*/
package jalview.bin;
-import jalview.ext.so.SequenceOntology;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.PromptUserConfig;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.BioJsHTMLOutput;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
-import jalview.io.FileLoader;
-import jalview.io.HtmlSvgOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
+import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
+import java.util.Locale;
import java.util.Map;
+import java.util.Properties;
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.bin.ArgParser.Arg;
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.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
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;
*/
public class Jalview
{
+ 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");
+ }
+
/*
* singleton instance of this class
*/
static
{
- // grab all the rights we can the JVM
- Policy.setPolicy(new Policy()
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- @Override
- public PermissionCollection getPermissions(CodeSource codesource)
+ // grab all the rights we can for the JVM
+ Policy.setPolicy(new Policy()
{
- Permissions perms = new Permissions();
- perms.add(new AllPermission());
- return (perms);
- }
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
- @Override
- public void refresh()
- {
- }
- });
+ @Override
+ public void refresh()
+ {
+ }
+ });
+ }
}
/**
*/
public static void main(String[] args)
{
+ // setLogging(); // BH - for event debugging in JavaScript
instance = new Jalview();
instance.doMain(args);
}
+ private static void logClass(String name)
+ {
+ // BH - for event debugging in JavaScript
+ ConsoleHandler consoleHandler = new ConsoleHandler();
+ consoleHandler.setLevel(Level.ALL);
+ Logger logger = Logger.getLogger(name);
+ logger.setLevel(Level.ALL);
+ logger.addHandler(consoleHandler);
+ }
+
+ @SuppressWarnings("unused")
+ private static void setLogging()
+ {
+
+ /**
+ * @j2sIgnore
+ *
+ */
+ {
+ System.out.println("not in js");
+ }
+
+ // BH - for event debugging in JavaScript (Java mode only)
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ Logger.getLogger("").setLevel(Level.ALL);
+ logClass("java.awt.EventDispatchThread");
+ logClass("java.awt.EventQueue");
+ logClass("java.awt.Component");
+ logClass("java.awt.focus.Component");
+ logClass("java.awt.focus.DefaultKeyboardFocusManager");
+ }
+
+ }
+
/**
* @param args
*/
void doMain(String[] args)
{
- System.setSecurityManager(null);
+
+ if (!Platform.isJS())
+ {
+ System.setSecurityManager(null);
+ }
+
+ // get args needed before proper ArgParser
+ Map<ArgParser.Arg, String> bootstrapArgs = ArgParser
+ .bootstrapArgs(args);
+
System.out
.println("Java version: " + System.getProperty("java.version"));
System.out.println("Java Home: " + System.getProperty("java.home"));
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+
String val = System.getProperty("sys.install4jVersion");
if (val != null)
{
System.out.println("Launcher version: " + val);
}
+ if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
+ {
+ System.setProperty("flatlaf.uiScale", "1");
+ }
+
+ // get bootstrap properties (mainly for the logger level)
+ Properties bootstrapProperties = Cache
+ .bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
+
// report Jalview version
Cache.loadBuildProperties(true);
+ // old ArgsParser
ArgsParser aparser = new ArgsParser(args);
+
+ // old
boolean headless = false;
+ // new
+ boolean headlessArg = false;
- if (aparser.contains("help") || aparser.contains("h"))
+ try
+ {
+ String logLevel = bootstrapArgs.containsKey(Arg.DEBUG) ? "DEBUG"
+ : null;
+ if (logLevel == null && !(bootstrapProperties == null))
+ {
+ logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
+ }
+ Console.initLogger(logLevel);
+ } catch (NoClassDefFoundError error)
{
- showUsage();
+ error.printStackTrace();
+ System.out.println("\nEssential logging libraries not found."
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
System.exit(0);
}
- if (aparser.contains("nodisplay") || aparser.contains("nogui")
- || aparser.contains("headless"))
+
+ // register SIGTERM listener
+ Runtime.getRuntime().addShutdownHook(new Thread()
{
- System.setProperty("java.awt.headless", "true");
- headless = true;
- }
- String usrPropsFile = aparser.getValue("props");
- Cache.loadProperties(usrPropsFile); // must do this before
+ 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
+ }
+ });
+
+ String usrPropsFile = bootstrapArgs.containsKey(Arg.PROPS)
+ ? bootstrapArgs.get(Arg.PROPS)
+ : aparser.getValue("props");
+ Cache.loadProperties(usrPropsFile);
if (usrPropsFile != null)
{
System.out.println(
"CMD [-props " + usrPropsFile + "] executed successfully!");
}
- // anything else!
