X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalview.java;h=50e3559272b0c3054c979567f18a092288608304;hb=7d52ef194d39e75fed7730041da25c48e456cf8c;hp=2524abd87dec2655613f3940b6cf23789c5b8506;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 2524abd..28d029c 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,156 +1,2054 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.bin;
-
-import jalview.gui.*;
-import javax.swing.*;
-import java.awt.event.*;
-import jalview.io.*;
-
-import org.apache.log4j.*;
-
-public class Jalview extends JApplet
-{
- public static JApplet applet;
- Desktop frame;
- public void init()
- {
- applet = this;
- Cache.loadProperties();
- jalview.gui.Preferences.initPreferences();
-
- frame = new Desktop();
- frame.setResizable(true);
- frame.setVisible(true);
- frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
- frame.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent e)
- {
- applet.stop();
- applet.destroy();
- }
- });
-
- String file = getParameter("alignment");
-
- if(file!=null)
- {
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);
- String protocol = "File";
- if (file.indexOf("http:") > -1)
- protocol = "URL";
-
- String format = jalview.io.IdentifyFile.Identify(file, protocol);
-
- frame.LoadFile(file, protocol, format);
- }
- }
-
- public void destroy()
- {
- if(applet!=null)
- applet.stop();
- else
- System.exit(0);
- frame.setVisible(false);
- }
-
- private static void initLogger() {
- Logger l = Logger.getLogger("org.apache.axis");
- if (Cache.getProperty("logs.Axis.Level")==null) {
- Cache.setProperty("logs.Axis.Level", Level.INFO.toString());
- }
-
- l.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),"System.err");
- ap.setName("Axis");
- l.addAppender(ap);
- }
- public static void main(String[] args) {
-
- Cache.loadProperties();
- jalview.gui.Preferences.initPreferences();
- try {
- initLogger();
- } catch (Exception e) {
- System.err.println("Problems initializing the log4j system\n");
- e.printStackTrace();
- }
- try{
- UIManager.setLookAndFeel(
- // "javax.swing.plaf.metal.MetalLookAndFeel"
- // "javax.swing.plaf.multi.MultiLookAndFeel"
- UIManager.getSystemLookAndFeelClassName()
- // UIManager.getCrossPlatformLookAndFeelClassName()
- // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
- // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
- // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
- );
- }
- catch (Exception ex)
- {}
-
- Desktop frame = new Desktop();
- frame.setResizable(true);
- frame.setVisible(true);
-
-
-
- if(args!=null && args.length>0)
- {
- String file=null;
- if(args[0].equals("-open"))
- file = args[1];
- else
- file = args[0];
-
- String protocol = "File";
- if(file.indexOf("http:")>-1)
- protocol = "URL";
-
- String format = jalview.io.IdentifyFile.Identify(file, protocol);
-
- frame.LoadFile(file, protocol, format);
- }
-
- if(jalview.gui.Preferences.showStartupFile &&
- jalview.gui.Preferences.startupFile!=null)
- {
- String file = jalview.gui.Preferences.startupFile;
- String protocol = "File";
- if (file.indexOf("http:") > -1)
- protocol = "URL";
-
- if(file.endsWith(".jar"))
- Jalview2XML.LoadJalviewAlign(file);
- else
- {
- String format = jalview.io.IdentifyFile.Identify(file, protocol);
- frame.LoadFile(file, protocol, format);
- }
- }
-
-
-
- }
-
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.bin;
+
+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.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 javax.swing.LookAndFeel;
+import javax.swing.UIManager;
+
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+import netscape.javascript.JSObject;
+
+/**
+ * Main class for Jalview Application
+ *
+ * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview
+ *
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ *
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview implements ApplicationSingletonI, JalviewJSApi
+{
+
+ 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;
+
+ 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())
+ /**
+ * 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()
+ {
+ }
+ });
+ }
+ }
+
+ /**
+ * keep track of feature fetching tasks.
+ *
+ * @author JimP
+ *
+ */
+ class FeatureFetcher
+ {
+ /*
+ * TODO: generalise to track all jalview events to orchestrate batch
+ * processing events.
+ */
+
+ private int queued = 0;
+
+ private int running = 0;
+
+ public FeatureFetcher()
+ {
+
+ }
+
+ public void addFetcher(final AlignFrame af,
+ final Vector dasSources)
+ {
+ final long id = System.currentTimeMillis();
+ queued++;
+ final FeatureFetcher us = this;
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ synchronized (us)
+ {
+ queued--;
+ running++;
+ }
+
+ af.setProgressBar(MessageManager
+ .getString("status.das_features_being_retrived"), id);
+ af.featureSettings_actionPerformed(null);
+ af.setProgressBar(null, id);
+ synchronized (us)
+ {
+ running--;
+ }
+ }
+ }).start();
+ }
+
+ public synchronized boolean allFinished()
+ {
+ return queued == 0 && running == 0;
+ }
+
+ }
+
+ /**
+ * main class for Jalview application
+ *
+ * @param args
+ * open filename
+ */
+ public static void main(String[] args)
+ {
+ // Platform.startJavaLogging();
+ getInstance().doMain(args);
+ }
+
+
+ @SuppressWarnings("unused")
+ /**
+ * @param args
+ */
+ void doMain(String[] args)
+ {
+
+ 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(System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
+
+ ArgsParser aparser = new ArgsParser(args);
+
+ 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(
+ "