import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import java.util.logging.ConsoleHandler;
import java.util.logging.Level;
import java.util.logging.Logger;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import javax.swing.UIManager.LookAndFeelInfo;
+import javax.swing.UnsupportedLookAndFeelException;
+import com.formdev.flatlaf.FlatLightLaf;
+import com.formdev.flatlaf.themes.FlatMacLightLaf;
+import com.formdev.flatlaf.util.SystemInfo;
import com.threerings.getdown.util.LaunchUtil;
+//import edu.stanford.ejalbert.launching.IBrowserLaunching;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.PromptUserConfig;
+import jalview.gui.QuitHandler;
+import jalview.gui.QuitHandler.QResponse;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.ChannelProperties;
import jalview.util.HttpUtils;
+import jalview.util.LaunchUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
static
{
Platform.getURLCommandArguments();
+ Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
+ Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
+ Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
+ Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
}
/*
if (!Platform.isJS())
{
System.setSecurityManager(null);
+
+ Runtime.getRuntime().addShutdownHook(new Thread()
+ {
+ public void run()
+ {
+ Console.debug("Running shutdown hook");
+ if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
+ {
+ // Got to here by a SIGTERM signal.
+ // Note we will not actually cancel the quit from here -- it's too
+ // late -- but we can wait for saving files.
+ Console.debug("Checking for saving files");
+ QuitHandler.getQuitResponse(false);
+ }
+ else
+ {
+ Console.debug("Nothing more to do");
+ }
+ Console.debug("Exiting, bye!");
+ // shutdownHook cannot be cancelled, JVM will now halt
+ }
+ });
}
System.out
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+
String val = System.getProperty("sys.install4jVersion");
if (val != null)
{
Cache.loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
+
boolean headless = false;
String usrPropsFile = aparser.getValue("props");
- Cache.loadProperties(usrPropsFile); // must do this before
+ Cache.loadProperties(usrPropsFile); // must do this
+ // before
if (usrPropsFile != null)
{
System.out.println(
}
// anything else!
+ // allow https handshakes to download intermediate certs if necessary
+ System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
+
final String jabawsUrl = aparser.getValue("jabaws");
if (jabawsUrl != null)
{
}
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+
try
{
- Cache.initLogger();
- } catch (NoClassDefFoundError error)
+ Console.initLogger();
+ } catch (
+
+ NoClassDefFoundError error)
{
error.printStackTrace();
System.out.println("\nEssential logging libraries not found."
JalviewTaskbar.setTaskbar(this);
} catch (Exception e)
{
- Cache.log.info("Cannot set Taskbar");
- Cache.log.error(e.getMessage());
+ Console.info("Cannot set Taskbar");
+ Console.error(e.getMessage());
// e.printStackTrace();
} catch (Throwable t)
{
- Cache.log.info("Cannot set Taskbar");
- Cache.log.error(t.getMessage());
+ Console.info("Cannot set Taskbar");
+ Console.error(t.getMessage());
// t.printStackTrace();
}
* @j2sIgnore
*/
{
+
+ /**
+ * Check to see that the JVM version being run is suitable for the Java
+ * version this Jalview was compiled for. Popup a warning if not.
+ */
+ if (!LaunchUtils.checkJavaVersion())
+ {
+ Console.warn("The Java version being used (Java "
+ + LaunchUtils.getJavaVersion()
+ + ") may lead to problems. This installation of Jalview should be used with Java "
+ + LaunchUtils.getJavaCompileVersion() + ".");
+
+ if (!LaunchUtils
+ .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
+ {
+ Object[] options = {
+ MessageManager.getString("label.continue") };
+ JOptionPane.showOptionDialog(null,
+ MessageManager.formatMessage(
+ "warning.wrong_jvm_version_message",
+ LaunchUtils.getJavaVersion(),
+ LaunchUtils.getJavaCompileVersion()),
+ MessageManager
+ .getString("warning.wrong_jvm_version_title"),
+ JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
+ }
+ }
+
if (!aparser.contains("nowebservicediscovery"))
{
desktop.startServiceDiscovery();
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
- Cache.log.debug("Starting questionnaire url at " + url);
+ Console.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
System.out.println("CMD questionnaire[-" + url
+ "] executed successfully!");
// String defurl =
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
- String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
- Cache.log.debug(
+ String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
+ Console.debug(
"Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
}
.println("CMD [-noquestionnaire] executed successfully!");
}
- if (!aparser.contains("nonews"))
+ if (!aparser.contains("nonews")
+ || Cache.getProperty("NONEWS") == null)
{
desktop.checkForNews();
}
- BioJsHTMLOutput.updateBioJS();
+ if (!aparser.contains("nohtmltemplates")
+ || Cache.getProperty("NOHTMLTEMPLATES") == null)
+ {
+ BioJsHTMLOutput.updateBioJS();
+ }
}
}
+ // Check if JVM and compile version might cause problems and log if it
+ // might.
