X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FJalview.java;h=59382fd6fec11a0d61de7ffacea6c49a4c8dc70c;hb=7d66757c0ac1b57953fb113cdae34dc94b03dd17;hp=ff1b18099190bfec774bd1928ba20fc8a9325edd;hpb=4e7511345e2d3b5c0ec47c280bf5582073c86c1e;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ff1b180..59382fd 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
@@ -20,40 +20,96 @@
*/
package jalview.bin;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
+import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
import java.io.OutputStreamWriter;
+import java.io.PrintStream;
import java.io.PrintWriter;
-import java.lang.reflect.Constructor;
import java.net.MalformedURLException;
import java.net.URI;
+import java.net.URISyntaxException;
import java.net.URL;
-import java.net.URLDecoder;
import java.security.AllPermission;
import java.security.CodeSource;
import java.security.PermissionCollection;
import java.security.Permissions;
import java.security.Policy;
-import java.util.Hashtable;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Locale;
import java.util.Map;
+import java.util.Properties;
import java.util.Vector;
-
+import java.util.logging.ConsoleHandler;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import java.util.stream.Collectors;
+
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
import javax.swing.UIManager;
+import javax.swing.UIManager.LookAndFeelInfo;
+import javax.swing.UnsupportedLookAndFeelException;
+
+import com.formdev.flatlaf.FlatLightLaf;
+import com.formdev.flatlaf.themes.FlatMacLightLaf;
+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.bin.argparser.Arg.Opt;
+import jalview.bin.argparser.Arg.Type;
+import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.BootstrapArgs;
+import jalview.ext.so.SequenceOntology;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.gui.QuitHandler;
+import jalview.gui.QuitHandler.QResponse;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+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;
/**
* Main class for Jalview Application
*
- * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview
+ *
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ *
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
*
* @author $author$
* @version $Revision$
@@ -62,20 +118,125 @@ public class Jalview
{
static
{
- // grab all the rights we can the JVM
- Policy.setPolicy(new Policy()
+ 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");
+ }
+
+ /*
+ * singleton instance of this class
+ */
+ private static Jalview instance;
+
+ private Desktop desktop;
+
+ protected Commands cmds;
+
+ public static AlignFrame currentAlignFrame;
+
+ public ArgParser argparser = null;
+
+ public BootstrapArgs bootstrapArgs = null;
+
+ private boolean QUIET = false;
+
+ public static boolean quiet()
+ {
+ return Jalview.getInstance() != null && Jalview.getInstance().QUIET;
+ }
+
+ static
+ {
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- public PermissionCollection getPermissions(CodeSource codesource)
+ // grab all the rights we can for the JVM
+ Policy.setPolicy(new Policy()
{
- Permissions perms = new Permissions();
- perms.add(new AllPermission());
- return (perms);
- }
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ @Override
+ public void refresh()
+ {
+ }
+ });
+ }
+ }
- public void refresh()
+ /**
+ * keep track of feature fetching tasks.
+ *
+ * @author JimP
+ *
+ */
+ class FeatureFetcher
+ {
+ /*
+ * TODO: generalise to track all jalview events to orchestrate batch processing
+ * events.
+ */
+
+ private int queued = 0;
+
+ private int running = 0;
+
+ public FeatureFetcher()
+ {
+
+ }
+
+ public void addFetcher(final AlignFrame af,
+ final Vector dasSources)
+ {
+ final long id = System.currentTimeMillis();
+ queued++;
+ final FeatureFetcher us = this;
+ new Thread(new Runnable()
{
- }
- });
+
+ @Override
+ public void run()
+ {
+ synchronized (us)
+ {
+ queued--;
+ running++;
+ }
+
+ af.setProgressBar(MessageManager
+ .getString("status.das_features_being_retrived"), id);
+ af.featureSettings_actionPerformed(null);
+ af.setProgressBar(null, id);
+ synchronized (us)
+ {
+ running--;
+ }
+ }
+ }).start();
+ }
+
+ public synchronized boolean allFinished()
+ {
+ return queued == 0 && running == 0;
+ }
+
+ }
+
+ public static Jalview getInstance()
+ {
+ return instance;
}
/**
@@ -86,64 +247,346 @@ public class Jalview
*/
public static void main(String[] args)
{
- System.out.println("Java version: "
- + System.getProperty("java.version"));
- System.out.println(System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version"));
- if (new Platform().isAMac())
- {
- System.setProperty("com.apple.mrj.application.apple.menu.about.name",
- "Jalview");
- System.setProperty("apple.laf.useScreenMenuBar", "true");
+ // setLogging(); // BH - for event debugging in JavaScript
+ instance = new Jalview();
+ instance.doMain(args);
+ }
+
+ private static void logClass(String name)
+ {
+ // BH - for event debugging in JavaScript
+ ConsoleHandler consoleHandler = new ConsoleHandler();
+ consoleHandler.setLevel(Level.ALL);
+ Logger logger = Logger.getLogger(name);
+ logger.setLevel(Level.ALL);
+ logger.addHandler(consoleHandler);
+ }
+
+ @SuppressWarnings("unused")
+ private static void setLogging()
+ {
+
+ /**
+ * @j2sIgnore
+ *
+ */
+ {
+ System.out.println("not in js");
}
+ // BH - for event debugging in JavaScript (Java mode only)
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ Logger.getLogger("").setLevel(Level.ALL);
+ logClass("java.awt.EventDispatchThread");
+ logClass("java.awt.EventQueue");
+ logClass("java.awt.Component");
+ logClass("java.awt.focus.Component");
+ logClass("java.awt.focus.DefaultKeyboardFocusManager");
+ }
+
+ }
+
+ /**
+ * @param args
+ */
+ void doMain(String[] args)
+ {
+ if (!Platform.isJS())
+ {
+ System.setSecurityManager(null);
+ }
+
+ if (args == null || args.length == 0 || (args.length == 1
+ && (args[0] == null || args[0].length() == 0)))
+ {
+ args = new String[] {};
+ }
+
+ // get args needed before proper ArgParser
+ bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+
+ if (!Platform.isJS())
+ {
+ // are we being --quiet ?
