X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e1fd5721ebd38c25f525ace51f0df71c7db43bf5;hb=refs%2Fheads%2FJAL-4152-typed-singleton-provider;hp=ac44bfebfc9f995ab7ffb71e93226a4a002966cd;hpb=d193330513f3b6aa8d1aaee0eb502601b2f7fec2;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index ac44bfe..e1fd572 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,6 +20,11 @@ */ package jalview.bin; +import java.util.Locale; + +import java.awt.GraphicsEnvironment; +import java.awt.Color; + import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; @@ -37,18 +42,26 @@ import java.security.PermissionCollection; 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.LookAndFeel; +import javax.swing.JOptionPane; +import javax.swing.SwingUtilities; import javax.swing.UIManager; +import javax.swing.UIManager.LookAndFeelInfo; +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.api.AlignCalcWorkerI; -import jalview.api.JalviewJSApp; import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; @@ -70,10 +83,12 @@ import jalview.io.NewickFile; 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; -//import netscape.javascript.JSObject; /** * Main class for Jalview Application
@@ -92,7 +107,6 @@ import jalview.ws.jws2.Jws2Discoverer; */ public class Jalview implements ApplicationSingletonI { - // for testing those nasty messages you cannot ever find. // static // { @@ -111,14 +125,19 @@ public class Jalview implements ApplicationSingletonI // } public static Jalview getInstance() { - return (Jalview) ApplicationSingletonProvider - .getInstance(Jalview.class); + return ApplicationSingletonProvider.getInstance(Jalview.class); } private Jalview() { + 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"); } + private boolean headless; private Desktop desktop; @@ -155,9 +174,15 @@ public class Jalview implements ApplicationSingletonI static { - if (Platform.isJS()) { - Platform.getURLCommandArguments(); - } else /** @j2sIgnore */ + if (Platform.isJS()) + { + Platform.getURLCommandArguments(); + } else + /** + * Java only + * + * @j2sIgnore + */ { // grab all the rights we can for the JVM Policy.setPolicy(new Policy() @@ -251,8 +276,13 @@ public class Jalview implements ApplicationSingletonI { Platform.startJavaLogging(); } + getInstance().doMain(args); + } + + + /** * @param args @@ -266,6 +296,11 @@ public class Jalview implements ApplicationSingletonI System.setSecurityManager(null); } + /* + * @j2sNative J2S.db._DirectDatabaseCalls["compbio.dundee.ac.uk"]=null; + * @j2sNative J2S.db._DirectDatabaseCalls["jalview.org"]=null; + * + */ System.out .println("Java version: " + System.getProperty("java.version")); System.out.println("Java Home: " + System.getProperty("java.home")); @@ -295,9 +330,9 @@ public class Jalview implements ApplicationSingletonI headless = false; String usrPropsFile = aparser.getValue("props"); - Cache.loadProperties(usrPropsFile); // must do this before - + boolean allowServices = true; + if (isJS) { j2sAppletID = Platform.getAppID(null); @@ -307,6 +342,7 @@ public class Jalview implements ApplicationSingletonI appletResourcePath = (String) aparser.getAppletValue("resourcepath", null, true); } + else /** * Java only @@ -314,7 +350,6 @@ public class Jalview implements ApplicationSingletonI * @j2sIgnore */ { - if (usrPropsFile != null) { System.out.println( @@ -325,19 +360,25 @@ public class Jalview implements ApplicationSingletonI showUsage(); System.exit(0); } - // ?>> + // BH note: Only -nodisplay is official; others are deprecated? if (aparser.contains("nodisplay") || aparser.contains("nogui") - || aparser.contains("headless")) + || aparser.contains("headless") + || GraphicsEnvironment.isHeadless()) { - System.setProperty("java.awt.headless", "true"); + if (!isJS) { + // BH Definitely not a good idea in JavaScript; + // probably should not be here for Java, either. + System.setProperty("java.awt.headless", "true"); + } headless = true; } - // < -1) - { - protocol = DataSourceType.URL; - } - - if (file.endsWith(".jar")) - { - format = FileFormat.Jalview; - } - else - { - try - { - format = new