+ if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
+ {
+ Console.warn("The Java version being used (Java "
+ + LaunchUtils.getJavaVersion()
+ + ") may lead to problems. This installation of Jalview should be used with Java "
+ + LaunchUtils.getJavaCompileVersion() + ".");
+ }
+
// Move any new getdown-launcher-new.jar into place over old
// getdown-launcher.jar
String appdirString = System.getProperty("getdownappdir");
}
String file = null, data = null;
+
FileFormatI format = null;
+
DataSourceType protocol = null;
+
FileLoader fileLoader = new FileLoader(!headless);
String groovyscript = null; // script to execute after all loading is
System.out.println("No files to open!");
System.exit(1);
}
+
long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
}
}
}
+
AlignFrame startUpAlframe = null;
// We'll only open the default file if the desktop is visible.
// And the user
*/
{
file = Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_7.jar");
- if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+ + "/examples/exampleFile_2_7.jvp");
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+ || file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
+ file.replace("http:", "https:");
// hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
+ file.replace("_2_3", "_2_7");
+ file.replace("2_7.jar", "2_7.jvp");
// and remove the stale setting
Cache.removeProperty("STARTUP_FILE");
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
+ // don't ask to save when quitting if only the startup file has been
+ // opened
+ Console.debug("Resetting up-to-date flag for startup file");
+ startUpAlframe.getViewport().setSavedUpToDate(true);
// extract groovy arguments before anything else.
}
lafSet = setCrossPlatformLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "system":
lafSet = setSystemLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "gtk":
lafSet = setGtkLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "metal":
lafSet = setMetalLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "nimbus":
lafSet = setNimbusLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "flat":
lafSet = setFlatLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
- }
- break;
- case "quaqua":
- lafSet = setQuaquaLookAndFeel();
- if (!lafSet)
- {
- Cache.log.error("Could not set requested laf=" + laf);
- }
- break;
- case "vaqua":
- lafSet = setVaquaLookAndFeel();
- if (!lafSet)
- {
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "mac":
lafSet = setMacLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "none":
break;
default:
- Cache.log.error("Requested laf=" + laf + " not implemented");
+ Console.error("Requested laf=" + laf + " not implemented");
}
if (!lafSet)
{
setSystemLookAndFeel();
if (Platform.isLinux())
{
- setMetalLookAndFeel();
+ setLinuxLookAndFeel();
}
if (Platform.isMac())
{
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
{
if (info.getName() != null && nameStartsWith
- ? info.getName().toLowerCase()
- .startsWith(name.toLowerCase())
- : info.getName().equalsIgnoreCase(name.toLowerCase()))
+ ? info.getName().toLowerCase(Locale.ROOT)
+ .startsWith(name.toLowerCase(Locale.ROOT))
+ : info.getName().toLowerCase(Locale.ROOT)
+ .equals(name.toLowerCase(Locale.ROOT)))
{
className = info.getClassName();
break;
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
private static boolean setFlatLookAndFeel()
{
- boolean set = setSpecificLookAndFeel("flatlaf light",
- "com.formdev.flatlaf.FlatLightLaf", false);
+ boolean set = false;
+ if (SystemInfo.isMacOS)
+ {
+ try
+ {
+ UIManager.setLookAndFeel(
+ "com.formdev.flatlaf.themes.FlatMacLightLaf");
+ set = true;
+ Console.debug("Using FlatMacLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ System.setProperty("apple.awt.application.name",
+ ChannelProperties.getProperty("app_name"));
+ System.setProperty("apple.awt.application.appearance", "system");
+ if (SystemInfo.isMacFullWindowContentSupported
+ && Desktop.desktop != null)
+ {
+ Console.debug("Setting transparent title bar");
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.fullWindowContent", true);