+ if (bootstrapArgs.contains(Arg.QUIET))
+ {
+ QUIET = true;
+ OutputStream devNull = new OutputStream()
+ {
+
+ @Override
+ public void write(int b)
+ {
+ // DO NOTHING
+ }
+ };
+ System.setOut(new PrintStream(devNull));
+ // redirecting stderr not working
+ if (bootstrapArgs.getList(Arg.QUIET).size() > 1)
+ {
+ System.setErr(new PrintStream(devNull));
+ }
+ }
+
+ if (bootstrapArgs.contains(Arg.HELP)
+ || bootstrapArgs.contains(Arg.VERSION))
+ {
+ QUIET = true;
+ }
+ }
+
+ // Move any new getdown-launcher-new.jar into place over old
+ // getdown-launcher.jar
+ String appdirString = System.getProperty("getdownappdir");
+ if (appdirString != null && appdirString.length() > 0)
+ {
+ final File appdir = new File(appdirString);
+ new Thread()
+ {
+
+ @Override
+ public void run()
+ {
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+ }.start();
+ }
+
+ if (!quiet() || bootstrapArgs.contains(Arg.VERSION))
+ {
+ System.out.println(
+ "Java version: " + System.getProperty("java.version"));
+ System.out.println("Java home: " + System.getProperty("java.home"));
+ System.out.println("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);
+ }
+ val = System.getProperty("installer_template_version");
+ if (val != null)
+ {
+ System.out.println("Install4j template version: " + val);
+ }
+ val = System.getProperty("launcher_version");
+ if (val != null)
+ {
+ System.out.println("Launcher version: " + val);
+ }
+ }
+
+ if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
+ {
+ System.setProperty("flatlaf.uiScale", "1");
+ }
+
+ // get bootstrap properties (mainly for the logger level)
+ Properties bootstrapProperties = Cache
+ .bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
+
+ // report Jalview version
+ Cache.loadBuildProperties(
+ !quiet() || bootstrapArgs.contains(Arg.VERSION));
+
+ // stop now if only after --version
+ if (bootstrapArgs.contains(Arg.VERSION))
+ {
+ Jalview.exit(null, 0);
+ }
+
+ // old ArgsParser
ArgsParser aparser = new ArgsParser(args);
+
+ // old
boolean headless = false;
+ // new
+ boolean headlessArg = false;
- if (aparser.contains("help") || aparser.contains("h"))
+ try
{
- showUsage();
- System.exit(0);
+ String logLevel = null;
+ if (bootstrapArgs.contains(Arg.TRACE))
+ {
+ logLevel = "TRACE";
+ }
+ else if (bootstrapArgs.contains(Arg.DEBUG))
+ {
+ logLevel = "DEBUG";
+ }
+ if (logLevel == null && !(bootstrapProperties == null))
+ {
+ logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
+ }
+ Console.initLogger(logLevel);
+ } 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);
}
- if (aparser.contains("nodisplay") || aparser.contains("nogui")
- || aparser.contains("headless"))
+
+ // register SIGTERM listener
+ Runtime.getRuntime().addShutdownHook(new Thread()
{
- System.setProperty("java.awt.headless", "true");
- headless = true;
+ public void run()
+ {
+ Console.debug("Running shutdown hook");
+ if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
+ {
+ // Got to here by a SIGTERM signal.
+ // Note we will not actually cancel the quit from here -- it's too
+ // late -- but we can wait for saving files.
+ Console.debug("Checking for saving files");
+ QuitHandler.getQuitResponse(false);
+ }
+ else
+ {
+ Console.debug("Nothing more to do");
+ }
+ Console.debug("Exiting, bye!");
+ // shutdownHook cannot be cancelled, JVM will now halt
+ }
+ });
+
+ String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
+ ? bootstrapArgs.get(Arg.PROPS)
+ : aparser.getValue("props");
+ // if usrPropsFile == null, loadProperties will use the Channel
+ // preferences.file
+ Cache.loadProperties(usrPropsFile);
+ if (usrPropsFile != null)
+ {
+ System.out.println(
+ "CMD [-props " + usrPropsFile + "] executed successfully!");
+ testoutput(bootstrapArgs, Arg.PROPS,
+ "test/jalview/bin/testProps.jvprops", usrPropsFile);
}
- Cache.loadProperties(aparser.getValue("props")); // must do this before
- // anything else!
- final String jabawsUrl = aparser.getValue("jabaws");
- if (jabawsUrl != null)
+ // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
+ if (bootstrapArgs.contains(Arg.ARGFILE))
{
- try
+ argparser = ArgParser.parseArgFiles(
+ bootstrapArgs.getValueList(Arg.ARGFILE),
+ bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+ bootstrapArgs);
+ }
+ else
+ {
+ argparser = new ArgParser(args,
+ bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+ bootstrapArgs);
+ }
+
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ if (bootstrapArgs.contains(Arg.HELP))
{
- Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
- } catch (MalformedURLException e)
+ List> helpArgs = bootstrapArgs
+ .getList(Arg.HELP);
+ System.out.println(Arg.usage(helpArgs.stream().map(e -> e.getKey())
+ .collect(Collectors.toList())));
+ Jalview.exit(null, 0);
+ }
+ if (aparser.contains("help") || aparser.contains("h"))
+ {
+ /*
+ * Now using new usage statement.
+ showUsage();
+ */
+ System.out.println(Arg.usage());
+ Jalview.exit(null, 0);
+ }
+
+ if (bootstrapArgs.contains(Arg.HEADLESS))
+ {
+ System.setProperty("java.awt.headless", "true");
+ // new
+ headlessArg = bootstrapArgs.getBoolean(Arg.HEADLESS);
+ }
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
{
- System.err.println("Invalid jabaws parameter: " + jabawsUrl
- + " ignored");
+ System.setProperty("java.awt.headless", "true");
+ // old
+ headless = true;
+ }
+ // anything else!
