X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e98ea638a5b8d0cc0844d8beca81dcd1612c6d79;hb=564c47bdd60cf84046269e45d2f85f39408e4441;hp=7cbbd7df24f2594286bb297f925675ba64d8cbce;hpb=d9f0a24d9662a0b530fd79b51108dd074d03d6e0;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 7cbbd7d..e98ea63 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,27 +20,6 @@
*/
package jalview.bin;
-import jalview.ext.so.SequenceOntology;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.PromptUserConfig;
-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.FileLoader;
-import jalview.io.HtmlSvgOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
@@ -58,17 +37,58 @@ 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;
+import jalview.api.AlignCalcWorkerI;
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
+import jalview.api.StructureSelectionManagerProvider;
+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 netscape.javascript.JSObject;
/**
* Main class for Jalview Application
@@ -85,55 +105,80 @@ import groovy.util.GroovyScriptEngine;
* @author $author$
* @version $Revision$
*/
-public class Jalview
+public class Jalview implements JalviewJSApi
{
- /**
- * // find first query parameter (if any) that doesn't start with j2s // and
- * set as space-delimited arguments to Jalview main
- *
- * @j2sNative
- *
- * var hr = decodeURI(document.location.href); var 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; } } }
- */
+ static
+ {
+ Platform.getURLCommandArguments();
+ }
+
+ private boolean headless;
+
+ // singleton instance of this class
- /*
- * singleton instance of this class
- */
private static Jalview instance;
private Desktop desktop;
public static 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;
+ }
+
static
{
if (!Platform.isJS())
/**
* Java only
*
- * @j2sNative
+ * @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()
- {
- }
- });
+ Policy.setPolicy(new Policy()
+ {
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ @Override
+ public void refresh()
+ {
+ }
+ });
}
}
@@ -146,8 +191,8 @@ public class Jalview
class FeatureFetcher
{
/*
- * TODO: generalise to track all jalview events to orchestrate batch
- * processing events.
+ * TODO: generalise to track all jalview events to orchestrate batch processing
+ * events.
*/
private int queued = 0;
@@ -200,6 +245,9 @@ public class Jalview
{
return instance;
}
+
+
+ private final static boolean doPlatformLogging = false;
/**
* main class for Jalview application
@@ -209,44 +257,14 @@ public class Jalview
*/
public static void main(String[] args)
{
-// setLogging(); // BH - for event debugging in JavaScript
+ if (doPlatformLogging)
+ {
+ Platform.startJavaLogging();
+ }
+
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 (!Platform.isJS())// !(/** @j2sNative true ||*/false))
- /**
- * Java only
- *
- * @j2sNative
- */
- {
- 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");
- }
-
}
-
-
-
/**
* @param args
@@ -254,49 +272,91 @@ public class Jalview
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"));
+ 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);
+ }
+ val = System.getProperty("installer_template_version");
+ if (val != null)
+ {
+ System.out.println("Install4j template version: " + val);
+ }
+ val = System.getProperty("launcher_version");
+ if (val != null)
+ {
+ System.out.println("Launcher version: " + val);
+ }
+
+ // report Jalview version
+ 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!");
+ "