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;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.ChannelProperties;
import jalview.util.HttpUtils;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
import jalview.util.LaunchUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
* @author $author$
* @version $Revision$
*/
-public class Jalview
+public class Jalview implements JalviewObjectI
{
static
{
protected Commands cmds;
- public static AlignFrame currentAlignFrame;
+ public AlignFrame currentAlignFrame = null;
- public ArgParser argparser = null;
+ private ArgParser argparser = null;
- public BootstrapArgs bootstrapArgs = null;
+ private BootstrapArgs bootstrapArgs = null;
private boolean QUIET = false;
public void addFetcher(final AlignFrame af,
final Vector<String> dasSources)
{
- final long id = System.currentTimeMillis();
+ final long id = IdUtils.newId(IdType.PROGRESS);
queued++;
final FeatureFetcher us = this;
new Thread(new Runnable()
*
*/
{
- System.out.println("not in js");
+ Console.outPrintln("not in js");
}
// BH - for event debugging in JavaScript (Java mode only)
{
System.setSecurityManager(null);
}
+ else
+ {
+ setJSNamespace();
+ }
if (args == null || args.length == 0 || (args.length == 1
&& (args[0] == null || args[0].length() == 0)))
}.start();
}
- if (!quiet() || bootstrapArgs.contains(Arg.VERSION))
+ if (!quiet() || !bootstrapArgs.outputToStdout()
+ || bootstrapArgs.contains(Arg.VERSION))
{
- System.out.println(
+ Console.outPrintln(
"Java version: " + System.getProperty("java.version"));
- System.out.println("Java home: " + System.getProperty("java.home"));
- System.out.println("Java arch: " + System.getProperty("os.arch") + " "
+ Console.outPrintln("Java home: " + System.getProperty("java.home"));
+ Console.outPrintln("Java arch: " + System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
String val = System.getProperty("sys.install4jVersion");
if (val != null)
{
- System.out.println("Install4j version: " + val);
+ Console.outPrintln("Install4j version: " + val);
}
val = System.getProperty("installer_template_version");
if (val != null)
{
- System.out.println("Install4j template version: " + val);
+ Console.outPrintln("Install4j template version: " + val);
}
val = System.getProperty("launcher_version");
if (val != null)
{
- System.out.println("Launcher version: " + val);
+ Console.outPrintln("Launcher version: " + val);
}
}
// stop now if only after --version
if (bootstrapArgs.contains(Arg.VERSION))
{
- Jalview.exit(null, 0);
+ Jalview.exit(null, ExitCode.OK);
}
// old ArgsParser
}
else if (bootstrapArgs.contains(Arg.DEBUG))
{
- logLevel = "DEBUG";
+ logLevel = bootstrapArgs.getBoolean(Arg.DEBUG) ? "DEBUG" : "INFO";
}
if (logLevel == null && !(bootstrapProperties == null))
{
error.printStackTrace();
String message = "\nEssential logging libraries not found."
+ "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
- Jalview.exit(message, 0);
+ Jalview.exit(message, ExitCode.OK);
}
// register SIGTERM listener
Runtime.getRuntime().addShutdownHook(new Thread()
{
+ @Override
public void run()
{
Console.debug("Running shutdown hook");
Cache.loadProperties(usrPropsFile);
if (usrPropsFile != null)
{
- System.out.println(
+ Console.outPrintln(
"CMD [-props " + usrPropsFile + "] executed successfully!");
testoutput(bootstrapArgs, Arg.PROPS,
"test/jalview/bin/testProps.jvprops", usrPropsFile);
{
List<Map.Entry<Type, String>> helpArgs = bootstrapArgs
.getList(Arg.HELP);
- System.out.println(Arg.usage(helpArgs.stream().map(e -> e.getKey())
+ Console.outPrintln(Arg.usage(helpArgs.stream().map(e -> e.getKey())
.collect(Collectors.toList())));
- Jalview.exit(null, 0);
+ Jalview.exit(null, ExitCode.OK);
}
if (aparser.contains("help") || aparser.contains("h"))
{
/*
- * Now using new usage statement.