+
+ // allow https handshakes to download intermediate certs if necessary
+ System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
+
+ String jabawsUrl = bootstrapArgs.get(Arg.JABAWS);
+ if (jabawsUrl == null)
+ jabawsUrl = aparser.getValue("jabaws");
+ if (jabawsUrl != null)
+ {
+ try
+ {
+ Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println(
+ "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+ testoutput(bootstrapArgs, Arg.JABAWS,
+ "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
+ } catch (MalformedURLException e)
+ {
+ System.err.println(
+ "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+ }
}
}
- String defs = aparser.getValue("setprop");
- while (defs != null)
+ List setprops = new ArrayList<>();
+ if (bootstrapArgs.contains(Arg.SETPROP))
+ {
+ setprops = bootstrapArgs.getValueList(Arg.SETPROP);
+ }
+ else
+ {
+ String sp = aparser.getValue("setprop");
+ while (sp != null)
+ {
+ setprops.add(sp);
+ sp = aparser.getValue("setprop");
+ }
+ }
+ for (String setprop : setprops)
{
- int p = defs.indexOf('=');
+ int p = setprop.indexOf('=');
if (p == -1)
{
- System.err.println("Ignoring invalid setprop argument : " + defs);
+ System.err
+ .println("Ignoring invalid setprop argument : " + setprop);
}
else
{
- System.out.println("Executing setprop argument: " + defs);
+ System.out.println("Executing setprop argument: " + setprop);
+ if (Platform.isJS())
+ {
+ Cache.setProperty(setprop.substring(0, p),
+ setprop.substring(p + 1));
+ }
// DISABLED FOR SECURITY REASONS
// TODO: add a property to allow properties to be overriden by cli args
- // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+ // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
}
- defs = aparser.getValue("setprop");
}
if (System.getProperty("java.awt.headless") != null
&& System.getProperty("java.awt.headless").equals("true"))
@@ -152,194 +595,270 @@ public class Jalview
}
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+
try
{
- Cache.initLogger();
- } catch (java.lang.NoClassDefFoundError error)
+ Console.initLogger();
+ } catch (
+
+ NoClassDefFoundError error)
{
error.printStackTrace();
- System.out
- .println("\nEssential logging libraries not found."
- + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
- System.exit(0);
+ String message = "\nEssential logging libraries not found."
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
+ Jalview.exit(message, 0);
}
+ desktop = null;
- Desktop desktop = null;
+ if (!(headless || headlessArg))
+ setLookAndFeel();
- try
- {
- UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
- } catch (Exception ex)
+ /*
+ * 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))
{
+ SequenceOntologyFactory.setInstance(new SequenceOntology());
}
- if (!headless)
+ if (!(headless || headlessArg))
{
+ Desktop.nosplash = "false".equals(bootstrapArgs.get(Arg.SPLASH))
+ || aparser.contains("nosplash")
+ || Cache.getDefault("SPLASH", "true").equals("false");
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
- desktop.setVisible(true);
- desktop.startServiceDiscovery();
- if (!aparser.contains("nousagestats"))
+
+ try
{
- startUsageStats(desktop);
- }
- if (!aparser.contains("noquestionnaire"))
+ JalviewTaskbar.setTaskbar(this);
+ } catch (Exception e)
{
- String url = aparser.getValue("questionnaire");
- if (url != null)
- {
- // Start the desktop questionnaire prompter with the specified
- // questionnaire
- Cache.log.debug("Starting questionnaire url at " + url);
- desktop.checkForQuestionnaire(url);
- }
- else
- {
- if (Cache.getProperty("NOQUESTIONNAIRES") == null)
- {
- // Start the desktop questionnaire prompter with the specified
- // questionnaire
- // String defurl =
- // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
- // //
- String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
- Cache.log.debug("Starting questionnaire with default url: "
- + defurl);
- desktop.checkForQuestionnaire(defurl);
-
- }
- }
+ Console.info("Cannot set Taskbar");
+ Console.error(e.getMessage());
+ // e.printStackTrace();
+ } catch (Throwable t)
+ {
+ Console.info("Cannot set Taskbar");
+ Console.error(t.getMessage());
+ // t.printStackTrace();
}
- desktop.checkForNews();
- }
- String file = null, protocol = null, format = null, data = null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
- Vector getFeatures = null; // vector of das source nicknames to fetch
- // features from
- // loading is done.
- String groovyscript = null; // script to execute after all loading is
- // completed one way or another
- // extract groovy argument and execute if necessary
- groovyscript = aparser.getValue("groovy", true);
- file = aparser.getValue("open", true);
+ // set Proxy settings before all the internet calls
+ Cache.setProxyPropertiesFromPreferences();
- if (file == null && desktop == null)
- {
- System.out.println("No files to open!");
- System.exit(1);
- }
- String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser
- .getValue("vsess");
- if (vamsasImport != null || vamsasSession != null)
- {
- if (desktop == null || headless)
- {
- System.out
- .println("Headless vamsas sessions not yet supported. Sorry.");
- System.exit(1);
- }
- // if we have a file, start a new session and import it.
