X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=7535f6013fa00b77eea606728b0f7d45abcc17b4;hb=84ff3a3c7824890b0a201e6a4ec8fa1c9b6e9e64;hp=d70326e30f7597ad814d8943744cb129156e6568;hpb=0788111a588187a04dd0d254d70b055274cf2c9d;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index d70326e..7535f60 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -49,9 +49,11 @@ import java.util.Vector; import java.util.logging.ConsoleHandler; import java.util.logging.Level; import java.util.logging.Logger; +import java.util.stream.Collectors; import javax.swing.JDialog; import javax.swing.JFrame; +import javax.swing.JInternalFrame; import javax.swing.JOptionPane; import javax.swing.SwingUtilities; import javax.swing.UIManager; @@ -67,6 +69,8 @@ import com.threerings.getdown.util.LaunchUtil; import groovy.lang.Binding; import groovy.util.GroovyScriptEngine; import jalview.bin.argparser.Arg; +import jalview.bin.argparser.Arg.Opt; +import jalview.bin.argparser.Arg.Type; import jalview.bin.argparser.ArgParser; import jalview.bin.argparser.BootstrapArgs; import jalview.ext.so.SequenceOntology; @@ -75,6 +79,7 @@ import jalview.gui.Desktop; import jalview.gui.PromptUserConfig; import jalview.gui.QuitHandler; import jalview.gui.QuitHandler.QResponse; +import jalview.gui.StructureViewerBase; import jalview.io.AppletFormatAdapter; import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; @@ -133,6 +138,17 @@ public class Jalview public static AlignFrame currentAlignFrame; + public ArgParser argparser = null; + + public BootstrapArgs bootstrapArgs = null; + + private boolean QUIET = false; + + public static boolean quiet() + { + return Jalview.getInstance() != null && Jalview.getInstance().QUIET; + } + static { if (!Platform.isJS()) @@ -288,38 +304,24 @@ public class Jalview System.setSecurityManager(null); } - if (args == null) - args = new String[] {}; - - // Move any new getdown-launcher-new.jar into place over old - // getdown-launcher.jar - String appdirString = System.getProperty("getdownappdir"); - if (appdirString != null && appdirString.length() > 0) + if (args == null || args.length == 0 || (args.length == 1 + && (args[0] == null || args[0].length() == 0))) { - final File appdir = new File(appdirString); - new Thread() - { - @Override - public void run() - { - LaunchUtil.upgradeGetdown( - new File(appdir, "getdown-launcher-old.jar"), - new File(appdir, "getdown-launcher.jar"), - new File(appdir, "getdown-launcher-new.jar")); - } - }.start(); + args = new String[] {}; } // get args needed before proper ArgParser - BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args); + bootstrapArgs = BootstrapArgs.getBootstrapArgs(args); if (!Platform.isJS()) { // are we being --quiet ? if (bootstrapArgs.contains(Arg.QUIET)) { + QUIET = true; OutputStream devNull = new OutputStream() { + @Override public void write(int b) { @@ -333,29 +335,58 @@ public class Jalview System.setErr(new PrintStream(devNull)); } } - } - - 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("Install4j version: " + val); + if (bootstrapArgs.contains(Arg.HELP) + || bootstrapArgs.contains(Arg.VERSION)) + { + QUIET = true; + } } - val = System.getProperty("installer_template_version"); - if (val != null) + + // Move any new getdown-launcher-new.jar into place over old + // getdown-launcher.jar + String appdirString = System.getProperty("getdownappdir"); + if (appdirString != null && appdirString.length() > 0) { - System.out.println("Install4j template version: " + val); + final File appdir = new File(appdirString); + new Thread() + { + + @Override + public void run() + { + LaunchUtil.upgradeGetdown( + new File(appdir, "getdown-launcher-old.jar"), + new File(appdir, "getdown-launcher.jar"), + new File(appdir, "getdown-launcher-new.jar")); + } + }.start(); } - val = System.getProperty("launcher_version"); - if (val != null) + + if (!quiet() || bootstrapArgs.contains(Arg.VERSION)) { - System.out.println("Launcher version: " + val); + System.out.println( + "Java