- showUsage();
- */
- System.out.println(Arg.usage());
- Jalview.exit(null, 0);
+ * Now using new usage statement. showUsage();
+ */
+ Console.outPrintln(Arg.usage());
+ Jalview.exit(null, ExitCode.OK);
}
// new CLI
try
{
Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
- System.out.println(
+ Console.outPrintln(
"CMD [-jabaws " + jabawsUrl + "] executed successfully!");
testoutput(bootstrapArgs, Arg.JABAWS,
"http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
} catch (MalformedURLException e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Invalid jabaws parameter: " + jabawsUrl + " ignored");
}
}
}
else
{
- System.out.println("Executing setprop argument: " + setprop);
+ jalview.bin.Console
+ .errPrintln("Executing setprop argument: " + setprop);
if (Platform.isJS())
{
Cache.setProperty(setprop.substring(0, p),
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, 0);
+ Jalview.exit(message, ExitCode.NO_LOGGING);
}
desktop = null;
setLookAndFeel();
/*
- * 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
+ * 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
*/
boolean soDefault = !Platform.isJS();
if (Cache.getDefault("USE_FULL_SO", soDefault))
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
+ mixedCliWarning();
+
try
{
JalviewTaskbar.setTaskbar(this);
}
else
{
- System.out.println("CMD [-nousagestats] executed successfully!");
+ Console.outPrintln("CMD [-nousagestats] executed successfully!");
testoutput(argparser, Arg.NOUSAGESTATS);
}
// questionnaire
Console.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
- System.out.println("CMD questionnaire[-" + url
+ Console.outPrintln("CMD questionnaire[-" + url
+ "] executed successfully!");
}
else
}
else
{
- System.out
- .println("CMD [-noquestionnaire] executed successfully!");
+ Console.outPrintln(
+ "CMD [-noquestionnaire] executed successfully!");
testoutput(argparser, Arg.QUESTIONNAIRE);
}
}
}
}
- // Run Commands from cli
- cmds = new Commands(argparser, headlessArg);
- boolean commandsSuccess = cmds.argsWereParsed();
+ else
+ {
- if (commandsSuccess)
+ if (getArgParser().isMixedStyle())
+ {
+ String warning = MessageManager.formatMessage(
+ "warning.using_mixed_command_line_arguments",
+ getArgParser().getMixedExamples());
+ Console.warn(warning);
+ Jalview.exit(
+ "Exiting due to mixed old and new command line arguments",
+ ExitCode.INVALID_ARGUMENT);
+ }
+ if (getArgParser().isOldStyle())
+ {
+ String warning = MessageManager
+ .getString("warning.using_old_command_line_arguments")
+ .replace("\n", " ")
+ + "https://www.jalview.org/help/html/features/commandline.html";
+ Console.warn(warning);
+ }
+
+ }
+
+ // Run Commands from cli
+ boolean commandsSuccess = false;
+ if (!(argparser.isMixedStyle() || argparser.isOldStyle()))
{
- if (headlessArg)
+ cmds = new Commands(argparser, headlessArg);
+ cmds.processArgs();
+ commandsSuccess = cmds.argsWereParsed();
+
+ if (commandsSuccess)
{
- if (argparser.getBoolean(Arg.NOQUIT))
+ if (headlessArg)
{
- Console.warn(
- "Completed " + Arg.HEADLESS.getName() + " commands, but "
- + Arg.NOQUIT + " is set so not quitting!");
- }
- else
- {
- // record usage stats if in headless mode
- if (Cache.getDefault("USAGESTATS", false)
- && !argparser.getBoolean(Arg.NOUSAGESTATS))
+ if (argparser.getBoolean(Arg.NOQUIT))
+ {
+ Console.warn("Completed " + Arg.HEADLESS.getName()
+ + " commands, but " + Arg.NOQUIT
+ + " is set so not quitting!");
+ }
+ else
{
- Cache.initAnalytics(headlessArg);
+ Jalview.exit("Successfully completed commands in headless mode",
+ ExitCode.OK);
}
- Jalview.exit("Successfully completed commands in headless mode",
