X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e343b0fc4cdf3f0713badb2b1c8e6d283752f909;hb=refs%2Fheads%2Fbug%2FJAL-4290_headless_alignment_figure_with_sse;hp=51e8a82b976e552c987a0b7e1e8609734c192fd9;hpb=985d5f40db480896f550db914297cf948a32e963;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 51e8a82..e343b0f 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -73,9 +73,12 @@ import jalview.bin.argparser.Arg.Opt; import jalview.bin.argparser.Arg.Type; import jalview.bin.argparser.ArgParser; import jalview.bin.argparser.BootstrapArgs; +import jalview.bin.groovy.JalviewObject; +import jalview.bin.groovy.JalviewObjectI; import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.PromptUserConfig; import jalview.gui.QuitHandler; import jalview.gui.QuitHandler.QResponse; @@ -117,7 +120,7 @@ import jalview.ws.jws2.Jws2Discoverer; * @author $author$ * @version $Revision$ */ -public class Jalview +public class Jalview implements JalviewObjectI { static { @@ -137,7 +140,7 @@ public class Jalview protected Commands cmds; - public static AlignFrame currentAlignFrame; + public AlignFrame currentAlignFrame = null; private ArgParser argparser = null; @@ -446,7 +449,7 @@ public class Jalview } else if (bootstrapArgs.contains(Arg.DEBUG)) { - logLevel = "DEBUG"; + logLevel = bootstrapArgs.getBoolean(Arg.DEBUG) ? "DEBUG" : "INFO"; } if (logLevel == null && !(bootstrapProperties == null)) { @@ -641,14 +644,12 @@ public class Jalview try { Console.initLogger(); - } catch ( - - NoClassDefFoundError error) + } catch (NoClassDefFoundError error) { error.printStackTrace(); String message = "\nEssential logging libraries not found." + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview"; - Jalview.exit(message, ExitCode.OK); + Jalview.exit(message, ExitCode.NO_LOGGING); } desktop = null; @@ -673,6 +674,8 @@ public class Jalview desktop = new Desktop(); desktop.setInBatchMode(true); // indicate we are starting up + mixedCliWarning(); + try { JalviewTaskbar.setTaskbar(this); @@ -1247,6 +1250,8 @@ public class Jalview } desktop.setInBatchMode(false); } + + cliWarning(); } private static void setLookAndFeel() @@ -1627,9 +1632,8 @@ public class Jalview */ PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop, "USAGESTATS", - MessageManager.getString("prompt.plausible_analytics_title"), - MessageManager.getString("prompt.plausible_analytics"), - new Runnable() + MessageManager.getString("prompt.analytics_title"), + MessageManager.getString("prompt.analytics"), new Runnable() { @Override public void run() @@ -1747,12 +1751,11 @@ public class Jalview } try { + JalviewObjectI j = new JalviewObject(this); Map vbinding = new HashMap<>(); - vbinding.put("Jalview", this); - if (af != null) - { - vbinding.put("currentAlFrame", af); - } + vbinding.put(JalviewObjectI.jalviewObjectName, j); + vbinding.put(JalviewObjectI.currentAlFrameName, + af != null ? af : getCurrentAlignFrame()); Binding gbinding = new Binding(vbinding); GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile }); gse.run(sfile.toString(), gbinding); @@ -1768,7 +1771,6 @@ public class Jalview .errPrintln("Exception Whilst trying to execute file " + sfile + " as a groovy script."); e.printStackTrace(System.err); - } } @@ -1782,30 +1784,32 @@ public class Jalview return false; } + @Override public AlignFrame[] getAlignFrames() { return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() } - : Desktop.getAlignFrames(); - + : Desktop.getDesktopAlignFrames(); } /** * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit */ + @Override public void quit() { // System.exit will run the shutdownHook first Jalview.exit("Quitting now. Bye!", ExitCode.OK); } - public static AlignFrame getCurrentAlignFrame() + @Override + public AlignFrame getCurrentAlignFrame() { - return Jalview.currentAlignFrame; + return currentAlignFrame; } - public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + public void setCurrentAlignFrame(AlignFrame af) { - Jalview.currentAlignFrame = currentAlignFrame; + this.currentAlignFrame = af; } public Commands getCommands() @@ -1857,7 +1861,7 @@ public class Jalview // only add new ones to the end of the list (to preserve ordinal values) OK, FILE_NOT_FOUND, FILE_NOT_READABLE, NO_FILES, INVALID_FORMAT, INVALID_ARGUMENT, INVALID_VALUE, MIXED_CLI_ARGUMENTS, - ERROR_RUNNING_COMMANDS; + ERROR_RUNNING_COMMANDS, NO_LOGGING, GROOVY_ERROR; } /****************************** @@ -2020,4 +2024,71 @@ public class Jalview || getInstance().desktop.isInBatchMode()); } + /** + * Warning about old or mixed command line arguments + */ + private void mixedCliWarning() + { + Jalview j = Jalview.getInstance(); + boolean mixedStyle = j.getArgParser() != null + && j.getArgParser().isMixedStyle(); + String title = MessageManager.getString("label.command_line_arguments"); + if (mixedStyle) + { + String warning = MessageManager.formatMessage( + "warning.using_mixed_command_line_arguments", + j.getArgParser().getMixedExamples()); + String quit = MessageManager.getString("action.quit"); + + Desktop.instance.nonBlockingDialog(title, warning, null, quit, + JvOptionPane.WARNING_MESSAGE, false, false, true, 30000); + + Jalview.exit( + "Exiting due to mixed old and new command line arguments.", + ExitCode.MIXED_CLI_ARGUMENTS); + } + } + + private void cliWarning() + { + Jalview j = Jalview.getInstance(); + Commands c = j.getCommands(); + boolean oldStyle = j.getArgParser() != null + && j.getArgParser().isOldStyle(); + String title = MessageManager.getString("label.command_line_arguments"); + if (oldStyle) + { + String warning = MessageManager + .getString("warning.using_old_command_line_arguments"); + String url = "https://www.jalview.org/help/html/features/commandline.html"; + if (Desktop.instance != null) + { + String cont = MessageManager.getString("label.continue"); + + Desktop.instance.nonBlockingDialog(title, warning, url, cont, + JvOptionPane.WARNING_MESSAGE, false, true, true, 30000); + } + } + if (j.getCommands() != null && j.getCommands().getErrors().size() > 0) + { + if (Desktop.instance != null) + { + String message = MessageManager + .getString("warning.the_following_errors"); + String ok = MessageManager.getString("action.ok"); + int shortest = 60; + List errors = j.getCommands().getErrors(); + for (int i = 0; i < errors.size(); i++) + { + shortest = Math.min(shortest, errors.get(i).length()); + } + Desktop.instance.nonBlockingDialog( + Math.max(message.length(), Math.min(60, shortest)), + Math.min(errors.size(), 20), title, message, + j.getCommands().errorsToString(), ok, + JvOptionPane.WARNING_MESSAGE, true, false, true, -1); + } + } + } + }