X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e98ea638a5b8d0cc0844d8beca81dcd1612c6d79;hb=564c47bdd60cf84046269e45d2f85f39408e4441;hp=98dc0399a5d420471d75fc4d7ae311cc3e75e554;hpb=b93f8af382bb2fbdb0c974558bcef57750d1bdd6;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 98dc039..e98ea63 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,6 +20,34 @@
*/
package jalview.bin;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+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.Hashtable;
+import java.util.Map;
+import java.util.Vector;
+
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
+
+import com.threerings.getdown.util.LaunchUtil;
+
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.JalviewApp;
@@ -31,9 +59,11 @@ import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
+import jalview.gui.Preferences;
import jalview.gui.PromptUserConfig;
import jalview.gui.StructureViewer;
import jalview.io.AppletFormatAdapter;
@@ -42,6 +72,7 @@ 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;
@@ -59,39 +90,6 @@ import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
import netscape.javascript.JSObject;
-import java.applet.AppletContext;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-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.Hashtable;
-import java.util.Map;
-import java.util.Vector;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import javax.swing.LookAndFeel;
-import javax.swing.UIManager;
-
-import com.threerings.getdown.util.LaunchUtil;
-
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
/**
* Main class for Jalview Application
*
@@ -114,6 +112,8 @@ public class Jalview implements JalviewJSApi
Platform.getURLCommandArguments();
}
+ private boolean headless;
+
// singleton instance of this class
private static Jalview instance;
@@ -154,7 +154,6 @@ public class Jalview implements JalviewJSApi
return !noAnnotation;
}
-
static
{
if (!Platform.isJS())
@@ -165,21 +164,21 @@ public class Jalview implements JalviewJSApi
*/
{
// 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()
- {
- }
- });
+ Policy.setPolicy(new Policy()
+ {
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ @Override
+ public void refresh()
+ {
+ }
+ });
}
}
@@ -246,23 +245,26 @@ public class Jalview implements JalviewJSApi
{
return instance;
}
+
+
+ private final static boolean doPlatformLogging = false;
/**
* main class for Jalview application
*
* @param args
- * open filename
+ * open filename
*/
public static void main(String[] args)
{
- if (false)
+ if (doPlatformLogging)
{
Platform.startJavaLogging();
}
instance = new Jalview();
instance.doMain(args);
-}
+ }
/**
* @param args
@@ -270,28 +272,35 @@ public class Jalview implements JalviewJSApi
void doMain(String[] args)
{
- if (!Platform.isJS())
+ boolean isJS = Platform.isJS();
+ if (isJS)
+ {
+ Platform.setAppClass(this);
+ }
+ else
{
System.setSecurityManager(null);
}
System.out
- .println("Java version: "
- + System.getProperty("java.version"));
+ .println("Java version: " + System.getProperty("java.version"));
System.out.println("Java Home: " + System.getProperty("java.home"));
System.out.println(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);
+ if (val != null)
+ {
+ System.out.println("Install4j version: " + val);
}
val = System.getProperty("installer_template_version");
- if (val != null) {
+ if (val != null)
+ {
System.out.println("Install4j template version: " + val);
}
val = System.getProperty("launcher_version");
- if (val != null) {
+ if (val != null)
+ {
System.out.println("Launcher version: " + val);
}
@@ -299,37 +308,55 @@ public class Jalview implements JalviewJSApi
Cache.loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
- boolean headless = false;
+ headless = false;
String usrPropsFile = aparser.getValue("props");
+
Cache.loadProperties(usrPropsFile); // must do this before
- if (usrPropsFile != null)
+
+ if (isJS)
{
+ isJavaAppletTag = aparser.isApplet();
+ if (isJavaAppletTag)
+ {
+ Preferences.setAppletDefaults();
+ Cache.loadProperties(usrPropsFile); // again, because we
+ // might be changing defaults here?
+ }
System.out.println(
- "CMD [-props " + usrPropsFile + "] executed successfully!");
+ "