- 0);
}
+ Console.info("Successfully completed commands");
}
- Console.info("Successfully completed commands");
- }
- else
- {
- if (headlessArg)
+ else
{
- Jalview.exit("Error when running Commands in headless mode", 1);
+ if (headlessArg)
+ {
+ Jalview.exit("Error when running Commands in headless mode",
+ ExitCode.ERROR_RUNNING_COMMANDS);
+ }
+ Console.warn("Error when running commands");
}
- Console.warn("Error when running commands");
}
// Check if JVM and compile version might cause problems and log if it
if (file == null && desktop == null && !commandsSuccess)
{
- Jalview.exit("No files to open!", 1);
+ Jalview.exit("No files to open!", ExitCode.NO_FILES);
}
long progress = -1;
desktop.setProgressBar(
MessageManager
.getString("status.processing_commandline_args"),
- progress = System.currentTimeMillis());
+ progress = IdUtils.newId(IdType.PROGRESS));
}
- System.out.println("CMD [-open " + file + "] executed successfully!");
+ Console.outPrintln("CMD [-open " + file + "] executed successfully!");
if (!Platform.isJS())
/**
if (headless)
{
Jalview.exit(
- "Can't find file '" + file + "' in headless mode", 1);
+ "Can't find file '" + file + "' in headless mode",
+ ExitCode.FILE_NOT_FOUND);
}
Console.warn("Can't find file'" + file + "'");
}
format);
if (af == null)
{
- System.out.println("error");
+ Console.outPrintln("error");
}
else
{
if (cs != null)
{
- System.out.println(
+ Console.outPrintln(
"CMD [-colour " + data + "] executed successfully!");
}
af.changeColour(cs);
{
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
- // System.out.println("Added " + data);
- System.out.println(
+ // Console.outPrintln("Added " + data);
+ Console.outPrintln(
"CMD groups[-" + data + "] executed successfully!");
}
data = aparser.getValue("features", true);
{
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
- // System.out.println("Added " + data);
- System.out.println(
+ // Console.outPrintln("Added " + data);
+ Console.outPrintln(
"CMD [-features " + data + "] executed successfully!");
}
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
- // System.out.println("Added " + data);
- System.out.println(
+ // Console.outPrintln("Added " + data);
+ Console.outPrintln(
"CMD [-annotations " + data + "] executed successfully!");
}
// set or clear the sortbytree flag.
af.getViewport().setSortByTree(true);
if (af.getViewport().getSortByTree())
{
- System.out.println("CMD [-sortbytree] executed successfully!");
+ Console.outPrintln("CMD [-sortbytree] executed successfully!");
}
}
if (aparser.contains("no-annotation"))
af.getViewport().setShowAnnotation(false);
if (!af.getViewport().isShowAnnotation())
{
- System.out.println("CMD no-annotation executed successfully!");
+ Console.outPrintln("CMD no-annotation executed successfully!");
}
}
if (aparser.contains("nosortbytree"))
af.getViewport().setSortByTree(false);
if (!af.getViewport().getSortByTree())
{
- System.out
- .println("CMD [-nosortbytree] executed successfully!");
+ Console.outPrintln(
+ "CMD [-nosortbytree] executed successfully!");
}
}
data = aparser.getValue("tree", true);
{
try
{
- System.out.println(
+ Console.outPrintln(
"CMD [-tree " + data + "] executed successfully!");
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
.setCurrentTree(af.showNewickTree(nf, data).getTree());
} catch (IOException ex)
{
- System.err.println("Couldn't add tree " + data);
+ jalview.bin.Console.errPrintln("Couldn't add tree " + data);
ex.printStackTrace(System.err);
}
}
{
// Execute the groovy script after we've done all the rendering stuff
// and before any images or figures are generated.