+ // new ArgParser
+ ArgParser argparser;
+ // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
+ if (bootstrapArgs.containsKey(Arg.ARGFILE))
+ {
+ argparser = ArgParser.parseArgFile(bootstrapArgs.get(Arg.ARGFILE));
+ }
+ else
+ {
+ argparser = new ArgParser(args);
+ }
- final String jabawsUrl = aparser.getValue("jabaws");
- if (jabawsUrl != null)
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- try
+ if (aparser.contains("help") || aparser.contains("h")
+ || argparser.getBool(Arg.HELP))
+ {
+ showUsage();
+ System.exit(0);
+ }
+
+ if (argparser.isSet(Arg.HEADLESS))
{
- Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
- System.out.println(
- "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
- } catch (MalformedURLException e)
+ System.setProperty("java.awt.headless", "true");
+ // new
+ headlessArg = argparser.getBool(Arg.HEADLESS);
+ }
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
{
- System.err.println(
- "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+ System.setProperty("java.awt.headless", "true");
+ // old
+ headless = true;
+ }
+ // 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)
+ {
+ try
+ {
+ Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println(
+ "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+ } catch (MalformedURLException e)
+ {
+ System.err.println(
+ "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+ }
}
}
else
{
System.out.println("Executing setprop argument: " + defs);
+ if (Platform.isJS())
+ {
+ Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
+ }
// DISABLED FOR SECURITY REASONS
// TODO: add a property to allow properties to be overriden by cli args
// Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
}
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."
+ "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
System.exit(0);
}
-
desktop = null;
- setLookAndFeel();
+ if (!(headless || headlessArg))
+ setLookAndFeel();
/*
- * configure 'full' SO model if preferences say to, else use the default (SO
- * Lite)
+ * configure 'full' SO model if preferences say to, else use the default (full SO)
+ * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
*/
- if (Cache.getDefault("USE_FULL_SO", true))
+ boolean soDefault = !Platform.isJS();
+ if (Cache.getDefault("USE_FULL_SO", soDefault))
{
SequenceOntologyFactory.setInstance(new SequenceOntology());
}
- if (!headless)
+ if (!(headless || headlessArg))
{
-
+ Desktop.nosplash = aparser.contains("nosplash");
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
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();
}
+ // set Proxy settings before all the internet calls
+ Cache.setProxyPropertiesFromPreferences();
+
desktop.setVisible(true);
- desktop.startServiceDiscovery();
- if (!aparser.contains("nousagestats"))
- {
- startUsageStats(desktop);
- }
- else
- {
- System.err.println("CMD [-nousagestats] executed successfully!");
- }
- if (!aparser.contains("noquestionnaire"))
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- String url = aparser.getValue("questionnaire");
- if (url != null)
+
+ /**
+ * 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())
{
- // Start the desktop questionnaire prompter with the specified
- // questionnaire
- Cache.log.debug("Starting questionnaire url at " + url);
- desktop.checkForQuestionnaire(url);
- System.out.println(
- "CMD questionnaire[-" + url + "] executed successfully!");
+ 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();
+ }
+ if (!aparser.contains("nousagestats"))
+ {
+ startUsageStats(desktop);
}
else
{
- if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+
+ if (!aparser.contains("noquestionnaire"))
+ {
+ String url = aparser.getValue("questionnaire");
+ if (url != null)
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
- // String defurl =
- // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
- // //
- String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
- Cache.log.debug(
- "Starting questionnaire with default url: " + defurl);
- desktop.checkForQuestionnaire(defurl);
+ Console.debug("Starting questionnaire url at " + url);
+ desktop.checkForQuestionnaire(url);
+ System.out.println("CMD questionnaire[-" + url
+ + "] executed successfully!");
+ }
+ else
+ {
+ if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ {
+ // Start the desktop questionnaire prompter with the specified
+ // questionnaire
+ // String defurl =
+ // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
+ // //
+ String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
+ Console.debug(
+ "Starting questionnaire with default url: " + defurl);
+ desktop.checkForQuestionnaire(defurl);
+ }
}
}
- }
- else
- {
- System.err.println("CMD [-noquestionnaire] executed successfully!");
- }
+ else
+ {
+ System.err
+ .println("CMD [-noquestionnaire] executed successfully!");
+ }
- if (!aparser.contains("nonews"))
- {
- desktop.checkForNews();
+ if (!aparser.contains("nonews")
+ || Cache.getProperty("NONEWS") == null)
+ {
+ desktop.checkForNews();
+ }
+
+ if (!aparser.contains("nohtmltemplates")
+ || Cache.getProperty("NOHTMLTEMPLATES") == null)
+ {
+ BioJsHTMLOutput.updateBioJS();
+ }
}
+ }
+ // Run Commands from cli
+ boolean commandsSuccess = Commands.processArgs(argparser, headlessArg);
+ if (commandsSuccess)
+ {
+ Console.info("Successfully completed commands");
+ if (headlessArg)
+ System.exit(0);
+ }
+ else
+ {
+ Console.warn("Error when running commands");
+ if (headlessArg)
+ System.exit(1);
+ }
- 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
}
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)
}
System.out.println("CMD [-open " + file + "] executed successfully!");
-
-
- protocol = AppletFormatAdapter.checkProtocol(file);
-
- if (protocol == DataSourceType.FILE)
+ if (!Platform.isJS())
+ /**
+ * ignore in JavaScript -- can't just file existence - could load it?