- boolean inSession = false;
- if (vamsasImport != null)
+ desktop.setVisible(true);
+
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- try
+
+ /**
+ * 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())
{
- String viprotocol = jalview.io.AppletFormatAdapter
- .checkProtocol(vamsasImport);
- if (viprotocol == jalview.io.FormatAdapter.FILE)
- {
- inSession = desktop.vamsasImport(new File(vamsasImport));
- }
- else if (viprotocol == jalview.io.FormatAdapter.URL)
+ 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"))
{
- inSession = desktop.vamsasImport(new URL(vamsasImport));
+ 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]);
}
+ }
- } catch (Exception e)
+ boolean webservicediscovery = bootstrapArgs
+ .getBoolean(Arg.WEBSERVICEDISCOVERY);
+ if (aparser.contains("nowebservicediscovery"))
+ webservicediscovery = false;
+ if (webservicediscovery)
{
- System.err.println("Exeption when importing " + vamsasImport
- + " as a vamsas document.");
- e.printStackTrace();
+ desktop.startServiceDiscovery();
}
- if (!inSession)
+ else
{
- System.err.println("Failed to import " + vamsasImport
- + " as a vamsas document.");
+ testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
}
- else
+
+ boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
+ if (aparser.contains("nousagestats"))
+ usagestats = false;
+ if (usagestats)
{
- System.out.println("Imported Successfully into new session "
- + desktop.getVamsasApplication().getCurrentSession());
+ startUsageStats(desktop);
+ testoutput(argparser, Arg.USAGESTATS);
}
- }
- if (vamsasSession != null)
- {
- if (vamsasImport != null)
+ else
{
- // close the newly imported session and import the Jalview specific
- // remnants into the new session later on.
- desktop.vamsasStop_actionPerformed(null);
+ System.out.println("CMD [-nousagestats] executed successfully!");
+ testoutput(argparser, Arg.USAGESTATS);
}
- // now join the new session
- try
+
+ boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
+ if (aparser.contains("noquestionnaire"))
+ questionnaire = false;
+ if (questionnaire)
{
- if (desktop.joinVamsasSession(vamsasSession))
+ String url = aparser.getValue("questionnaire");
+ if (url != null)
{
- System.out.println("Successfully joined vamsas session "
- + vamsasSession);
+ // Start the desktop questionnaire prompter with the specified
+ // questionnaire
+ Console.debug("Starting questionnaire url at " + url);
+ desktop.checkForQuestionnaire(url);
+ System.out.println("CMD questionnaire[-" + url
+ + "] executed successfully!");
}
else
{
- System.err.println("WARNING: Failed to join vamsas session "
- + vamsasSession);
+ if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ {
+ // Start the desktop questionnaire prompter with the specified
+ // questionnaire
+ // String defurl =
+ // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
+ // //
+ String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
+ Console.debug(
+ "Starting questionnaire with default url: " + defurl);
+ desktop.checkForQuestionnaire(defurl);
+ }
}
- } catch (Exception e)
+ }
+ else
{
- System.err.println("ERROR: Failed to join vamsas session "
- + vamsasSession);
- e.printStackTrace();
+ System.out
+ .println("CMD [-noquestionnaire] executed successfully!");
+ testoutput(argparser, Arg.QUESTIONNAIRE);
}
- if (vamsasImport != null)
+
+ if ((!aparser.contains("nonews")
+ && Cache.getProperty("NONEWS") == null
+ && !"false".equals(bootstrapArgs.get(Arg.NEWS)))
+ || "true".equals(bootstrapArgs.get(Arg.NEWS)))
{
- // the Jalview specific remnants can now be imported into the new
- // session at the user's leisure.
- Cache.log
- .info("Skipping Push for import of data into existing vamsas session."); // TODO:
- // enable
- // this
- // when
- // debugged
- // desktop.getVamsasApplication().push_update();
+ desktop.checkForNews();
}
+
+ if (!aparser.contains("nohtmltemplates")
+ && Cache.getProperty("NOHTMLTEMPLATES") == null)
+ {
+ BioJsHTMLOutput.updateBioJS();
+ }
+ }
+ }
+ // Run Commands from cli
+ cmds = new Commands(argparser, headlessArg);
+ boolean commandsSuccess = cmds.argsWereParsed();
+ if (commandsSuccess)
+ {
+ if (headlessArg)
+ {
+ Jalview.exit("Successfully completed commands in headless mode", 0);
}
+ Console.info("Successfully completed commands");
+ }
+ else
+ {
+ if (headlessArg)
+ {
+ Jalview.exit("Error when running Commands in headless mode", 1);
+ }
+ Console.warn("Error when running commands");
+ }
+
+ // 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() + ".");
+ }
+
+ String file = null, data = null;
+
+ FileFormatI format = null;
+
+ DataSourceType protocol = null;
+
+ FileLoader fileLoader = new FileLoader(!headless);
+
+ String groovyscript = null; // script to execute after all loading is
+ // completed one way or another
+ // extract groovy argument and execute if necessary
+ groovyscript = aparser.getValue("groovy", true);
+ file = aparser.getValue("open", true);
+
+ if (file == null && desktop == null && !commandsSuccess)
+ {
+ Jalview.exit("No files to open!", 1);
}
+
long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
{
if (!headless)
{
- desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
+ desktop.setProgressBar(
+ MessageManager
+ .getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
- System.out.println("Opening file: " + file);
+ System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!file.startsWith("http://"))
+ if (!Platform.isJS())
+ /**
+ * ignore in JavaScript -- can't just file existence - could load it?
+ *
+ * @j2sIgnore
+ */
{
- if (!(new java.io.File(file)).exists())
+ if (!HttpUtils.startsWithHttpOrHttps(file))
{
- System.out.println("Can't find " + file);
- if (headless)
+ if (!(new File(file)).exists())
{
- System.exit(1);
+ if (headless)
+ {
+ Jalview.exit(
+ "Can't find file '" + file + "' in headless mode", 1);
+ }
+ Console.warn("Can't find file'" + file + "'");
}
}
}
- protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
+ protocol = AppletFormatAdapter.checkProtocol(file);
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e1)
+ {
+ // TODO ?
