X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=fae2b7597ec10ca45093e7a9347c8cfe726dd022;hb=5014beeca83ef54a5740388c443d85f532a34db6;hp=2595c4dcf3c1133855e7eeae43010963487e32d4;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 2595c4d..fae2b75 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,29 +20,50 @@
*/
package jalview.bin;
+import jalview.api.AlignCalcWorkerI;
+import jalview.api.AlignFrameI;
+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;
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;
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.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
+import java.applet.AppletContext;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
@@ -60,18 +81,16 @@ 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.Timer;
import javax.swing.UIManager;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
+import netscape.javascript.JSObject;
/**
* Main class for Jalview Application
@@ -88,60 +107,102 @@ import groovy.util.GroovyScriptEngine;
* @author $author$
* @version $Revision$
*/
-public class Jalview
+public class Jalview implements ApplicationSingletonI, JalviewJSApi
{
- /**
- * @j2sNative
- *
- * // find first query parameter (if any) that doesn't start with j2s
- * // and set as space-delimited arguments to Jalview main
- * hr = decodeURI(document.location.href);
- * pos = hr.indexOf("?");
- * if (pos > 0)
- * {
- * q = hr.substring(pos+1);
- * args = q.split("&");
- * for (i = 0 ; i < args.length; i++)
- * {
- * arg1 = args[i];
- * if (!arg1.startsWith("j2s"))
- * {
- * thisApplet.__Info.args = arg1.split(" ");
- * break;
- * }
- * }
- * }
- */
-
- /*
- * singleton instance of this class
- */
- private static Jalview instance;
+
+ public static Jalview getInstance()
+ {
+ return (Jalview) ApplicationSingletonProvider
+ .getInstance(Jalview.class);
+ }
+
+ private Jalview()
+ {
+ }
+
+ static
+ {
+ Platform.getURLCommandArguments();
+ }
+
+ private boolean headless;
+
+ public static boolean isHeadlessMode()
+ {
+ return getInstance().headless;
+ }
private Desktop desktop;
- public static AlignFrame currentAlignFrame;
+ private AlignFrame currentAlignFrame;
+
+ public boolean isJavaAppletTag;
+
+ public String appletResourcePath;
+
+ JalviewAppLoader appLoader;
+
+ protected JSFunctionExec jsFunctionExec;
+
+ 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;
+ }
+
+ public static AlignFrame getCurrentAlignFrame()
+ {
+ return getInstance().currentAlignFrame;
+ }
+
+ public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+ {
+ getInstance().currentAlignFrame = currentAlignFrame;
+ }
static
{
if (!Platform.isJS())
- { // BH 2018
- // 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()
- {
- }
- });
+ /**
+ * Java only
+ *
+ * @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()
+ {
+ }
+ });
}
}
@@ -204,11 +265,6 @@ public class Jalview
}
- public static Jalview getInstance()
- {
- return instance;
- }
-
/**
* main class for Jalview application
*
@@ -217,47 +273,24 @@ public class Jalview
*/
public static void main(String[] args)
{
-// setLogging(); // BH - for event debugging in JavaScript
- instance = new Jalview();
- instance.doMain(args);
-}
-
- private static void logClass(String name)
- {
- // BH - for event debugging in JavaScript
- ConsoleHandler consoleHandler = new ConsoleHandler();
- consoleHandler.setLevel(Level.ALL);
- Logger logger = Logger.getLogger(name);
- logger.setLevel(Level.ALL);
- logger.addHandler(consoleHandler);
- }
-
- @SuppressWarnings("unused")
- private static void setLogging()
- {
- // BH - for event debugging in JavaScript (Java mode only)
- if (!(/** @j2sNative true ||*/false))
- {
- Logger.getLogger("").setLevel(Level.ALL);
- logClass("java.awt.EventDispatchThread");
- logClass("java.awt.EventQueue");
- logClass("java.awt.Component");
- logClass("java.awt.focus.Component");
- logClass("java.awt.focus.DefaultKeyboardFocusManager");
- }
-
+ // Platform.startJavaLogging();
+ getInstance().doMain(args);
}
-
-
+ @SuppressWarnings("unused")
/**
* @param args
*/
void doMain(String[] args)
{
- if (!Platform.isJS())
+ boolean isJS = Platform.isJS();
+ if (isJS)
+ {
+ Platform.setAppClass(this);
+ }
+ else
{
System.setSecurityManager(null);
}
@@ -269,41 +302,56 @@ public class Jalview
+ System.getProperty("os.version"));
ArgsParser aparser = new ArgsParser(args);
- boolean headless = false;
- String usrPropsFile = aparser.getValue("props");
- Cache.loadProperties(usrPropsFile); // must do this before
- if (usrPropsFile != null)
+ String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
+ Cache.loadProperties(usrPropsFile);
+ 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!");
+ "