IdentifyFile().identify(file, protocol); - } catch (FileFormatException e) - { - // TODO what? - } - } - - af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); - + af.getViewport().getCalcManager().shutdown(); } } // extract groovy arguments before anything else. @@ -906,8 +822,12 @@ public class Jalview implements ApplicationSingletonI { if (Cache.groovyJarsPresent()) { + // TODO: DECIDE IF THIS SECOND PASS AT GROOVY EXECUTION IS STILL REQUIRED !! System.out.println("Executing script " + groovyscript); executeGroovyScript(groovyscript, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); + } else { @@ -926,13 +846,170 @@ public class Jalview implements ApplicationSingletonI } desktop.setInBatchMode(false); } - - if (isJS && isStartup) - { + + if (jsApp != null) { jsApp.callInitCallback(); } } + /** + * Set general display parameters irrespective of file loading or headlessness. + * + * @param aparser + */ + private void setDisplayParameters(ArgsParser aparser) + { + if (aparser.contains(ArgsParser.NOMENUBAR)) + { + noMenuBar = true; + System.out.println("CMD [nomenu] executed successfully!"); + } + + if (aparser.contains(ArgsParser.NOSTATUS)) + { + noStatus = true; + System.out.println("CMD [nostatus] executed successfully!"); + } + + if (aparser.contains(ArgsParser.NOANNOTATION) + || aparser.contains(ArgsParser.NOANNOTATION2)) + { + noAnnotation = true; + System.out.println("CMD no-annotation executed successfully!"); + } + if (aparser.contains(ArgsParser.NOCALCULATION)) + { + noCalculation = true; + System.out.println("CMD [nocalculation] executed successfully!"); + } + } + + private void setFrameDependentProperties(ArgsParser aparser, + AlignFrame af) + { + String data = aparser.getValue(ArgsParser.COLOUR, true); + if (data != null) + { + data.replaceAll("%20", " "); + + ColourSchemeI cs = ColourSchemeProperty.getColourScheme( + af.getViewport(), af.getViewport().getAlignment(), data); + + if (cs != null) + { + System.out.println( + "CMD [-color " + data + "] executed successfully!"); + } + af.changeColour(cs); + } + + // Must maintain ability to use the groups flag + data = aparser.getValue(ArgsParser.GROUPS, true); + if (data != null) + { + af.parseFeaturesFile(data, + AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println( + "CMD groups[-" + data + "] executed successfully!"); + } + data = aparser.getValue(ArgsParser.FEATURES, true); + if (data != null) + { + af.parseFeaturesFile(data, + AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println( + "CMD [-features " + data + "] executed successfully!"); + } + data = aparser.getValue(ArgsParser.ANNOTATIONS, true); + if (data != null) + { + af.loadJalviewDataFile(data, null, null, null); + // System.out.println("Added " + data); + System.out.println( + "CMD [-annotations " + data + "] executed successfully!"); + } + + // JavaScript feature + + if (aparser.contains(ArgsParser.SHOWOVERVIEW)) + { + af.overviewMenuItem_actionPerformed(null); + System.out.println("CMD [showoverview] executed successfully!"); + } + + // set or clear the sortbytree flag. + if (aparser.contains(ArgsParser.SORTBYTREE)) + { + af.getViewport().setSortByTree(true); + if (af.getViewport().getSortByTree()) + { + System.out.println("CMD [-sortbytree] executed successfully!"); + } + } + + boolean doUpdateAnnotation = false; + /** + * we do this earlier in JalviewJS because of a complication with + * SHOWOVERVIEW + * + * For now, just fixing this in JalviewJS. + * + * + * @j2sIgnore + * + */ + { + if (noAnnotation) + { + af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) + { + doUpdateAnnotation = true; + } + } + + } + + if (aparser.contains(ArgsParser.NOSORTBYTREE)) + { + af.getViewport().setSortByTree(false); + if (!af.getViewport().getSortByTree()) + { + doUpdateAnnotation = true; + System.out + .println("CMD [-nosortbytree] executed successfully!"); + } + } + if (doUpdateAnnotation) + { // BH 2019.07.24 + af.setMenusForViewport(); + af.alignPanel.updateLayout(); + } + + data = aparser.getValue(ArgsParser.TREE, true); + if (data != null) + { + try + { + NewickFile nf = new