+ }
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
@@ -349,24 +868,20 @@ public class Jalview
}
else
{
-
+ setCurrentAlignFrame(af);
data = aparser.getValue("colour", true);
if (data != null)
{
data.replaceAll("%20", " ");
- jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
- .getColour(af.getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
- if (cs == null)
+ if (cs != null)
{
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- "white");
- ucs.parseAppletParameter(data);
- cs = ucs;
+ System.out.println(
+ "CMD [-colour " + data + "] executed successfully!");
}
-
- System.out.println("colour is " + data);
af.changeColour(cs);
}
@@ -375,46 +890,66 @@ public class Jalview
if (data != null)
{
af.parseFeaturesFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD groups[-" + data + "] executed successfully!");
}
data = aparser.getValue("features", true);
if (data != null)
{
af.parseFeaturesFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD [-features " + data + "] executed successfully!");
}
data = aparser.getValue("annotations", true);
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD [-annotations " + data + "] executed successfully!");
}
// set or clear the sortbytree flag.
if (aparser.contains("sortbytree"))
{
af.getViewport().setSortByTree(true);
+ if (af.getViewport().getSortByTree())
+ {
+ System.out.println("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!");
+ }
}
if (aparser.contains("nosortbytree"))
{
af.getViewport().setSortByTree(false);
+ if (!af.getViewport().getSortByTree())
+ {
+ System.out
+ .println("CMD [-nosortbytree] executed successfully!");
+ }
}
data = aparser.getValue("tree", true);
if (data != null)
{
- jalview.io.NewickFile fin = null;
try
{
- fin = new jalview.io.NewickFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
- if (fin != null)
- {
- af.getViewport().setCurrentTree(
- af.ShowNewickTree(fin, data).getTree());
- System.out.println("Added tree " + data);
- }
+ System.out.println(
+ "CMD [-tree " + data + "] executed successfully!");
+ NewickFile nf = new NewickFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ af.getViewport()
+ .setCurrentTree(af.showNewickTree(nf, data).getTree());
} catch (IOException ex)
{
System.err.println("Couldn't add tree " + data);
@@ -424,88 +959,113 @@ public class Jalview
// TODO - load PDB structure(s) to alignment JAL-629
// (associate with identical sequence in alignment, or a specified
// sequence)
-
- getFeatures = checkDasArguments(aparser);
- if (af != null && getFeatures != null)
- {
- FeatureFetcher ff = startFeatureFetching(getFeatures);
- if (ff != null)
- {
- while (!ff.allFinished() || af.operationInProgress())
- {
- // wait around until fetching is finished.
- try
- {
- Thread.sleep(100);
- } catch (Exception e)
- {
-
- }
- }
- }
- getFeatures = null; // have retrieved features - forget them now.
- }
if (groovyscript != null)
{
// Execute the groovy script after we've done all the rendering stuff
// and before any images or figures are generated.
- if (jalview.bin.Cache.groovyJarsPresent())
- {
- System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[]
- { desktop, af });
- }
- else
- {
- System.err
- .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
- + groovyscript);
- }
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, af);
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
groovyscript = null;
}
String imageName = "unnamed.png";
while (aparser.getSize() > 1)
{
- format = aparser.nextValue();
+ String outputFormat = aparser.nextValue();
file = aparser.nextValue();
- if (format.equalsIgnoreCase("png"))
+ if (outputFormat.equalsIgnoreCase("png"))
{
- af.createPNG(new java.io.File(file));
- imageName = (new java.io.File(file)).getName();
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
System.out.println("Creating PNG image: " + file);
continue;
}
- else if (format.equalsIgnoreCase("svg"))
+ else if (outputFormat.equalsIgnoreCase("svg"))
{
- File imageFile = new java.io.File(file);
+ File imageFile = new File(file);
imageName = imageFile.getName();
af.createSVG(imageFile);
System.out.println("Creating SVG image: " + file);
continue;
}
- else if (format.equalsIgnoreCase("imgMap"))
+ else if (outputFormat.equalsIgnoreCase("html"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(file);
+
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ {
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
+ System.out
+ .println("Creating BioJS MSA Viwer HTML file: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("imgMap"))
{
- af.createImageMap(new java.io.File(file), imageName);
+ af.createImageMap(new File(file), imageName);
System.out.println("Creating image map: " + file);
continue;
}
- else if (format.equalsIgnoreCase("eps"))
+ else if (outputFormat.equalsIgnoreCase("eps"))
{
- System.out.println("Creating EPS file: " + file);
- af.createEPS(new java.io.File(file));
+ File outputFile = new File(file);
+ System.out.println(
+ "Creating EPS file: " + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
continue;
}
-
- if (af.saveAlignment(file, format))
+ FileFormatI outFormat = null;
+ try
+ {
+ outFormat = FileFormats.getInstance().forName(outputFormat);
+ } catch (Exception formatP)
{
- System.out.println("Written alignment in " + format
- + " format to " + file);
+ System.out.println("Couldn't parse " + outFormat
+ + " as a valid Jalview format string.");
}
- else
+ if (outFormat != null)
{
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ if (!outFormat.isWritable())
+ {
+ System.out.println(
+ "This version of Jalview does not support alignment export as "
+ + outputFormat);
+ }
+ else
+ {
+ af.saveAlignment(file, outFormat);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println("Written alignment in "
+ + outFormat.getName() + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + outFormat.getName() + " format!!");
+ }
+ }
}
}
@@ -516,72 +1076,76 @@ public class Jalview
}
}
}
+
AlignFrame startUpAlframe = null;
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
- if (!headless && file == null && vamsasImport == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ if (!Platform.isJS() && !headless && file == null
+ && Cache.getDefault("SHOW_STARTUP_FILE", true)
+ && !cmds.commandArgsProvided())
+ // don't open the startup file if command line args have been processed
+ // (&& !Commands.commandArgsProvided())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- file = jalview.bin.Cache.getDefault(
- "STARTUP_FILE",
- jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
- + "/examples/exampleFile_2_7.jar");
- if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ 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(
+ "http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
+ file.replace("http:", "https:");
// hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
+ file.replace("_2_3", "_2_7");
+ file.replace("2_7.jar", "2_7.jvp");
// and remove the stale setting
- jalview.bin.Cache.removeProperty("STARTUP_FILE");
+ Cache.removeProperty("STARTUP_FILE");
}
- protocol = "File";
-
- if (file.indexOf("http:") > -1)
- {
- protocol = "URL";
- }
+ protocol = AppletFormatAdapter.checkProtocol(file);
if (file.endsWith(".jar"))
{
- format = "Jalview";
+ format = FileFormat.Jalview;
}
else
{
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e)
+ {
+ // TODO what?