+ *
+ * @j2sIgnore
+ */
{
- if (!(new File(file)).exists())
+ if (!HttpUtils.startsWithHttpOrHttps(file))
{
- System.out.println("Can't find " + file);
- if (headless)
+ if (!(new File(file)).exists())
{
- System.exit(1);
+ System.out.println("Can't find " + file);
+ if (headless)
+ {
+ System.exit(1);
+ }
}
}
}
+ protocol = AppletFormatAdapter.checkProtocol(file);
+
try
{
format = new IdentifyFile().identify(file, protocol);
if (cs != null)
{
System.out.println(
- "CMD [-color " + data + "] executed successfully!");
+ "CMD [-colour " + data + "] executed successfully!");
}
af.changeColour(cs);
}
af.createEPS(outputFile);
continue;
}
- FileFormatI outFormat=null;
- try {
+ FileFormatI outFormat = null;
+ try
+ {
outFormat = FileFormats.getInstance().forName(outputFormat);
- } catch (Exception formatP) {
- System.out.println("Couldn't parse "+outFormat+" as a valid Jalview format string.");
+ } catch (Exception formatP)
+ {
+ System.out.println("Couldn't parse " + outFormat
+ + " as a valid Jalview format string.");
}
if (outFormat != null)
{
}
else
{
- if (af.saveAlignment(file, outFormat))
+ af.saveAlignment(file, outFormat);
+ if (af.isSaveAlignmentSuccessful())
{
- System.out.println("Written alignment in " + format
- + " format to " + file);
+ System.out.println("Written alignment in "
+ + outFormat.getName() + " format to " + file);
}
else
{
System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ + outFormat.getName() + " format!!");
}
}
}
+
}
while (aparser.getSize() > 0)
}
}
}
+
AlignFrame startUpAlframe = null;
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
- if (!headless && file == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ if (!Platform.isJS() && !headless && file == null
+ && Cache.getDefault("SHOW_STARTUP_FILE", true)
+ && !Commands.commandArgsProvided())
+ // don't open the startup file if command line args have been processed
+ // (&& !Commands.commandArgsProvided())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- file = jalview.bin.Cache.getDefault("STARTUP_FILE",
- jalview.bin.Cache.getDefault("www.jalview.org",
- "https://www.jalview.org")
+ file = Cache.getDefault("STARTUP_FILE",
+ 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(
+ 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:");
file.replace("_2_3", "_2_7");
file.replace("2_7.jar", "2_7.jvp");
// and remove the stale setting
- jalview.bin.Cache.removeProperty("STARTUP_FILE");
+ Cache.removeProperty("STARTUP_FILE");
}
- protocol = DataSourceType.FILE;
-
- if (file.indexOf("http:") > -1)
- {
- protocol = DataSourceType.URL;
- }
+ protocol = AppletFormatAdapter.checkProtocol(file);
if (file.endsWith(".jar"))
{
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.
}
private static void setLookAndFeel()
{
- // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
- // "mac"
+ // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
+ // "mac" or "flat"
// If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
// try Quaqua/Vaqua.
String lafProp = System.getProperty("laf");
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 "quaqua":
- lafSet = setQuaquaLookAndFeel();
+ case "flat":
+ lafSet = setFlatLookAndFeel();
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.isAMac())
+ if (Platform.isMac())
{
setMacLookAndFeel();
}
private static boolean setCrossPlatformLookAndFeel()
{
- return setGenericLookAndFeel(false);
+ boolean set = false;
+ try
+ {
+ UIManager.setLookAndFeel(
+ UIManager.getCrossPlatformLookAndFeelClassName());
+ set = true;
+ } catch (Exception ex)
+ {
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
+ }
+ return set;
}
private static boolean setSystemLookAndFeel()
{
- return setGenericLookAndFeel(true);
- }
-
- private static boolean setGenericLookAndFeel(boolean system)
- {
boolean set = false;
try
{
- UIManager.setLookAndFeel(
- system ? UIManager.getSystemLookAndFeelClassName()
- : UIManager.getCrossPlatformLookAndFeelClassName());
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
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().toLowerCase().equals(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;
}
"javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
}
- private static boolean setQuaquaLookAndFeel()
+ private static boolean setFlatLookAndFeel()
{
- return setSpecificLookAndFeel("quaqua",
- ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
- .getName(),
- 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;
+ }
- private static boolean setVaquaLookAndFeel()
- {
- return setSpecificLookAndFeel("vaqua",
- "org.violetlib.aqua.AquaLookAndFeel", false);
+ 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);
+ }
+
+ Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
+ return set;
}
private static boolean setMacLookAndFeel()
{
boolean set = false;
System.setProperty("com.apple.mrj.application.apple.menu.about.name",
- "Jalview");
+ 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;
}
@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()