version: " + System.getProperty("java.version")); + System.out.println("Java home: " + System.getProperty("java.home")); + System.out.println("Java arch: " + System.getProperty("os.arch") + " " + + System.getProperty("os.name") + " " + + System.getProperty("os.version")); + + String val = System.getProperty("sys.install4jVersion"); + if (val != null) + { + System.out.println("Install4j version: " + val); + } + val = System.getProperty("installer_template_version"); + if (val != null) + { + System.out.println("Install4j template version: " + val); + } + val = System.getProperty("launcher_version"); + if (val != null) + { + System.out.println("Launcher version: " + val); + } } if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11) @@ -368,7 +399,14 @@ public class Jalview .bootstrapProperties(bootstrapArgs.get(Arg.PROPS)); // report Jalview version - Cache.loadBuildProperties(true); + Cache.loadBuildProperties( + !quiet() || bootstrapArgs.contains(Arg.VERSION)); + + // stop now if only after --version + if (bootstrapArgs.contains(Arg.VERSION)) + { + Jalview.exit(null, 0); + } // old ArgsParser ArgsParser aparser = new ArgsParser(args); @@ -380,7 +418,15 @@ public class Jalview try { - String logLevel = bootstrapArgs.contains(Arg.DEBUG) ? "DEBUG" : null; + String logLevel = null; + if (bootstrapArgs.contains(Arg.TRACE)) + { + logLevel = "TRACE"; + } + else if (bootstrapArgs.contains(Arg.DEBUG)) + { + logLevel = "DEBUG"; + } if (logLevel == null && !(bootstrapProperties == null)) { logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL); @@ -400,11 +446,29 @@ public class Jalview public void run() { Console.debug("Running shutdown hook"); + QuitHandler.startForceQuit(); + boolean closeExternal = Cache + .getDefault("DEFAULT_CLOSE_EXTERNAL_VIEWERS", false) + || Cache.getDefault("ALWAYS_CLOSE_EXTERNAL_VIEWERS", false); + StructureViewerBase.setQuitClose(closeExternal); + if (desktop != null) + { + for (JInternalFrame frame : Desktop.desktop.getAllFrames()) + { + if (frame instanceof StructureViewerBase) + { + ((StructureViewerBase) frame).closeViewer(closeExternal); + } + } + } + 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. + // late -- but we can wait for saving files and close external viewers + // if configured. + // Close viewers/Leave viewers open Console.debug("Checking for saving files"); QuitHandler.getQuitResponse(false); } @@ -427,21 +491,23 @@ public class Jalview { System.out.println( "CMD [-props " + usrPropsFile + "] executed successfully!"); + testoutput(bootstrapArgs, Arg.PROPS, + "test/jalview/bin/testProps.jvprops", usrPropsFile); } - // new ArgParser - ArgParser argparser; // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS if (bootstrapArgs.contains(Arg.ARGFILE)) { argparser = ArgParser.parseArgFiles( - bootstrapArgs.getList(Arg.ARGFILE), - bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS)); + bootstrapArgs.getValueList(Arg.ARGFILE), + bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS), + bootstrapArgs); } else { argparser = new ArgParser(args, - bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS)); + bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS), + bootstrapArgs); } if (!Platform.isJS()) @@ -453,26 +519,33 @@ public class Jalview { if (bootstrapArgs.contains(Arg.HELP)) { - System.out.println(Arg.usage()); + List> helpArgs = bootstrapArgs + .getList(Arg.HELP); + System.out.println(Arg.usage(helpArgs.stream().map(e -> e.getKey()) + .collect(Collectors.toList()))); Jalview.exit(null, 0); } if (aparser.contains("help") || aparser.contains("h")) { + /* + * Now using new usage statement. showUsage(); + */ + System.out.println(Arg.usage()); Jalview.exit(null, 0); } - if (bootstrapArgs.contains(Arg.HEADLESS)) + // new CLI + headlessArg = isHeadless(bootstrapArgs); + if (headlessArg) { System.setProperty("java.awt.headless", "true"); - // new - headlessArg = argparser.getBool(Arg.HEADLESS); } + // old CLI if (aparser.contains("nodisplay") || aparser.contains("nogui") || aparser.contains("headless")) { System.setProperty("java.awt.headless", "true"); - // old headless = true; } // anything else! @@ -480,7 +553,9 @@ public class Jalview // allow https handshakes to download intermediate certs if necessary System.setProperty("com.sun.security.enableAIAcaIssuers", "true"); - final String jabawsUrl = aparser.getValue("jabaws"); + String jabawsUrl = bootstrapArgs.get(Arg.JABAWS); + if (jabawsUrl == null) + jabawsUrl = aparser.getValue("jabaws"); if (jabawsUrl != null) { try @@ -488,6 +563,8 @@ public class Jalview Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); System.out.println( "CMD [-jabaws " + jabawsUrl + "] executed successfully!"); + testoutput(bootstrapArgs, Arg.JABAWS, + "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl); } catch (MalformedURLException e) { System.err.println( @@ -499,7 +576,7 @@ public class Jalview List setprops = new ArrayList<>(); if (bootstrapArgs.contains(Arg.SETPROP)) { - setprops = bootstrapArgs.getList(Arg.SETPROP); + setprops = bootstrapArgs.getValueList(Arg.SETPROP); } else { @@ -630,20 +707,37 @@ public class Jalview } } - if (!aparser.contains("nowebservicediscovery")) + boolean webservicediscovery = bootstrapArgs + .getBoolean(Arg.WEBSERVICEDISCOVERY); + if (aparser.contains("nowebservicediscovery")) + webservicediscovery = false; + if (webservicediscovery) { desktop.startServiceDiscovery(); } - if (!aparser.contains("nousagestats")) + else + { + testoutput(argparser, Arg.WEBSERVICEDISCOVERY); + } + + boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS); + if (aparser.contains("nousagestats")) + usagestats = false; + if (usagestats) { startUsageStats(desktop); + testoutput(argparser, Arg.USAGESTATS); } else { - System.err.println("CMD [-nousagestats] executed successfully!"); + System.out.println("CMD [-nousagestats] executed successfully!"); + testoutput(argparser, Arg.USAGESTATS); } - if (!aparser.contains("noquestionnaire")) + boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE); + if (aparser.contains("noquestionnaire")) + questionnaire = false; + if (questionnaire) { String url = aparser.getValue("questionnaire"); if (url != null) @@ -673,8 +767,9 @@ public class Jalview } else { - System.err + System.out .println("CMD [-noquestionnaire] executed successfully!"); + testoutput(argparser, Arg.QUESTIONNAIRE); } if ((!aparser.contains("nonews") @@ -699,7 +794,17 @@ public class Jalview { if (headlessArg) { - Jalview.exit("Successfully completed commands in headless mode", 0); + if (argparser.getBoolean(Arg.NOQUIT)) + { + Console.warn( + "Completed " + Arg.HEADLESS.getName() + " commands, but " + + Arg.NOQUIT + " is set so not quitting!"); + } + else + { + Jalview.exit("Successfully completed commands in headless mode", + 0); + } } Console.info("Successfully completed commands"); } @@ -1161,7 +1266,12 @@ public class Jalview } if (!lafSet) { - setSystemLookAndFeel(); + // Flatlaf default for everyone! + lafSet = setFlatLookAndFeel(); + if (!lafSet) + { + setSystemLookAndFeel(); + } if (Platform.isLinux()) { setLinuxLookAndFeel(); @@ -1358,6 +1468,8 @@ public class Jalview UIManager.put("TabbedPane.smoothScrolling", true); UIManager.put("TabbedPane.tabWidthMode", "compact"); UIManager.put("TabbedPane.selectedBackground", Color.white); + UIManager.put("TabbedPane.background", new Color(236, 236, 236)); + UIManager.put("TabbedPane.hoverColor", Color.lightGray); } Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true)); @@ -1395,6 +1507,7 @@ public class Jalview return set; } + /* private static void showUsage() { System.out.println( @@ -1437,6 +1550,7 @@ public class Jalview + "-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 https://www.jalview.org for description of Features and Annotations file~\n\n"); } + */ private static void startUsageStats(final Desktop desktop) { @@ -1478,7 +1592,7 @@ public class Jalview * the Jalview Desktop object passed in to the groovy binding as the * 