+ }
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
- getFeatures = checkDasArguments(aparser);
+ // don't ask to save when quitting if only the startup file has been
+ // opened
+ Console.debug("Resetting up-to-date flag for startup file");
+ startUpAlframe.getViewport().setSavedUpToDate(true);
// extract groovy arguments before anything else.
}
- // If the user has specified features to be retrieved,
- // or a groovy script to be executed, do them if they
- // haven't been done already
- // fetch features for the default alignment
- if (getFeatures != null)
- {
- if (startUpAlframe != null)
- {
- startFeatureFetching(getFeatures);
- }
- }
+
// Once all other stuff is done, execute any groovy scripts (in order)
if (groovyscript != null)
{
- if (jalview.bin.Cache.groovyJarsPresent())
+ if (Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[]
- { desktop, startUpAlframe });
+ executeGroovyScript(groovyscript, startUpAlframe);
}
else
{
- System.err
- .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ System.err.println(
+ "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ groovyscript);
}
}
@@ -596,10 +1160,320 @@ public class Jalview
}
}
+ 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 "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())
+ {
+ setLinuxLookAndFeel();
+ }
+ 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 = false;
+ if (SystemInfo.isMacOS)
+ {
+ try
+ {
+ UIManager.setLookAndFeel(
+ "com.formdev.flatlaf.themes.FlatMacLightLaf");
+ set = true;
+ Console.debug("Using FlatMacLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ 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)
+ {
+ Console.debug("Setting transparent title bar");
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.fullWindowContent", true);
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.transparentTitleBar", true);
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.fullscreenable", true);
+ }
+ SwingUtilities.invokeLater(() -> {
+ FlatMacLightLaf.setup();
+ });
+ Console.debug("Using FlatMacLightLaf");
+ set = true;
+ }
+ if (!set)
+ {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+ set = true;
+ Console.debug("Using FlatLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ // Windows specific properties here
+ SwingUtilities.invokeLater(() -> {
+ FlatLightLaf.setup();
+ });
+ Console.debug("Using FlatLightLaf");
+ set = true;
+ }
+ else if (SystemInfo.isLinux)
+ {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+ set = true;
+ Console.debug("Using FlatLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ // enable custom window decorations
+ JFrame.setDefaultLookAndFeelDecorated(true);
+ JDialog.setDefaultLookAndFeelDecorated(true);
+ SwingUtilities.invokeLater(() -> {
+ FlatLightLaf.setup();
+ });
+ Console.debug("Using FlatLightLaf");
+ set = true;
+ }
+
+ if (!set)
+ {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+ set = true;
+ Console.debug("Using FlatLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ }
+
+ if (set)
+ {
+ UIManager.put("TabbedPane.tabType", "card");
+ UIManager.put("TabbedPane.showTabSeparators", true);
+ UIManager.put("TabbedPane.showContentSeparator", 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);
+ }
+
+ Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
+ return set;
+ }
+
+ 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 boolean setLinuxLookAndFeel()
+ {
+ boolean set = false;
+ set = setFlatLookAndFeel();
+ if (!set)
+ set = setMetalLookAndFeel();
+ // avoid GtkLookAndFeel -- not good results especially on HiDPI
+ if (!set)
+ set = setNimbusLookAndFeel();
+ return set;
+ }
+
private static void showUsage()
{
- System.out
- .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ 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"
@@ -613,26 +1487,30 @@ public class Jalview
+ "-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 google 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)"
+ // "-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"
- + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
- + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
- + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
- // +
- // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
- // + "-vses vamsas-session\tJoin session with given URN\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)
@@ -640,27 +1518,27 @@ public class Jalview
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
- desktop.desktop,
- "USAGESTATS",
- "Jalview Usage Statistics",
+ PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
+ "USAGESTATS", "Jalview Usage Statistics",
"Do you want to help make Jalview better by enabling "
+ "the collection of usage statistics with Google Analytics ?"
+ "\n\n(you can enable or disable usage tracking in the preferences)",
new Runnable()
{
+ @Override
public void run()
{
- Cache.log
- .debug("Initialising googletracker for usage stats.");
+ 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);
@@ -675,14 +1553,8 @@ public class Jalview
* the Jalview Desktop object passed in to the groovy binding as the
* 'Jalview' object.
