X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FJalview.java;h=ef16e5553ac3eea7e7ad7c25d0a3bb3be04714e5;hb=2b08c849bd54a0799ddf251f602a421d4696005e;hp=2899abb7f8c7b1eb985e110f700b0aeb76e5a9e7;hpb=6a9c2893f6ac47be883141c0a716d36f9dc67db1;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 2899abb..07fd4d6 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,295 +1,1369 @@
-/*
- * 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.util.Vector;
-
-
-/**
- * Main class for Jalview Application
- *
- *
start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
- *
- * @author $author$
- * @version $Revision$
- */
-public class Jalview
-{
-
- /**
- * main class for Jalview application
- *
- * @param args open filename
- */
- public static void main(String[] args)
- {
- 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);
- boolean headless = false;
-
- if( aparser.contains("help") || aparser.contains("h") )
- {
- System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
- +"-nodisplay\tRun Jalview without User Interface.\n"
- +"-props FILE\tUse the given Jalview properties file instead of users default.\n"
- +"-groups FILE\tUse the given file to mark groups on the alignment. \nGroups file is in the following tab delimited format\n"
- +"TEXTSEQUENCE_IDSEQUENCE_INDEXSTART_RESIDUEEND_RESIDUECOLOUR\n"
- +"SequenceID is used in preference to SequenceIndex if both are provided.\n"
- +"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"
- +"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\n"
- +"-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
- +"-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
- +"-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
- +"-msf FILE\tCreate alignment file FILE in MSF format.\n"
- +"-pileup FILE\tCreate alignment file FILE in Pileup format\n"
- +"-pir FILE\tCreate alignment file FILE in PIR format.\n"
- +"-blc FILE\tCreate alignment file FILE in BLC format.\n"
- +"-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
- +"-png FILE\tCreate PNG image FILE from alignment.\n"
- +"-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
- +"-eps FILE\tCreate EPS file FILE from alignment.");
- System.exit(0);
- }
-
-
- if (aparser.contains("nodisplay"))
- {
- System.setProperty("java.awt.headless", "true");
- }
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
- {
- headless = true;
- }
-
- try
- {
- Cache.initLogger();
- }
- catch (java.lang.NoClassDefFoundError error)
- {
- error.printStackTrace();
- System.out.println(
- "\nEssential logging libraries not found."
- +"\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
- System.exit(0);
- }
-
- Cache.loadProperties(aparser.getValue("props"));
-
- Desktop desktop = null;
- if( !headless )
- {
- try
- {
- UIManager.setLookAndFeel(
- UIManager.getSystemLookAndFeelClassName()
- // UIManager.getCrossPlatformLookAndFeelClassName()
-//"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
-//"javax.swing.plaf.metal.MetalLookAndFeel"
-//"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
-//"com.sun.java.swing.plaf.motif.MotifLookAndFeel"
-
- );
- }
- catch (Exception ex)
- {
- }
-
- desktop = new Desktop();
- desktop.setVisible(true);
- desktop.discoverer.start();
- }
-
-
- String file = null, protocol = null, format = null, groups=null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
-
- file = aparser.getValue("open");
-
- if (file == null && desktop==null)
- {
- System.out.println("No files to open!");
- System.exit(1);
- }
-
- if(file!=null)
- {
-
- if (!file.startsWith("http://"))
- {
- if (! (new java.io.File(file)).exists())
- {
- System.out.println("Can't find " + file);
- if(headless)
- System.exit(1);
- }
- }
-
- protocol = "File";
-
- if (file.indexOf("http:") > -1)
- {
- protocol = "URL";
- }
-
- if (file.endsWith(".jar"))
- format = "Jalview";
- else
- format = jalview.io.IdentifyFile.Identify(file, protocol);
-
- System.out.println("Opening: " + format + " file " + file);
-
- AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
-
- groups = aparser.getValue("groups");
- if (groups != null)
- {
- af.parseGroupsFile(groups);
- }
-
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
- {
- format = aparser.nextValue();
- file = aparser.nextValue();
-
- if (format.equalsIgnoreCase("png"))
- {
- af.createPNG(new java.io.File(file));
- imageName = (new java.io.File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
- }
- else if (format.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new java.io.File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
- }
- else if (format.equalsIgnoreCase("eps"))
- {
- System.out.println("Creating EPS file: " + file);
- af.createEPS(new java.io.File(file));
- continue;
- }
-
- if (af.saveAlignment(file, format))
- System.out.println("Written alignment in " + format +
- " format to " + file);
- else
- System.out.println("Error writing file " + file + " in " + format +
- " format!!");
-
- }
-
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
- }
- }
-
- // We'll only open the default file if the desktop is visible.
- //////////////////////
- if (
- !headless &&
- jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
- {
-
- file = jalview.bin.Cache.getDefault("STARTUP_FILE",
- "http://www.jalview.org/examples/exampleFile.jar");
- protocol = "File";
-
- if (file.indexOf("http:") > -1)
- {
- protocol = "URL";
- }
-
- if (file.endsWith(".jar"))
- {
- Jalview2XML.LoadJalviewAlign(file);
- }
- else
- {
- format = jalview.io.IdentifyFile.Identify(file, protocol);
- desktop.LoadFile(file, protocol, format);
- }
- }
- }
-}
-
- class ArgsParser
- {
- Vector vargs = null;
- public ArgsParser(String [] args)
- {
- vargs = new Vector();
- for (int i = 0; i < args.length; i++)
- {
- String arg = args[i].trim();
- if (arg.charAt(0) == '-')
- arg = arg.substring(1);
- vargs.addElement(arg);
- }
- }
-
- public String getValue(String arg)
- {
- int index = vargs.indexOf(arg);
- String ret = null;
- if (index != -1)
- {
- ret = vargs.elementAt(index + 1).toString();
- vargs.removeElementAt(index);
- vargs.removeElementAt(index);
- }
- return ret;
- }
-
- public boolean contains(String arg)
- {
- if(vargs.contains(arg))
- {
- vargs.removeElement(arg);
- return true;
- }
- else
- return false;
- }
-
- public String nextValue()
- {
- return vargs.remove(0).toString();
- }
-
- public int getSize()
- {
- return vargs.size();
- }
-
- }
+/*
+ * 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.AlignViewportI;
+import jalview.api.JalviewApp;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.so.SequenceOntology;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+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.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;
+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.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 groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
+/**
+ * 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
+{
+
+ 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;
+
+ 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)
+ {
+ // setLogging(); // BH - for event debugging in JavaScript
+ getInstance().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()
+ {
+
+ /**
+ * @j2sIgnore
+ *
+ */
+ {
+ System.out.println("not in js");
+ }
+
+ // BH - for event debugging in JavaScript (Java mode only)
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ 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
+ */
+ void doMain(String[] args)
+ {
+
+ boolean isJS = Platform.isJS();
+ if (!isJS)
+ {
+ 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(
+ "