'Jalview' object. */ - private void executeGroovyScript(String groovyscript, AlignFrame af) + protected void executeGroovyScript(String groovyscript, AlignFrame af) { /** * for scripts contained in files @@ -1630,13 +1744,168 @@ public class Jalview public static void exit(String message, int exitcode) { - Console.debug("Using Jalview.exit"); - if (message != null) - if (exitcode == 0) - Console.info(message); - else - Console.error(message); + if (Console.log == null) + { + // Don't start the logger just to exit! + if (message != null) + { + if (exitcode == 0) + { + System.out.println(message); + } + else + { + System.err.println(message); + } + } + } + else + { + Console.debug("Using Jalview.exit"); + if (message != null) + { + if (exitcode == 0) + { + Console.info(message); + } + else + { + Console.error(message); + } + } + } if (exitcode > -1) + { System.exit(exitcode); + } + } + + /* + * testoutput for string values + */ + protected static void testoutput(ArgParser ap, Arg a, String s1, + String s2) + { + BootstrapArgs bsa = ap.getBootstrapArgs(); + if (!bsa.getBoolean(Arg.TESTOUTPUT)) + return; + if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2)))) + { + Console.debug("testoutput with unmatching values '" + s1 + "' and '" + + s2 + "' for arg " + a.argString()); + return; + } + boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a) + : ap.isSet(a); + if (!isset) + { + Console.warn("Arg '" + a.getName() + "' not set at all"); + return; + } + testoutput(true, a, s1, s2); + } + + protected static void testoutput(BootstrapArgs bsa, Arg a, String s1, + String s2) + { + if (!bsa.getBoolean(Arg.TESTOUTPUT)) + return; + if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2)))) + { + Console.debug("testoutput with unmatching values '" + s1 + "' and '" + + s2 + "' for arg " + a.argString()); + return; + } + if (!a.hasOption(Opt.BOOTSTRAP)) + { + Console.error("Non-bootstrap Arg '" + a.getName() + + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs"); + } + if (!bsa.contains(a)) + { + Console.warn("Arg '" + a.getName() + "' not set at all"); + return; + } + testoutput(true, a, s1, s2); + } + + private static void testoutput(boolean yes, Arg a, String s1, String s2) + { + if (yes && ((s1 == null && s2 == null) + || (s1 != null && s1.equals(s2)))) + { + System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1 + + "' was set"); + } + } + + /* + * testoutput for boolean values + */ + protected static void testoutput(ArgParser ap, Arg a) + { + if (ap == null) + return; + BootstrapArgs bsa = ap.getBootstrapArgs(); + if (bsa == null) + return; + if (!bsa.getBoolean(Arg.TESTOUTPUT)) + return; + boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a) + : ap.getBoolean(a); + boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a) + : ap.isSet(a); + if (!isset) + { + Console.warn("Arg '" + a.getName() + "' not set at all"); + return; + } + testoutput(val, a); + } + + protected static void testoutput(BootstrapArgs bsa, Arg a) + { + if (!bsa.getBoolean(Arg.TESTOUTPUT)) + return; + if (!a.hasOption(Opt.BOOTSTRAP)) + { + Console.warn("Non-bootstrap Arg '" + a.getName() + + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs"); + + } + if (!bsa.contains(a)) + { + Console.warn("Arg '" + a.getName() + "' not set at all"); + return; + } + testoutput(bsa.getBoolean(a), a); + } + + private static void testoutput(boolean yes, Arg a) + { + System.out.println("[TESTOUTPUT] arg " + + (yes ? a.argString() : a.negateArgString()) + " was set"); + } + + private static boolean isHeadless(BootstrapArgs bootstrapArgs) + { + if (bootstrapArgs == null) + { + return false; + } + boolean isHeadless = false; + if (bootstrapArgs.contains(Arg.GUI)) + { + isHeadless = !bootstrapArgs.getBoolean(Arg.GUI); + } + else if (bootstrapArgs.contains(Arg.HEADLESS)) + { + isHeadless = bootstrapArgs.getBoolean(Arg.HEADLESS); + } + else if (bootstrapArgs.argsHaveOption(Opt.OUTPUTFILE)) + { + isHeadless = true; + } + return isHeadless; } }