X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;fp=src%2Fjalview%2Fbin%2FJalview.java;h=08b4a1b713f99f88a2675e42de13f6b497705766;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=d437f1ba44fc864310dcc1d9da9715bf68e4e5a7;hpb=3609d4b908fa64cab35f2348401baab3347188fc;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index d437f1b..08b4a1b 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -60,6 +60,9 @@ import java.security.Policy; import java.util.HashMap; 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.LookAndFeel; import javax.swing.UIManager; @@ -86,9 +89,13 @@ import groovy.util.GroovyScriptEngine; */ public class Jalview { - /* - * singleton instance of this class - */ + static + { + Platform.getURLCommandArguments(); + } + + // singleton instance of this class + private static Jalview instance; private Desktop desktop; @@ -97,22 +104,30 @@ public class Jalview 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) - { - Permissions perms = new Permissions(); - perms.add(new AllPermission()); - return (perms); - } - - @Override - public void refresh() + // grab all the rights we can for the JVM + Policy.setPolicy(new Policy() { - } - }); + @Override + public PermissionCollection getPermissions(CodeSource codesource) + { + Permissions perms = new Permissions(); + perms.add(new AllPermission()); + return (perms); + } + + @Override + public void refresh() + { + } + }); + } } /** @@ -187,16 +202,65 @@ public class Jalview */ 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); + } + System.out .println("Java version: " + System.getProperty("java.version")); @@ -223,17 +287,6 @@ public class Jalview ArgsParser aparser = new ArgsParser(args); boolean headless = false; - if (aparser.contains("help") || aparser.contains("h")) - { - showUsage(); - System.exit(0); - } - if (aparser.contains("nodisplay") || aparser.contains("nogui") - || aparser.contains("headless")) - { - System.setProperty("java.awt.headless", "true"); - headless = true; - } String usrPropsFile = aparser.getValue("props"); Cache.loadProperties(usrPropsFile); // must do this before if (usrPropsFile != null) @@ -242,23 +295,42 @@ public class Jalview "CMD [-props " + usrPropsFile + "] executed successfully!"); } - // anything else! - - final String jabawsUrl = aparser.getValue("jabaws"); - if (jabawsUrl != null) + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ { - try + if (aparser.contains("help") || aparser.contains("h")) { - Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); - System.out.println( - "CMD [-jabaws " + jabawsUrl + "] executed successfully!"); - } catch (MalformedURLException e) + showUsage(); + System.exit(0); + } + if (aparser.contains("nodisplay") || aparser.contains("nogui") + || aparser.contains("headless")) { - System.err.println( - "Invalid jabaws parameter: " + jabawsUrl + " ignored"); + System.setProperty("java.awt.headless", "true"); + headless = true; + } + // anything else! + + 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"); + } } - } + } String defs = aparser.getValue("setprop"); while (defs != null) { @@ -270,9 +342,10 @@ public class Jalview else { System.out.println("Executing setprop argument: " + defs); - // 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)); + if (Platform.isJS()) + { + Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); + } } defs = aparser.getValue("setprop"); } @@ -304,7 +377,7 @@ public class Jalview System.err.println("Unexpected Look and Feel Exception"); ex.printStackTrace(); } - if (Platform.isAMac()) + if (Platform.isAMacAndNotJS()) { LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager @@ -343,9 +416,11 @@ public class Jalview } /* - * configure 'full' SO model + * 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()); } @@ -358,66 +433,71 @@ public class Jalview try { JalviewTaskbar.setTaskbar(this); - } catch (Exception e) - { - System.out.println("Cannot set Taskbar"); - // e.printStackTrace(); } catch (Throwable t) { - System.out.println("Cannot set Taskbar"); - // t.printStackTrace(); + System.out.println("Error setting Taskbar: " + t.getMessage()); } 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) + desktop.startServiceDiscovery(); + if (!aparser.contains("nousagestats")) { - // 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!"); + 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 = "http://www.jalview.org/cgi-bin/questionnaire.pl"; - Cache.log.debug( - "Starting questionnaire with default url: " + defurl); - desktop.checkForQuestionnaire(defurl); + Cache.log.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 = "http://www.jalview.org/cgi-bin/questionnaire.pl"; + Cache.log.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")) + { + desktop.checkForNews(); + } - BioJsHTMLOutput.updateBioJS(); + BioJsHTMLOutput.updateBioJS(); + } } // Move any new getdown-launcher-new.jar into place over old @@ -468,19 +548,28 @@ public class Jalview } System.out.println("CMD [-open " + file + "] executed successfully!"); - if (!file.startsWith("http://")) + if (!Platform.isJS()) + /** + * ignore in JavaScript -- can't just file existence - could load it? + * + * @j2sIgnore + */ { - if (!(new File(file)).exists()) + if (!file.startsWith("http://") && !file.startsWith("https://")) + // BH 2019 added https check for Java { - 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); + protocol = AppletFormatAdapter.checkProtocol(file); try { @@ -666,7 +755,8 @@ public class Jalview continue; } - if (af.saveAlignment(file, format)) + af.saveAlignment(file, format); + if (af.isSaveAlignmentSuccessful()) { System.out.println("Written alignment in " + format + " format to " + file); @@ -690,11 +780,16 @@ public class Jalview // 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)) + /** + * Java only + * + * @j2sIgnore + */ { - file = jalview.bin.Cache.getDefault("STARTUP_FILE", - jalview.bin.Cache.getDefault("www.jalview.org", + file = Cache.getDefault("STARTUP_FILE", + Cache.getDefault("www.jalview.org", "http://www.jalview.org") + "/examples/exampleFile_2_7.jar"); if (file.equals( @@ -703,7 +798,7 @@ public class Jalview // hardwire upgrade of the startup file file.replace("_2_3.jar", "_2_7.jar"); // and remove the stale setting - jalview.bin.Cache.removeProperty("STARTUP_FILE"); + Cache.removeProperty("STARTUP_FILE"); } protocol = DataSourceType.FILE;