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.transparentTitleBar", true);
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.fullscreenable", true);
+ }
+ SwingUtilities.invokeLater(() -> {
+ FlatMacLightLaf.setup();
+ });
+ Console.debug("Using FlatMacLightLaf");
+ set = true;
+ }
+ if (!set)
+ {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+ set = true;
+ Console.debug("Using FlatLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ // Windows specific properties here
+ SwingUtilities.invokeLater(() -> {
+ FlatLightLaf.setup();
+ });
+ Console.debug("Using FlatLightLaf");
+ set = true;
+ }
+ else if (SystemInfo.isLinux)
+ {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+ set = true;
+ Console.debug("Using FlatLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ // enable custom window decorations
+ JFrame.setDefaultLookAndFeelDecorated(true);
+ JDialog.setDefaultLookAndFeelDecorated(true);
+ SwingUtilities.invokeLater(() -> {
+ FlatLightLaf.setup();
+ });
+ Console.debug("Using FlatLightLaf");
+ set = true;
+ }
+
+ if (!set)
+ {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+ set = true;
+ Console.debug("Using FlatLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ }
+
if (set)
{
+ UIManager.put("TabbedPane.tabType", "card");
UIManager.put("TabbedPane.showTabSeparators", true);
+ UIManager.put("TabbedPane.showContentSeparator", true);
UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
+ UIManager.put("TabbedPane.tabsOverlapBorder", true);
+ UIManager.put("TabbedPane.hasFullBorder", true);
+ UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
+ UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
+ UIManager.put("TabbedPane.smoothScrolling", true);
+ UIManager.put("TabbedPane.tabWidthMode", "compact");
UIManager.put("TabbedPane.selectedBackground", Color.white);
}
- return set;
- }
-
- private static boolean setQuaquaLookAndFeel()
- {
- return setSpecificLookAndFeel("quaqua",
- ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
- .getName(),
- false);
- }
- private static boolean setVaquaLookAndFeel()
- {
- return setSpecificLookAndFeel("vaqua",
- "org.violetlib.aqua.AquaLookAndFeel", false);
+ Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
+ return set;
}
private static boolean setMacLookAndFeel()
System.setProperty("com.apple.mrj.application.apple.menu.about.name",
ChannelProperties.getProperty("app_name"));
System.setProperty("apple.laf.useScreenMenuBar", "true");
+ /*
+ * broken native LAFs on (ARM?) macbooks
set = setQuaquaLookAndFeel();
if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
- .toLowerCase().contains("quaqua"))
+ .toLowerCase(Locale.ROOT).contains("quaqua"))
{
set = setVaquaLookAndFeel();
}
+ */
+ set = setFlatLookAndFeel();
+ return set;
+ }
+
+ private static boolean setLinuxLookAndFeel()
+ {
+ boolean set = false;
+ set = setFlatLookAndFeel();
+ if (!set)
+ set = setMetalLookAndFeel();
+ // avoid GtkLookAndFeel -- not good results especially on HiDPI
+ if (!set)
+ set = setNimbusLookAndFeel();
return set;
}
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
- + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
}
private static void startUsageStats(final Desktop desktop)
@Override
public void run()
{
- Cache.log.debug(
+ Console.debug(
"Initialising googletracker for usage stats.");
Cache.initGoogleTracker();
- Cache.log.debug("Tracking enabled.");
+ Console.debug("Tracking enabled.");
}
}, new Runnable()
{
@Override
public void run()
{
- Cache.log.debug("Not enabling Google Tracking.");
+ Console.debug("Not enabling Google Tracking.");
}
}, null, true);
desktop.addDialogThread(prompter);
}
/**
- * Quit method delegates to Desktop.quit - unless running in headless mode
- * when it just ends the JVM
+ * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
*/
public void quit()
{
- if (desktop != null)
- {
- desktop.quit();
- }
- else
- {
- System.exit(0);
- }
+ // System.exit will run the shutdownHook first
+ System.exit(0);
}
public static AlignFrame getCurrentAlignFrame()
git://source.jalview.org / jalview.git / blobdiff