X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalview.java;h=a988a09d3453b389dff1798e8e36299cb9bfb0e4;hb=0de37d1a047209510bab82225109ae2a47931f79;hp=f4d340b731b669eedabe392caa9bf63f86e9ec39;hpb=3a457987342ea69ca6b9e8d37573ea28ce8568f5;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index f4d340b..a988a09 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -45,17 +45,26 @@ import java.util.logging.ConsoleHandler; import java.util.logging.Level; import java.util.logging.Logger; +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.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; @@ -72,6 +81,7 @@ 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; @@ -96,6 +106,10 @@ 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"); } /* @@ -261,6 +275,28 @@ public class Jalview 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 @@ -269,6 +305,7 @@ public class Jalview System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); + String val = System.getProperty("sys.install4jVersion"); if (val != null) { @@ -288,17 +325,56 @@ public class Jalview // report Jalview version Cache.loadBuildProperties(true); + // old ArgsParser ArgsParser aparser = new ArgsParser(args); + boolean headless = false; + try + { + 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); + } + 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( "CMD [-props " + usrPropsFile + "] executed successfully!"); } + // set log level from cache properties + Console.setLogLevel(Cache.getDefault(Cache.JALVIEWLOGLEVEL, "INFO")); + + // new ArgParser + ArgParser argparser = new ArgParser(args); // do this after + // Console.initLogger, but TODO + // want --props before then + // CATCH22 + + if (argparser.isSet(Arg.HEADLESS)) + headless = argparser.getBool(Arg.HEADLESS); + boolean commandsSuccess = Commands.processArgs(argparser, headless); + if (commandsSuccess) + { + Console.info("Successfully completed commands"); + if (headless) + System.exit(0); + } + else + { + Console.warn("Error when running commands"); + if (headless) + System.exit(1); + } + if (!Platform.isJS()) /** * Java only @@ -306,13 +382,18 @@ public class Jalview * @j2sIgnore */ { + if (argparser.isSet(Arg.HEADLESS)) + { + headless = argparser.getBool(Arg.HEADLESS); + } + if (aparser.contains("help") || aparser.contains("h")) { showUsage(); System.exit(0); } - if (aparser.contains("nodisplay") || aparser.contains("nogui") - || aparser.contains("headless")) + if (headless || aparser.contains("nodisplay") + || aparser.contains("nogui") || aparser.contains("headless")) { System.setProperty("java.awt.headless", "true"); headless = true; @@ -366,16 +447,6 @@ public class Jalview } System.setProperty("http.agent", "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown")); - try - { - Cache.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; @@ -402,13 +473,13 @@ public class Jalview 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(); } @@ -424,6 +495,35 @@ public class Jalview * @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(); @@ -444,7 +544,7 @@ public class Jalview { // 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!"); @@ -459,7 +559,7 @@ public class Jalview // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; // // String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl"; - Cache.log.debug( + Console.debug( "Starting questionnaire with default url: " + defurl); desktop.checkForQuestionnaire(defurl); } @@ -471,15 +571,30 @@ public class Jalview .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"); @@ -500,8 +615,11 @@ public class Jalview } 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 @@ -515,6 +633,7 @@ public class Jalview System.out.println("No files to open!"); System.exit(1); } + long progress = -1; // Finally, deal with the remaining input data. if (file != null) @@ -774,6 +893,7 @@ public class Jalview } } } + AlignFrame startUpAlframe = null; // We'll only open the default file if the desktop is visible. // And the user @@ -787,12 +907,11 @@ public class Jalview * @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:"); @@ -875,76 +994,76 @@ public class Jalview 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); + Console.error("Could not set requested laf=" + laf); } break; case "quaqua": lafSet = setQuaquaLookAndFeel(); if (!lafSet) { - Cache.log.error("Could not set requested laf=" + laf); + Console.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()) { - setFlatLookAndFeel(); + setLinuxLookAndFeel(); } if (Platform.isMac()) { @@ -963,9 +1082,9 @@ public class Jalview 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; } @@ -979,9 +1098,9 @@ public class Jalview 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; } @@ -997,7 +1116,8 @@ public class Jalview if (info.getName() != null && nameStartsWith ? info.getName().toLowerCase(Locale.ROOT) .startsWith(name.toLowerCase(Locale.ROOT)) - : info.getName().toLowerCase(Locale.ROOT).equals(name.toLowerCase(Locale.ROOT))) + : info.getName().toLowerCase(Locale.ROOT) + .equals(name.toLowerCase(Locale.ROOT))) { className = info.getClassName(); break; @@ -1007,9 +1127,9 @@ public class Jalview 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; } @@ -1034,20 +1154,63 @@ public class Jalview private static boolean setFlatLookAndFeel() { - boolean set = setSpecificLookAndFeel("flatlaf light", - "com.formdev.flatlaf.FlatLightLaf", false); + boolean set = false; + if (Platform.isMac()) { + try + { + UIManager.setLookAndFeel("com.formdev.flatlaf.themes.FlatMacLightLaf"); + set = true; + } catch (ClassNotFoundException | InstantiationException + | IllegalAccessException | UnsupportedLookAndFeelException e) + { + Console.debug("Exception loading FlatMacLightLaf", e); + } + } + if (!set) { + try + { + UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf"); + set = true; + } catch (ClassNotFoundException | InstantiationException + | IllegalAccessException | UnsupportedLookAndFeelException e) + { + Console.debug("Exception loading FlatLightLaf", e); + } + } if (set) { + if (Platform.isMac()) + { + 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) + { + Desktop.desktop.getRootPane() + .putClientProperty("apple.awt.fullWindowContent", true); + Desktop.desktop.getRootPane() + .putClientProperty("apple.awt.transparentTitleBar", true); + } + + SwingUtilities.invokeLater(() -> { + FlatLightLaf.setup(); + }); + } + UIManager.put("TabbedPane.showTabSeparators", true); UIManager.put("TabbedPane.tabSeparatorsFullHeight", true); UIManager.put("TabbedPane.tabsOverlapBorder", true); - //UIManager.put("TabbedPane.hasFullBorder", 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; } @@ -1071,12 +1234,28 @@ public class Jalview 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(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; } @@ -1138,17 +1317,17 @@ public class Jalview @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); @@ -1290,19 +1469,12 @@ public class Jalview } /** - * 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()