/*
 * 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 <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.bin;

import java.awt.GraphicsEnvironment;
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 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.bin.ApplicationSingletonProvider.ApplicationSingletonI;
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.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;

/**
 * Main class for Jalview Application <br>
 * <br>
 * 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
{

  // for testing those nasty messages you cannot ever find.
  // static
  // {
  // System.setOut(new PrintStream(new ByteArrayOutputStream())
  // {
  // @Override
  // public void println(Object o)
  // {
  // if (o != null)
  // {
  // System.err.println(o);
  // }
  // }
  //
  // });
  // }
  public static Jalview getInstance()
  {
    System.out.println("Hello, MW!!!!!!!!!!!!");
    return (Jalview) ApplicationSingletonProvider
            .getInstance(Jalview.class);
  }

  private Jalview()
  {
  }

  private boolean headless;

  private Desktop desktop;

  public AlignFrame currentAlignFrame;

  public String appletResourcePath;

  public String j2sAppletID;

  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()) {
        Platform.getURLCommandArguments();
    } else /** @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<String> 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;
    }

  }

  private final static boolean doPlatformLogging = false;

  /**
   * main class for Jalview application
   * 
   * @param args
   *          open <em>filename</em>
   */
  public static void main(String[] args)
  {
    if (doPlatformLogging)
    {
      Platform.startJavaLogging();
    }
    getInstance().doMain(args);
  }

  /**
   * @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("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.getInstance().loadBuildProperties(true);

    ArgsParser aparser = new ArgsParser(args);
    headless = false;

    String usrPropsFile = aparser.getValue("props");

    Cache.loadProperties(usrPropsFile); // must do this before

    boolean allowServices = true;
    
    if (isJS)
    {
      j2sAppletID = Platform.getAppID(null);
      Preferences.setAppletDefaults();
      Cache.loadProperties(usrPropsFile); // again, because we
      // might be changing defaults here?
      appletResourcePath = (String) aparser.getAppletValue("resourcepath",
              null, true);
    }
    else
    /**
     * Java only
     * 
     * @j2sIgnore
     */
    {

      if (usrPropsFile != null)
      {
        System.out.println(
                "CMD [-props " + usrPropsFile + "] executed successfully!");
      }
      if (aparser.contains("help") || aparser.contains("h"))
      {
        showUsage();
        System.exit(0);
      }
      // BH note: Only -nodisplay is official; others are deprecated?
      if (aparser.contains("nodisplay") || aparser.contains("nogui")
              || aparser.contains("headless")
              || GraphicsEnvironment.isHeadless())
      {
        if (!isJS) {
          // BH Definitely not a good idea in JavaScript; 
          // probably should not be here for Java, either.  
          System.setProperty("java.awt.headless", "true");
        }
        headless = true;
      }
      if (GraphicsEnvironment.isHeadless())
      {
        headless = true;
      }
      // <<?

      // anything else!

      final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
      allowServices = !("none".equals(jabawsUrl));
      if (allowServices && jabawsUrl != null)
      {
        try
        {
          Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl);
          System.out.println(
                  "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
        } catch (MalformedURLException e)
        {
          System.err.println(
                  "Invalid jabaws parameter: " + jabawsUrl + " ignored");
        }
      }

    }
    String defs = aparser.getValue(ArgsParser.SETPROP);
    while (defs != null)
    {
      int p = defs.indexOf('=');
      if (p == -1)
      {
        System.err.println("Ignoring invalid setprop argument : " + defs);
      }
      else
      {
        System.out.println("Executing setprop argument: " + defs);
        if (isJS)
        {
          Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
        }
      }
      defs = aparser.getValue("setprop");
    }
    System.setProperty("http.agent",
            "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
    try
    {
      Cache.initLogger();
    } catch (NoClassDefFoundError error)
    {
      error.printStackTrace();
      System.out.println("\nEssential logging libraries not found."
              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
      System.exit(0);
    }

    if (!isJS)
    /** @j2sIgnore */
    {
      try
      {
        UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
      } catch (Exception ex)
      {
        System.err.println("Unexpected Look and Feel Exception");
        ex.printStackTrace();
      }
      if (Platform.isMac())
      {

        LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
                .getLookAndFeel();
        System.setProperty(
                "com.apple.mrj.application.apple.menu.about.name",
                "Jalview");
        System.setProperty("apple.laf.useScreenMenuBar", "true");
        if (lookAndFeel != null)
        {
          try
          {
            UIManager.setLookAndFeel(lookAndFeel);
          } catch (Throwable e)
          {
            System.err.println(
                    "Failed to set QuaQua look and feel: " + e.toString());
          }
        }
        if (lookAndFeel == null
                || !(lookAndFeel.getClass().isAssignableFrom(
                        UIManager.getLookAndFeel().getClass()))
                || !UIManager.getLookAndFeel().getClass().toString()
                        .toLowerCase().contains("quaqua"))
        {
          try
          {
            System.err.println(
                    "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
            UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
          } catch (Throwable e)
          {
            System.err.println(
                    "Failed to reset look and feel: " + e.toString());
          }
        }
      }
    }
    /*
     * configure 'full' SO model if preferences say to, else use the default (full SO)
     * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
     */
    boolean soDefault = !isJS;
    if (Cache.getDefault("USE_FULL_SO", soDefault))
    {
      SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
    }


