X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=d6da4052ee1152ec984a6153be3ef7d99bb8dd30;hb=4ad3af6fae856880fea0a982e6f0dc65f3109567;hp=ece610a85113dadd2974f9580d03f74e7e3260a0;hpb=1bd2350fdb5cce781548ce2e2188ab14bd412b6d;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ece610a..d6da405 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -52,6 +52,11 @@ import java.net.MalformedURLException;
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;
@@ -59,7 +64,7 @@ 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;
@@ -93,8 +98,6 @@ public class Jalview
static
{
// grab all the rights we can the JVM
- Policy.createEmptyPolicy();
- /*
Policy.setPolicy(new Policy()
{
@Override
@@ -110,7 +113,6 @@ public class Jalview
{
}
});
- */
}
/**
@@ -181,7 +183,7 @@ public class Jalview
* main class for Jalview application
*
* @param args
- * open filename
+ * open filename
*/
public static void main(String[] args)
{
@@ -304,8 +306,9 @@ public class Jalview
"Failed to set QuaQua look and feel: " + e.toString());
}
}
- if (lookAndFeel == null || !(lookAndFeel.getClass()
- .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
+ if (lookAndFeel == null
+ || !(lookAndFeel.getClass().isAssignableFrom(
+ UIManager.getLookAndFeel().getClass()))
|| !UIManager.getLookAndFeel().getClass().toString()
.toLowerCase().contains("quaqua"))
{
@@ -323,10 +326,9 @@ public class Jalview
}
/*
- * configure 'full' SO model if preferences say to,
- * else use the default (SO Lite)
+ * configure 'full' SO model
*/
- if (Cache.getDefault("USE_FULL_SO", false))
+ if (Cache.getDefault("USE_FULL_SO", true))
{
SequenceOntologyFactory.setInstance(new SequenceOntology());
}
@@ -341,10 +343,12 @@ public class Jalview
JalviewTaskbar.setTaskbar(this);
} catch (Exception e)
{
- e.printStackTrace();
+ System.out.println("Cannot set Taskbar");
+ // e.printStackTrace();
} catch (Throwable t)
{
- t.printStackTrace();
+ System.out.println("Cannot set Taskbar");
+ // t.printStackTrace();
}
desktop.setVisible(true);
@@ -399,6 +403,25 @@ public class Jalview
BioJsHTMLOutput.updateBioJS();
}
+ // 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();
+ }
+
String file = null, data = null;
FileFormatI format = null;
DataSourceType protocol = null;
@@ -415,91 +438,6 @@ public class Jalview
System.out.println("No files to open!");
System.exit(1);
}
- String vamsasImport = aparser.getValue("vdoc");
- String 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)
- {
- try
- {
- DataSourceType viprotocol = AppletFormatAdapter
- .checkProtocol(vamsasImport);
- if (viprotocol == DataSourceType.FILE)
- {
- inSession = desktop.vamsasImport(new File(vamsasImport));
- }
- else if (viprotocol == DataSourceType.URL)
- {
- inSession = desktop.vamsasImport(new URL(vamsasImport));
- }
-
- } catch (Exception e)
- {
- System.err.println("Exeption when importing " + vamsasImport
- + " as a vamsas document.");
- e.printStackTrace();
- }
- if (!inSession)
- {
- System.err.println("Failed to import " + vamsasImport
- + " as a vamsas document.");
- }
- else
- {
- System.out.println("Imported Successfully into new session "
- + desktop.getVamsasApplication().getCurrentSession());
- }
- }
- if (vamsasSession != null)
- {
- if (vamsasImport != null)
- {
- // close the newly imported session and import the Jalview specific
- // remnants into the new session later on.
- desktop.vamsasStop_actionPerformed(null);
- }
- // now join the new session
- try
- {
- if (desktop.joinVamsasSession(vamsasSession))
- {
- System.out.println(
- "Successfully joined vamsas session " + vamsasSession);
- }
- else
- {
- System.err.println("WARNING: Failed to join vamsas session "
- + vamsasSession);
- }
- } catch (Exception e)
- {
- System.err.println(
- "ERROR: Failed to join vamsas session " + vamsasSession);
- e.printStackTrace();
- }
- if (vamsasImport != null)
- {
- // 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();
- }
- }
- }
long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
@@ -549,9 +487,8 @@ public class Jalview
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty
- .getColourScheme(af.getViewport(),
- af.getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
if (cs != null)
{
@@ -736,7 +673,7 @@ public class Jalview
// And the user
// ////////////////////
- if (!headless && file == null && vamsasImport == null
+ if (!headless && file == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
file = jalview.bin.Cache.getDefault("STARTUP_FILE",
@@ -842,10 +779,6 @@ public class Jalview
// 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"
- // +
- // "-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");
}
@@ -885,10 +818,10 @@ public class Jalview
* Locate the given string as a file and pass it to the groovy interpreter.
*
* @param groovyscript
- * the script to execute
+ * the script to execute
* @param jalviewContext
- * the Jalview Desktop object passed in to the groovy binding as the
- * 'Jalview' object.
+ * the Jalview Desktop object passed in to the groovy
+ * binding as the 'Jalview' object.
*/
private void executeGroovyScript(String groovyscript, AlignFrame af)
{
@@ -1017,8 +950,8 @@ public class Jalview
}
/**
- * Quit method delegates to Desktop.quit - unless running in headless mode
- * when it just ends the JVM
+ * Quit method delegates to Desktop.quit - unless running in headless mode when
+ * it just ends the JVM
*/
public void quit()
{