X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=6238c7db80e5e87c2f65c01cb23b83c2b8739835;hb=453fa24ab502aaca4ffccf3590f97c897b9580b3;hp=1ae101455749d3c4b88c1c81048c380bdb12c9d8;hpb=d85279450741df748b662ca0e7757a489b8c6d01;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 1ae1014..6238c7d 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,8 +20,7 @@ */ package jalview.bin; -import java.util.Locale; - +import java.awt.Color; import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; @@ -39,19 +38,26 @@ 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.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.bin.ArgParser.Arg; import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; import jalview.gui.Desktop; @@ -72,6 +78,7 @@ 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 +103,10 @@ 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"); } /* @@ -288,7 +299,10 @@ public class Jalview // report Jalview version Cache.loadBuildProperties(true); + // old ArgsParser ArgsParser aparser = new ArgsParser(args); + // new ArgParser + ArgParser argparser = new ArgParser(args); boolean headless = false; String usrPropsFile = aparser.getValue("props"); @@ -306,13 +320,18 @@ 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; @@ -366,9 +385,10 @@ public class Jalview } System.setProperty("http.agent", "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown")); + try { - Cache.initLogger(); + Console.initLogger(); } catch (NoClassDefFoundError error) { error.printStackTrace(); @@ -402,13 +422,13 @@ 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 +444,35 @@ 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 +493,7 @@ 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 +508,7 @@ 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 +520,30 @@ 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"); @@ -499,6 +563,13 @@ public class Jalview }.start(); } + if (argparser.isSet(Arg.HEADLESS)) + headless = argparser.getBool(Arg.HEADLESS); + if (Commands.processArgs(argparser, headless)) + { + System.exit(1); + } + String file = null, data = null; FileFormatI format = null; DataSourceType protocol = null; @@ -787,12 +858,11 @@ 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:"); @@ -853,8 +923,8 @@ public class Jalview 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"); @@ -875,62 +945,69 @@ 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) + { + 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) { @@ -956,9 +1033,9 @@ 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; } @@ -972,9 +1049,9 @@ 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; } @@ -990,7 +1067,8 @@ 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; @@ -1000,9 +1078,9 @@ 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; } @@ -1025,6 +1103,45 @@ public class Jalview "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.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.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", @@ -1045,12 +1162,16 @@ 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; } @@ -1112,17 +1233,17 @@ 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);