+ // for testing those nasty messages you cannot ever find.
+ // static
+ // {
+ // System.setOut(new PrintStream(new ByteArrayOutputStream())
+ // {
+ // @Override
+ // public void println(Object o)
+ // {
+ // if (o != null)
+ // {
+ // System.err.println(o);
+ // }
+ // }
+ //
+ // });
+ // }
+ public static Jalview getInstance()
+ {
+ return (Jalview) ApplicationSingletonProvider
+ .getInstance(Jalview.class);
+ }
+
+ private Jalview()
+ {
+ }
+
+ private boolean headless;
+
+ private Desktop desktop;
+
+ public AlignFrame currentAlignFrame;
+
+ public String appletResourcePath;
+
+ public String j2sAppletID;
+
+ private boolean noCalculation, noMenuBar, noStatus;
+
+ private boolean noAnnotation;
+
+ public boolean getStartCalculations()
+ {
+ return !noCalculation;
+ }
+
+ public boolean getAllowMenuBar()
+ {
+ return !noMenuBar;
+ }
+
+ public boolean getShowStatus()
+ {
+ return !noStatus;
+ }
+
+ public boolean getShowAnnotation()
+ {
+ return !noAnnotation;
+ }
+
+ static
+ {
+ if (Platform.isJS()) {
+ Platform.getURLCommandArguments();
+ } else /** @j2sIgnore */
+ {
+ // grab all the rights we can for the JVM
+ Policy.setPolicy(new Policy()
+ {
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ @Override
+ 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<String> 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;
+ }
+
+ }
+
+ private final static boolean doPlatformLogging = false;
+