import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
-import java.security.AllPermission;
-import java.security.CodeSource;
-import java.security.PermissionCollection;
-import java.security.Permissions;
-import java.security.Policy;
import java.util.HashMap;
import java.util.Map;
import java.util.Vector;
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
+import com.sun.xml.ws.policy.Policy;
+import com.threerings.getdown.util.LaunchUtil;
+
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
static
{
// grab all the rights we can the JVM
+ Policy.createEmptyPolicy();
+ /*
Policy.setPolicy(new Policy()
{
@Override
perms.add(new AllPermission());
return (perms);
}
-
+
@Override
public void refresh()
{
}
});
+ */
}
/**
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+ 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();
+
+ }
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
{
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
+
+ try
+ {
+ JalviewTaskbar.setTaskbar(this);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } catch (Throwable t)
+ {
+ t.printStackTrace();
+ }
+
desktop.setVisible(true);
desktop.startServiceDiscovery();
if (!aparser.contains("nousagestats"))
data.replaceAll("%20", " ");
ColourSchemeI cs = ColourSchemeProperty
- .getColourScheme(af.getViewport().getAlignment(), data);
+ .getColourScheme(af.getViewport(),
+ af.getViewport().getAlignment(), data);
if (cs != null)
{
// (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
}
try
{
- Map<String, Object> vbinding = new HashMap<>();
+ Map<String, java.lang.Object> vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{