*/
- private static void executeGroovyScript(String groovyscript,
- Object[] jalviewContext)
+ protected void executeGroovyScript(String groovyscript, AlignFrame af)
{
- if (jalviewContext == null)
- {
- System.err
- .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
- }
/**
* for scripts contained in files
*/
@@ -697,10 +1569,10 @@ public class Jalview
try
{
tfile = File.createTempFile("jalview", "groovy");
- PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(tfile)));
+ PrintWriter outfile = new PrintWriter(
+ new OutputStreamWriter(new FileOutputStream(tfile)));
BufferedReader br = new BufferedReader(
- new java.io.InputStreamReader(System.in));
+ new InputStreamReader(System.in));
String line = null;
while ((line = br.readLine()) != null)
{
@@ -713,8 +1585,8 @@ public class Jalview
} catch (Exception ex)
{
System.err.println("Failed to read from STDIN into tempfile "
- + ((tfile == null) ? "(tempfile wasn't created)" : tfile
- .toString()));
+ + ((tfile == null) ? "(tempfile wasn't created)"
+ : tfile.toString()));
ex.printStackTrace();
return;
}
@@ -723,8 +1595,8 @@ public class Jalview
sfile = tfile.toURI().toURL();
} catch (Exception x)
{
- System.err
- .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ System.err.println(
+ "Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ tfile.toURI());
x.printStackTrace();
return;
@@ -764,76 +1636,23 @@ public class Jalview
}
}
}
- boolean success = false;
try
{
- /*
- * The following code performs the GroovyScriptEngine invocation using
- * reflection, and is equivalent to this fragment from the embedding
- * groovy documentation on the groovy site: import
- * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
- *
- * String[] roots = new String[] { "/my/groovy/script/path" };
- * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding
- * = new Binding(); binding.setVariable("input", "world");
- * gse.run("hello.groovy", binding);
- */
- Class[] bspec;
- Object[] binding;
- int blen = ((jalviewContext[0] == null) ? 0 : 1)
- + ((jalviewContext[1] == null) ? 0 : 1);
- String cnames[] = new String[]
- { "Jalview", "currentAlFrame" };
- bspec = new Class[blen * 2];
- binding = new Object[blen * 2];
- blen = 0;
- ClassLoader cl = null;
- Map vbinding = new Hashtable();
- for (int jc = 0; jc < jalviewContext.length; jc++)
- {
- if (jalviewContext[jc] != null)
- {
- if (cl == null)
- {
- cl = jalviewContext[jc].getClass().getClassLoader();
- }
- bspec[blen * 2] = String.class;
- bspec[blen * 2 + 1] = Object.class;
- binding[blen * 2] = cnames[jc];
- binding[blen * 2 + 1] = jalviewContext[jc];
- vbinding.put(cnames[jc], jalviewContext[jc]);
- blen++;
- }
+ Map vbinding = new HashMap<>();
+ vbinding.put("Jalview", this);
+ if (af != null)
+ {
+ vbinding.put("currentAlFrame", af);
}
- Class gbindingc = cl.loadClass("groovy.lang.Binding");
- Constructor gbcons;
- Object gbinding;
- try
+ Binding gbinding = new Binding(vbinding);
+ GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
+ gse.run(sfile.toString(), gbinding);
+ if ("STDIN".equals(groovyscript))
{
- gbcons = gbindingc.getConstructor(Map.class);
- gbinding = gbcons.newInstance(vbinding);
- } catch (NoSuchMethodException x)
- {
- // old style binding config - using series of string/object values to
- // setVariable.
- gbcons = gbindingc.getConstructor(null);
- gbinding = gbcons.newInstance(null);
- java.lang.reflect.Method setvar = gbindingc.getMethod(
- "setVariable", bspec);
- setvar.invoke(gbinding, binding);
+ // delete temp file that we made -
+ // only if it was successfully executed
+ tfile.delete();
}
- ;
- Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
- Constructor gseccons = gsec.getConstructor(new Class[]
- { URL[].class }); // String[].class });
- Object gse = gseccons.newInstance(new Object[]
- { new URL[]
- { sfile } }); // .toString() } });
- java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
- { String.class, gbindingc });
- run.invoke(gse, new Object[]
- { sfile.toString(), gbinding });
- success = true;
} catch (Exception e)
{
System.err.println("Exception Whilst trying to execute file " + sfile
@@ -841,266 +1660,191 @@ public class Jalview
e.printStackTrace(System.err);
}
- if (success && groovyscript.equals("STDIN"))
- {
- // delete temp file that we made - but only if it was successfully
- // executed
- tfile.delete();
- }
}
- /**
- * Check commandline for any das server definitions or any fetchfrom switches
- *
- * @return vector of DAS source nicknames to retrieve from
- */
- private static Vector checkDasArguments(ArgsParser aparser)
+ public static boolean isHeadlessMode()
{
- Vector source = null;
- String data;
- String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
- while ((data = aparser.getValue("dasserver", true)) != null)
- {
- String nickname = null;
- String url = null;
- boolean seq = false, feat = true;
- int pos = data.indexOf('=');
- // determine capabilities
- if (pos > 0)
- {
- nickname = data.substring(0, pos);
- }
- url = data.substring(pos + 1);
- if (url != null
- && (url.startsWith("http:") || url
- .startsWith("sequence:http:")))
- {
- if (nickname == null)
- {
- nickname = url;
- }
- if (locsources == null)
- {
- locsources = "";
- }
- else
- {
- locsources += "\t";
- }
- locsources = locsources + nickname + "|" + url;
- System.err
- .println("NOTE! dasserver parameter not yet really supported (got args of "
- + nickname + "|" + url);
- if (source == null)
- {
- source = new Vector();
- }
- source.addElement(nickname);
- }
- } // loop until no more server entries are found.
- if (locsources != null && locsources.indexOf('|') > -1)
+ String isheadless = System.getProperty("java.awt.headless");
+ if (isheadless != null && isheadless.equalsIgnoreCase("true"))
{
- Cache.log.debug("Setting local source list in properties file to:\n"
- + locsources);
- Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
- }
- while ((data = aparser.getValue("fetchfrom", true)) != null)
- {
- System.out.println("adding source '" + data + "'");
- if (source == null)
- {
- source = new Vector();
- }
- source.addElement(data);
+ return true;
}
- return source;
+ return false;
+ }
+
+ public AlignFrame[] getAlignFrames()
+ {
+ return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
+ : Desktop.getAlignFrames();
+
}
/**
- * start a feature fetcher for every alignment frame
- *
- * @param dasSources
+ * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
*/
- private static FeatureFetcher startFeatureFetching(final Vector dasSources)
+ public void quit()
{
- FeatureFetcher ff = new FeatureFetcher();
- AlignFrame afs[] = Desktop.getAlignframes();
- if (afs == null || afs.length == 0)
- {
- return null;
- }
- for (int i = 0; i < afs.length; i++)
- {
- ff.addFetcher(afs[i], dasSources);
- }
- return ff;
+ // System.exit will run the shutdownHook first
+ Jalview.exit("Quitting now. Bye!", 0);
}
-}
-
-/**
- * Notes: this argParser does not distinguish between parameter switches,
- * parameter values and argument text. If an argument happens to be identical to
- * a parameter, it will be taken as such (even though it didn't have a '-'
- * prefixing it).
