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;
* @author $author$
* @version $Revision$
*/
-public class Jalview
+public class Jalview implements JalviewObjectI
{
static
{
protected Commands cmds;
- public static AlignFrame currentAlignFrame;
+ public AlignFrame currentAlignFrame = null;
private ArgParser argparser = null;
}
else if (bootstrapArgs.contains(Arg.DEBUG))
{
- logLevel = "DEBUG";
+ logLevel = bootstrapArgs.getBoolean(Arg.DEBUG) ? "DEBUG" : "INFO";
}
if (logLevel == null && !(bootstrapProperties == null))
{
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;
cmds.processArgs();
boolean commandsSuccess = cmds.argsWereParsed();
- cliWarning();
-
if (commandsSuccess)
{
if (headlessArg)
}
desktop.setInBatchMode(false);
}
+
+ cliWarning();
}
private static void setLookAndFeel()
*/
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()
}
try
{
+ JalviewObjectI j = new JalviewObject(this);
Map<String, java.lang.Object> 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);
.errPrintln("Exception Whilst trying to execute file " + sfile
+ " as a groovy script.");
e.printStackTrace(System.err);
-
}
}
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()
// 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;
}
/******************************
j.getArgParser().getMixedExamples());
String quit = MessageManager.getString("action.quit");
- Desktop.instance.nonBlockingDialog(title, warning, quit,
- JvOptionPane.WARNING_MESSAGE, false, true);
+ 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.",
if (oldStyle)
{
String warning = MessageManager
- .getString("warning.using_old_command_line_arguments")
- + "https://www.jalview.org/help/html/features/commandline.html";
+ .getString("warning.using_old_command_line_arguments");
+ String url = "<a href=\"https://www.jalview.org/help/html/features/commandline.html\">https://www.jalview.org/help/html/features/commandline.html</a>";
if (Desktop.instance != null)
{
String cont = MessageManager.getString("label.continue");
- Desktop.instance.nonBlockingDialog(32, 2, title, warning, cont,
- JvOptionPane.WARNING_MESSAGE, false, false);
+ Desktop.instance.nonBlockingDialog(title, warning, url, cont,
+ JvOptionPane.WARNING_MESSAGE, false, true, true, 30000);
}
}
if (j.getCommands() != null && j.getCommands().getErrors().size() > 0)
String message = MessageManager
.getString("warning.the_following_errors");
String ok = MessageManager.getString("action.ok");
- Desktop.instance.nonBlockingDialog(60, 16, title,
- message + "\n" + j.getCommands().errorsToString(), ok,
- JvOptionPane.WARNING_MESSAGE, true, true);
+ int shortest = 60;
+ List<String> 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);
}
}
}