- System.out.println("Executing script " + groovyscript);
+ Console.outPrintln("Executing script " + groovyscript);
executeGroovyScript(groovyscript, af);
- System.out.println("CMD groovy[" + groovyscript
+ Console.outPrintln("CMD groovy[" + groovyscript
+ "] executed successfully!");
groovyscript = null;
}
if (outputFormat.equalsIgnoreCase("png"))
{
- System.out.println("Creating PNG image: " + file);
+ Console.outPrintln("Creating PNG image: " + file);
af.createPNG(new File(file));
imageName = (new File(file)).getName();
continue;
}
else if (outputFormat.equalsIgnoreCase("svg"))
{
- System.out.println("Creating SVG image: " + file);
+ Console.outPrintln("Creating SVG image: " + file);
File imageFile = new File(file);
imageName = imageFile.getName();
af.createSVG(imageFile);
imageName = imageFile.getName();
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- System.out.println("Creating HTML image: " + file);
+ Console.outPrintln("Creating HTML image: " + file);
htmlSVG.exportHTML(file);
continue;
}
{
if (file == null)
{
- System.err.println("The output html file must not be null");
+ jalview.bin.Console.errPrintln(
+ "The output html file must not be null");
return;
}
try
e.printStackTrace();
}
BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- System.out.println(
+ Console.outPrintln(
"Creating BioJS MSA Viwer HTML file: " + file);
bjs.exportHTML(file);
continue;
}
else if (outputFormat.equalsIgnoreCase("imgMap"))
{
- System.out.println("Creating image map: " + file);
+ Console.outPrintln("Creating image map: " + file);
af.createImageMap(new File(file), imageName);
continue;
}
else if (outputFormat.equalsIgnoreCase("eps"))
{
File outputFile = new File(file);
- System.out.println(
+ Console.outPrintln(
"Creating EPS file: " + outputFile.getAbsolutePath());
af.createEPS(outputFile);
continue;
outFormat = FileFormats.getInstance().forName(outputFormat);
} catch (Exception formatP)
{
- System.out.println("Couldn't parse " + outFormat
+ Console.outPrintln("Couldn't parse " + outFormat
+ " as a valid Jalview format string.");
}
if (outFormat != null)
{
if (!outFormat.isWritable())
{
- System.out.println(
+ Console.outPrintln(
"This version of Jalview does not support alignment export as "
+ outputFormat);
}
af.saveAlignment(file, outFormat);
if (af.isSaveAlignmentSuccessful())
{
- System.out.println("Written alignment in "
+ Console.outPrintln("Written alignment in "
+ outFormat.getName() + " format to " + file);
}
else
{
- System.out.println("Error writing file " + file + " in "
+ Console.outPrintln("Error writing file " + file + " in "
+ outFormat.getName() + " format!!");
}
}
}
} catch (ImageOutputException ioexc)
{
- System.out.println(
+ Console.outPrintln(
"Unexpected error whilst exporting image to " + file);
ioexc.printStackTrace();
}
while (aparser.getSize() > 0)
{
- System.out.println("Unknown arg: " + aparser.nextValue());
+ Console.outPrintln("Unknown arg: " + aparser.nextValue());
}
}
}
{
if (Cache.groovyJarsPresent())
{
- System.out.println("Executing script " + groovyscript);
+ Console.outPrintln("Executing script " + groovyscript);
executeGroovyScript(groovyscript, startUpAlframe);
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ groovyscript);
}
}
desktop.setInBatchMode(false);
}
+
+ cliWarning();
}
private static void setLookAndFeel()
UIManager.put("TabbedPane.tabType", "card");
UIManager.put("TabbedPane.showTabSeparators", true);
UIManager.put("TabbedPane.showContentSeparator", true);
- UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
+ // UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
UIManager.put("TabbedPane.tabsOverlapBorder", true);
UIManager.put("TabbedPane.hasFullBorder", true);
UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
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();
- }
+ * 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(
- "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
- + "-nodisplay\tRun Jalview without User Interface.\n"
- + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
- + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
- + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
- + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
- + "-features FILE\tUse the given file to mark features on the alignment.\n"
- + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
- + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
- + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
- + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
- + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
- + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
- + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
- + "-json FILE\tCreate alignment file FILE in JSON format.\n"
- + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
- + "-png FILE\tCreate PNG image FILE from alignment.\n"
- + "-svg FILE\tCreate SVG image FILE from alignment.\n"
- + "-html FILE\tCreate HTML file from alignment.\n"
- + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
- + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
- + "-eps FILE\tCreate EPS file FILE from alignment.\n"
- + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
- + "-noquestionnaire\tTurn off questionnaire check.\n"
- + "-nonews\tTurn off check for Jalview news.\n"
- + "-nousagestats\tTurn off analytics tracking for this session.\n"
- + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
- // +
- // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
- // after all other properties files have been read\n\t
- // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
- // passed in correctly)"
- + "-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"
- + "-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 showUsage() { jalview.bin.Console.outPrintln(
+ * "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n" +
+ * "-nodisplay\tRun Jalview without User Interface.\n" +
+ * "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+ * + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n" +
+ * "-annotations FILE\tAdd precalculated annotations to the alignment.\n" +
+ * "-tree FILE\tLoad the given newick format tree file onto the alignment\n" +
+ * "-features FILE\tUse the given file to mark features on the alignment.\n" +
+ * "-fasta FILE\tCreate alignment file FILE in Fasta format.\n" +
+ * "-clustal FILE\tCreate alignment file FILE in Clustal format.\n" +
+ * "-pfam FILE\tCreate alignment file FILE in PFAM format.\n" +
+ * "-msf FILE\tCreate alignment file FILE in MSF format.\n" +
+ * "-pileup FILE\tCreate alignment file FILE in Pileup format\n" +
+ * "-pir FILE\tCreate alignment file FILE in PIR format.\n" +
+ * "-blc FILE\tCreate alignment file FILE in BLC format.\n" +
+ * "-json FILE\tCreate alignment file FILE in JSON format.\n" +
+ * "-jalview FILE\tCreate alignment file FILE in Jalview format.\n" +
+ * "-png FILE\tCreate PNG image FILE from alignment.\n" +
+ * "-svg FILE\tCreate SVG image FILE from alignment.\n" +
+ * "-html FILE\tCreate HTML file from alignment.\n" +
+ * "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n" +
+ * "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n" +
+ * "-eps FILE\tCreate EPS file FILE from alignment.\n" +
+ * "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ * + "-noquestionnaire\tTurn off questionnaire check.\n" +
+ * "-nonews\tTurn off check for Jalview news.\n" +
+ * "-nousagestats\tTurn off analytics tracking for this session.\n" +
+ * "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
+ * // + // "-setprop PROPERTY=VALUE\tSet the given Jalview property, // after
+ * all other properties files have been read\n\t // (quote the 'PROPERTY=VALUE'
+ * pair to ensure spaces are // passed in correctly)" +
+ * "-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"
+ * +
+ * "-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)
{
*/
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()
} catch (Exception ex)
{
- System.err.println("Failed to read from STDIN into tempfile "
- + ((tfile == null) ? "(tempfile wasn't created)"
- : tfile.toString()));
+ jalview.bin.Console
+ .errPrintln("Failed to read from STDIN into tempfile "
+ + ((tfile == null) ? "(tempfile wasn't created)"
+ : tfile.toString()));
ex.printStackTrace();
return;
}
sfile = tfile.toURI().toURL();
} catch (Exception x)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ tfile.toURI());
x.printStackTrace();
tfile = new File(groovyscript);
if (!tfile.exists())
{
- System.err.println("File '" + groovyscript + "' does not exist.");
+ jalview.bin.Console.errPrintln(
+ "File '" + groovyscript + "' does not exist.");
return;
}
if (!tfile.canRead())
{
- System.err.println("File '" + groovyscript + "' cannot be read.");
+ jalview.bin.Console.errPrintln(
+ "File '" + groovyscript + "' cannot be read.");
return;
}
if (tfile.length() < 1)
{
- System.err.println("File '" + groovyscript + "' is empty.");
+ jalview.bin.Console
+ .errPrintln("File '" + groovyscript + "' is empty.");
return;
}
try
sfile = tfile.getAbsoluteFile().toURI().toURL();
} catch (Exception ex)
{
- System.err.println("Failed to create a file URL for "
+ jalview.bin.Console.errPrintln("Failed to create a file URL for "
+ tfile.getAbsoluteFile());
return;
}
}
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);
}
} catch (Exception e)
{
- System.err.println("Exception Whilst trying to execute file " + sfile
- + " as a groovy script.");
+ jalview.bin.Console
+ .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!", 0);
+ 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;
}
- protected Commands getCommands()
+ public Commands getCommands()
{
return cmds;
}
- public static void exit(String message, int exitcode)
+ public static void exit(String message, ExitCode ec)
{
+ int exitcode = ec == ExitCode.OK ? 0 : ec.ordinal() + 1;
if (Console.log == null)
{
// Don't start the logger just to exit!