NewickFile(data, + AppletFormatAdapter.checkProtocol(data)); + af.getViewport() + .setCurrentTree(af.showNewickTree(nf, data).getTree()); + System.out.println( + "CMD [-tree " + data + "] executed successfully!"); + } catch (IOException ex) + { + System.err.println("Couldn't add tree " + data); + ex.printStackTrace(System.err); + } + } + // TODO - load PDB structure(s) to alignment JAL-629 + // (associate with identical sequence in alignment, or a specified + // sequence) + + } /** * Writes an output file for each format (if any) specified in the @@ -950,18 +1027,18 @@ public class Jalview implements ApplicationSingletonI * corresponding alignment image output. * * @param aparser - * @param af * @param format */ - private void createOutputFiles(ArgsParser aparser, AlignFrame af, - FileFormatI format) + private void createOutputFiles(ArgsParser aparser, FileFormatI format) { + // logic essentially the same as 2.11.2/2.11.3 but uses a switch instead + AlignFrame af = currentAlignFrame; while (aparser.getSize() >= 2) { String outputFormat = aparser.nextValue(); File imageFile; String fname; - switch (outputFormat.toLowerCase()) + switch (outputFormat.toLowerCase(Locale.ROOT)) { case "png": imageFile = new File(aparser.nextValue()); @@ -1007,32 +1084,308 @@ public class Jalview implements ApplicationSingletonI System.out.println( "Creating image map: " + imageFile.getAbsolutePath()); continue; - } - if (!Platform.isJS()) /** @j2sIgnore */ - { - // skipping outputFormat? - System.out.println("Unknown arg: " + outputFormat); - fname = new File(aparser.nextValue()).getAbsolutePath(); - af.saveAlignment(fname, format); - if (af.isSaveAlignmentSuccessful()) + default: + // fall through - try to parse as an alignment data export format + FileFormatI outFormat = null; + try + { + outFormat = FileFormats.getInstance().forName(outputFormat); + } catch (Exception formatP) + { + } + if (outFormat == null) + { + System.out.println("Couldn't parse " + outputFormat + + " as a valid Jalview format string."); + continue; + } + if (!outFormat.isWritable()) { System.out.println( - "Written alignment in " + format + " format to " + fname); + "This version of Jalview does not support alignment export as " + + outputFormat); + continue; + } + // record file as it was passed to Jalview so it is recognisable to the CLI + // caller + String file; + fname = new File(file = aparser.nextValue()).getAbsolutePath(); + // JBPNote - yuck - really wish we did have a bean returned from this which gave + // success/fail like before ! + af.saveAlignment(fname, outFormat); + if (!af.isSaveAlignmentSuccessful()) + { + System.out.println("Written alignment in " + outputFormat + + " format to " + file); + continue; } else { - System.out.println("Error writing file " + fname + " in " + format - + " format!!"); + System.out.println("Error writing file " + file + " in " + + outputFormat + " format!!"); } } - break; } + // ??? Should report - 'ignoring' extra args here... while (aparser.getSize() > 0) { - System.out.println("Unknown arg: " + aparser.nextValue()); + System.out.println("Ignoring extra argument: " + aparser.nextValue()); } } + private static void setLookAndFeel() + { + // 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"); + String lafSetting = Cache.getDefault("PREFERRED_LAF", null); + String laf = "none"; + if (lafProp != null) + { + laf = lafProp; + } + else if (lafSetting != null) + { + laf = lafSetting; + } + boolean lafSet = false; + switch (laf) + { + case "crossplatform": + lafSet = setCrossPlatformLookAndFeel(); + if (!lafSet) + { + Console.error("Could not set requested laf=" + laf); + } + break; + case "system": + lafSet = setSystemLookAndFeel(); + if (!lafSet) + { + Console.error("Could not set requested laf=" + laf); + } + break; + case "gtk": + lafSet = setGtkLookAndFeel(); + if (!lafSet) + { + Console.error("Could not set requested laf=" + laf); + } + break; + case "metal": + lafSet = setMetalLookAndFeel(); + if (!lafSet) + { + Console.error("Could not set requested laf=" + laf); + } + break; + case "nimbus": + lafSet = setNimbusLookAndFeel(); + if (!lafSet) + { + Console.error("Could not set requested laf=" + laf); + } + break; + case "flat": + lafSet = setFlatLookAndFeel(); + if (!lafSet) + { + Console.error("Could not set requested laf=" + laf); + } + break; + case "quaqua": + lafSet = setQuaquaLookAndFeel(); + if (!lafSet) + { + Console.error("Could not set requested laf=" + laf); + } + break; + case "vaqua": + lafSet = setVaquaLookAndFeel(); + if (!lafSet) + { + Console.error("Could not set requested laf=" + laf); + } + break; + case "mac": + lafSet = setMacLookAndFeel(); + if (!lafSet) + { + Console.error("Could not set requested laf=" + laf); + } + break; + case "none": + break; + default: + Console.error("Requested laf=" + laf + " not implemented"); + } + if (!lafSet) + { + setSystemLookAndFeel(); + if (Platform.isLinux()) + { + setMetalLookAndFeel(); + } + if (Platform.isMac()) + { + setMacLookAndFeel(); + } + } + } + + private static boolean setCrossPlatformLookAndFeel() + { + 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() + { + boolean set = false; + try + { + UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); + 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 setSpecificLookAndFeel(String name, + String className, boolean nameStartsWith) + { + boolean set = false; + try + { + for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels()) + { + 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))) + { + className = info.getClassName(); + break; + } + } + UIManager.setLookAndFeel(className); + 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 setGtkLookAndFeel() + { + return setSpecificLookAndFeel("gtk", + "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true); + } + + private static boolean setMetalLookAndFeel() + { + return setSpecificLookAndFeel("metal", + "javax.swing.plaf.metal.MetalLookAndFeel", false); + } + + private static boolean setNimbusLookAndFeel() + { + return setSpecificLookAndFeel("nimbus", + "javax.swing.plaf.nimbus.NimbusLookAndFeel", false); + } + + private static boolean setFlatLookAndFeel() + { + boolean set = setSpecificLookAndFeel("flatlaf light", + "com.formdev.flatlaf.FlatLightLaf", false); + 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.getInstance() != null) + { + Desktop.getInstance().getRootPane() + .putClientProperty("apple.awt.fullWindowContent", true); + Desktop.getInstance().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.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); + } + + private static boolean setMacLookAndFeel() + { + boolean set = false; + 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 void showUsage() { System.out.println( @@ -1071,7 +1424,9 @@ public class Jalview implements ApplicationSingletonI + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n" + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" + "-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" - + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\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 https://www.jalview.org for description of Features and Annotations file~\n\n"); } private static void startUsageStats(final Desktop desktop) @@ -1089,17 +1444,17 @@ public class Jalview implements ApplicationSingletonI @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); @@ -1241,8 +1596,8 @@ public class Jalview implements ApplicationSingletonI } /** - * Quit method delegates to Desktop.quit - unless running in headless mode - * when it just ends the JVM + * Quit method delegates to Desktop.quit - unless running in headless mode when + * it just ends the JVM */ public void quit() { @@ -1265,12 +1620,23 @@ public class Jalview implements ApplicationSingletonI { Jalview.getInstance().currentAlignFrame = currentAlignFrame; } - public void notifyWorker(AlignCalcWorkerI worker, String status) { // System.out.println("Jalview worker " + worker.getClass().getSimpleName() // + " " + status); } - + + + private static boolean isInteractive = true; + + public static boolean isInteractive() + { + return isInteractive; + } + + public static void setInteractive(boolean tf) + { + isInteractive = tf; + } }