- *
- * @author Andrew Waterhouse and JBP documented.
- *
- */
-class rnabuttonlistener implements ActionListener
-{
- public void actionPerformed(ActionEvent arg0)
+ public static AlignFrame getCurrentAlignFrame()
{
- System.out.println("Good idea ! ");
-
+ return Jalview.currentAlignFrame;
}
-}
-class pbuttonlistener implements ActionListener
-{
- public void actionPerformed(ActionEvent arg0)
+ public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
-
+ Jalview.currentAlignFrame = currentAlignFrame;
}
-}
-class ArgsParser
-{
- Vector vargs = null;
+ protected Commands getCommands()
+ {
+ return cmds;
+ }
- public ArgsParser(String[] args)
+ public static void exit(String message, int exitcode)
{
- vargs = new Vector();
- for (int i = 0; i < args.length; i++)
+ if (Console.log == null)
{
- String arg = args[i].trim();
- if (arg.charAt(0) == '-')
+ // Don't start the logger just to exit!
+ if (message != null)
{
- arg = arg.substring(1);
+ if (exitcode == 0)
+ {
+ System.out.println(message);
+ }
+ else
+ {
+ System.err.println(message);
+ }
}
- vargs.addElement(arg);
}
- }
-
- /**
- * check for and remove first occurence of arg+parameter in arglist.
- *
- * @param arg
- * @return return the argument following the given arg if arg was in list.
- */
- public String getValue(String arg)
- {
- return getValue(arg, false);
- }
-
- public String getValue(String arg, boolean utf8decode)
- {
- int index = vargs.indexOf(arg);
- String dc = null, ret = null;
- if (index != -1)
+ else
{
- ret = vargs.elementAt(index + 1).toString();
- vargs.removeElementAt(index);
- vargs.removeElementAt(index);
- if (utf8decode && ret != null)
+ Console.debug("Using Jalview.exit");
+ if (message != null)
{
- try
+ if (exitcode == 0)
{
- dc = URLDecoder.decode(ret, "UTF-8");
- ret = dc;
- } catch (Exception e)
+ Console.info(message);
+ }
+ else
{
- // TODO: log failure to decode
+ Console.error(message);
}
}
}
- return ret;
+ if (exitcode > -1)
+ {
+ System.exit(exitcode);
+ }
}
- /**
- * check for and remove first occurence of arg in arglist.
- *
- * @param arg
- * @return true if arg was present in argslist.
+ /*
+ * testoutput for string values
*/
- public boolean contains(String arg)
+ protected static void testoutput(ArgParser ap, Arg a, String s1,
+ String s2)
{
- if (vargs.contains(arg))
+ BootstrapArgs bsa = ap.getBootstrapArgs();
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
{
- vargs.removeElement(arg);
- return true;
+ Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+ + s2 + "' for arg " + a.argString());
+ return;
}
- else
+ boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+ : ap.isSet(a);
+ if (!isset)
{
- return false;
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
}
+ testoutput(true, a, s1, s2);
}
- public String nextValue()
+ protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
+ String s2)
{
- return vargs.remove(0).toString();
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+ {
+ Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+ + s2 + "' for arg " + a.argString());
+ return;
+ }
+ if (!a.hasOption(Opt.BOOTSTRAP))
+ {
+ Console.error("Non-bootstrap Arg '" + a.getName()
+ + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
+ }
+ if (!bsa.contains(a))
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(true, a, s1, s2);
}
- public int getSize()
+ private static void testoutput(boolean yes, Arg a, String s1, String s2)
{
- return vargs.size();
+ if (yes && ((s1 == null && s2 == null)
+ || (s1 != null && s1.equals(s2))))
+ {
+ System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+ + "' was set");
+ }
}
-}
-
-/**
- * keep track of feature fetching tasks.
- *
- * @author JimP
- *
- */
-class FeatureFetcher
-{
/*
- * TODO: generalise to track all jalview events to orchestrate batch
- * processing events.
+ * testoutput for boolean values
*/
-
- private int queued = 0;
-
- private int running = 0;
-
- public FeatureFetcher()
+ protected static void testoutput(ArgParser ap, Arg a)
{
-
+ if (ap == null)
+ return;
+ BootstrapArgs bsa = ap.getBootstrapArgs();
+ if (bsa == null)
+ return;
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
+ : ap.getBoolean(a);
+ boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+ : ap.isSet(a);
+ if (!isset)
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(val, a);
}
- public void addFetcher(final AlignFrame af, final Vector dasSources)
+ protected static void testoutput(BootstrapArgs bsa, Arg a)
{
- final long id = System.currentTimeMillis();
- queued++;
- final FeatureFetcher us = this;
- new Thread(new Runnable()
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ if (!a.hasOption(Opt.BOOTSTRAP))
{
+ Console.warn("Non-bootstrap Arg '" + a.getName()
+ + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
- public void run()
- {
- synchronized (us)
- {
- queued--;
- running++;
- }
-
- af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
- af.featureSettings_actionPerformed(null);
- af.featureSettings.fetchDasFeatures(dasSources, true);
- af.setProgressBar(null, id);
- synchronized (us)
- {
- running--;
- }
- }
- }).start();
+ }
+ if (!bsa.contains(a))
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(bsa.getBoolean(a), a);
}
- public synchronized boolean allFinished()
+ private static void testoutput(boolean yes, Arg a)
{
- return queued == 0 && running == 0;
+ System.out.println("[TESTOUTPUT] arg "
+ + (yes ? a.argString() : a.negateArgString()) + " was set");
}
-
-};
+}