktop extends jalview.jbgui.GDesktop
} catch (InterruptedException x)
{
}
- ;
}
if (instance == null)
{
@@ -2812,34 +2861,45 @@ 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);
}
/**
* Explode the views in the given SplitFrame into separate SplitFrame windows.
- * This respects (remembers) any previous 'exploded geometry' i.e. the size
- * and location last time the view was expanded (if any). However it does not
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size and
+ * location last time the view was expanded (if any). However it does not
* remember the split pane divider location - this is set to match the
* 'exploding' frame.
*
@@ -3005,11 +3065,31 @@ 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