{
if (exitcode == 0)
{
- System.out.println(message);
+ Console.outPrintln(message);
}
else
{
- System.err.println(message);
+ jalview.bin.Console.errPrintln(message);
}
}
}
}
}
+ public enum ExitCode
+ {
+ // 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, NO_LOGGING, GROOVY_ERROR;
+ }
+
/******************************
*
* TEST OUTPUT METHODS
*
+ * these operate only when Arg.TESTOUTPUT has been passed, and variously check
+ * if an expected value / arg was set and report it to the test framework.
+ *
******************************/
/**
- * method for reporting string values parsed/processed during tests
+ * report string values parsed/processed during tests When the Bootstrap
+ * argument Arg.TESTOUTPUT is present - reports on debug if given s1 is not
+ * null and not equals s2, warns if given argument is not set, and calls
+ * testoutput(true,a,s1,s2) to report processing progress.
*
+ * @param ap
+ * - ArgParser handling parsing
+ * @param a
+ * - Arg currently being processed
+ * @param s1
+ * - expected
+ * @param s2
*/
protected static void testoutput(ArgParser ap, Arg a, String s1,
String s2)
}
/**
- * method for reporting string values parsed/processed during tests
+ * report values passed via bootstrap arguments
+ *
+ * TODO: significant code duplication with testouput(Argparser...) - move it
*/
protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
}
/**
- * report value set for string values parsed/processed during tests
+ * conditionally (on @param yes) report that expected value s1 was set during
+ * CommandsTest tests
*/
private static void testoutput(boolean yes, Arg a, String s1, String s2)
{
if (yes && ((s1 == null && s2 == null)
|| (s1 != null && s1.equals(s2))))
{
- System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+ Console.outPrintln("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+ "' was set");
}
}
{
message = a.argString() + (yes ? " was set" : " was not set");
}
- System.out.println("[TESTOUTPUT] arg " + message);
+ Console.outPrintln("[TESTOUTPUT] arg " + message);
+ }
+
+ public ArgParser getArgParser()
+ {
+ return argparser;
+ }
+
+ public BootstrapArgs getBootstrapArgs()
+ {
+ return bootstrapArgs;
}
+
+ public static boolean isBatchMode()
+ {
+ return getInstance() != null && (getInstance().desktop == null
+ || 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 = "<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(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<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);
+ }
+ }
+ }
+
+ /**
+ * Namespace (if set) by JalviewJS
+ */
+ private String JSNamespace = null;
+
+ private void setJSNamespace(String ns)
+ {
+ if (!Platform.isJS())
+ {
+ return;
+ }
+ Console.outPrintln("JSNamespace set to '" + ns + "'");
+ JSNamespace = ns;
+ }
+
+ public String getJSNamespace()
+ {
+ return JSNamespace;
+ }
+
+ public void setJSNamespace()
+ {
+ if (!Platform.isJS())
+ {
+ return;
+ }
+ String ns = null;
+ /**
+ * @j2sNative var namespace = J2S.thisApplet.__Info.namespace;
+ *
+ * if (namespace === undefined)
+ *
+ * {
+ *
+ * System.out.println("No namespace given");
+ *
+ * }
+ *
+ * else
+ *
+ * {
+ *
+ * ns = namespace;
+ *
+ * }
+ */
+ setJSNamespace(ns);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff