X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e1fd5721ebd38c25f525ace51f0df71c7db43bf5;hb=refs%2Fheads%2FJAL-4152-typed-singleton-provider;hp=963963d35576f9d2344f247551bd7c442fa44c9b;hpb=e82c0bb610425c3829037bec88b6c03509d07e36;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 963963d..e1fd572 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,6 +20,11 @@
*/
package jalview.bin;
+import java.util.Locale;
+
+import java.awt.GraphicsEnvironment;
+import java.awt.Color;
+
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
@@ -37,36 +42,33 @@ import java.security.PermissionCollection;
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
-import java.util.Hashtable;
+import java.util.Locale;
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.JOptionPane;
+import javax.swing.SwingUtilities;
import javax.swing.UIManager;
+import javax.swing.UIManager.LookAndFeelInfo;
+import com.formdev.flatlaf.FlatLightLaf;
+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.api.AlignCalcWorkerI;
-import jalview.api.AlignViewportI;
-import jalview.api.JalviewApp;
-import jalview.api.StructureSelectionManagerProvider;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-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;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
@@ -79,17 +81,14 @@ import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.gff.SequenceOntologyFactory;
-import jalview.javascript.JSFunctionExec;
-import jalview.javascript.MouseOverStructureListener;
-import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.structure.SelectionSource;
-import jalview.structure.VamsasSource;
+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;
-import netscape.javascript.JSObject;
/**
* Main class for Jalview Application
@@ -106,9 +105,8 @@ import netscape.javascript.JSObject;
* @author $author$
* @version $Revision$
*/
-public class Jalview implements ApplicationSingletonI, JalviewJSApi
+public class Jalview implements ApplicationSingletonI
{
-
// for testing those nasty messages you cannot ever find.
// static
// {
@@ -127,32 +125,28 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
// }
public static Jalview getInstance()
{
- return (Jalview) ApplicationSingletonProvider
- .getInstance(Jalview.class);
+ return ApplicationSingletonProvider.getInstance(Jalview.class);
}
private Jalview()
{
- }
-
- static
- {
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");
}
+
private boolean headless;
private Desktop desktop;
- public static AlignFrame currentAlignFrame;
-
- public boolean isJavaAppletTag;
+ public AlignFrame currentAlignFrame;
public String appletResourcePath;
- JalviewAppLoader appLoader;
-
- protected JSFunctionExec jsFunctionExec;
+ public String j2sAppletID;
private boolean noCalculation, noMenuBar, noStatus;
@@ -180,7 +174,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
static
{
- if (!Platform.isJS())
+ if (Platform.isJS())
+ {
+ Platform.getURLCommandArguments();
+ } else
/**
* Java only
*
@@ -279,8 +276,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
{
Platform.startJavaLogging();
}
+
getInstance().doMain(args);
+
}
+
+
+
/**
* @param args
@@ -289,15 +291,16 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
{
boolean isJS = Platform.isJS();
- if (isJS)
- {
- Platform.setAppClass(this);
- }
- else
+ if (!isJS)
{
System.setSecurityManager(null);
}
+ /*
+ * @j2sNative J2S.db._DirectDatabaseCalls["compbio.dundee.ac.uk"]=null;
+ * @j2sNative J2S.db._DirectDatabaseCalls["jalview.org"]=null;
+ *
+ */
System.out
.println("Java version: " + System.getProperty("java.version"));
System.out.println("Java Home: " + System.getProperty("java.home"));
@@ -327,22 +330,19 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
headless = false;
String usrPropsFile = aparser.getValue("props");
-
Cache.loadProperties(usrPropsFile); // must do this before
-
+ boolean allowServices = true;
+
if (isJS)
{
- isJavaAppletTag = aparser.isApplet();
- if (isJavaAppletTag)
- {
- Preferences.setAppletDefaults();
- Cache.loadProperties(usrPropsFile); // again, because we
- // might be changing defaults here?
- }
- System.out.println(
- "