    desktop = null;
    if (!headless)
    {
      desktop = Desktop.getInstance();
      desktop.setInBatchMode(true); // indicate we are starting up
      try
      {
        JalviewTaskbar.setTaskbar(this);
      } catch (Throwable t)
      {
        System.out.println("Error setting Taskbar: " + t.getMessage());
      }
      desktop.setVisible(true);

      if (!isJS)
      /**
       * Java only
       * 
       * @j2sIgnore
       */
      {
        if (allowServices)
          desktop.startServiceDiscovery();
        if (!aparser.contains("nousagestats"))
        {
          startUsageStats(desktop);
        }
        else
        {
          System.err.println("CMD [-nousagestats] executed successfully!");
        }

        if (!aparser.contains("noquestionnaire"))
        {
          String url = aparser.getValue("questionnaire");
          if (url != null)
          {
            // Start the desktop questionnaire prompter with the specified
            // questionnaire
            Cache.log.debug("Starting questionnaire url at " + url);
            desktop.checkForQuestionnaire(url);
            System.out.println("CMD questionnaire[-" + url
                    + "] executed successfully!");
          }
          else
          {
            if (Cache.getProperty("NOQUESTIONNAIRES") == null)
            {
              // Start the desktop questionnaire prompter with the specified
              // questionnaire
              // String defurl =
              // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
              // //
              String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
              Cache.log.debug(
                      "Starting questionnaire with default url: " + defurl);
              desktop.checkForQuestionnaire(defurl);
            }
          }
        }
        else
        {
          System.err
                  .println("CMD [-noquestionnaire] executed successfully!");
        }

        if (!aparser.contains("nonews"))
        {
          desktop.checkForNews();
        }

        BioJsHTMLOutput.updateBioJS();
      }
    }
    parseArguments(aparser, true);
  }

  /**
   * Parse all command-line String[] arguments as well as all JavaScript-derived
   * parameters from Info.
   * 
   * We allow for this method to be run from JavaScript. Basically allowing
   * simple scripting.
   * 
   * @param aparser
   * @param isStartup
   */
  public void parseArguments(ArgsParser aparser, boolean isStartup)
  {

    String groovyscript = null; // script to execute after all loading is
    boolean isJS = Platform.isJS();
    if (!isJS)
    /** @j2sIgnore */
    {
      // Move any new getdown-launcher-new.jar into place over old
      // getdown-launcher.jar
      String appdirString = System.getProperty("getdownappdir");
      if (appdirString != null && appdirString.length() > 0)
      {
        final File appdir = new File(appdirString);
        new Thread()
        {
          @Override
          public void run()
          {
            LaunchUtil.upgradeGetdown(
                    new File(appdir, "getdown-launcher-old.jar"),
                    new File(appdir, "getdown-launcher.jar"),
                    new File(appdir, "getdown-launcher-new.jar"));
          }
        }.start();
      }

      // completed one way or another
      // extract groovy argument and execute if necessary
      groovyscript = aparser.getValue("groovy", true);

    }

    String file = aparser.getValue("open", true);

    if (!isJS && file == null && desktop == null)
    {
      System.out.println("No files to open!");
      System.exit(1);
    }

    setDisplayParameters(aparser);
    
    // time to open a file.

    long progress = -1;
    DataSourceType protocol = null;
    FileLoader fileLoader = new FileLoader(!headless);
    FileFormatI format = null;
    // Finally, deal with the remaining input data.
    AlignFrame af = null;

    JalviewJSApp jsApp = (isJS ? new JalviewJSApp(this, aparser) : null);

    if (file == null)
    {
      if (isJS)
      {
        // JalviewJS allows sequence1 sequence2 ....
        
      }
      else if (!headless && Cache.getDefault("SHOW_STARTUP_FILE", true))
      /**
       * Java only
       * 
       * @j2sIgnore
       */
      {

        // We'll only open the default file if the desktop is visible.
        // And the user
        // ////////////////////

        file = Cache.getDefault("STARTUP_FILE",
                Cache.getDefault("www.jalview.org",
                        "http://www.jalview.org")
                        + "/examples/exampleFile_2_7.jar");
        if (file.equals(
                "http://www.jalview.org/examples/exampleFile_2_3.jar"))
        {
          // hardwire upgrade of the startup file
          file.replace("_2_3.jar", "_2_7.jar");
          // and remove the stale setting
          Cache.removeProperty("STARTUP_FILE");
        }

        protocol = DataSourceType.FILE;

        if (file.indexOf("http:") > -1)
        {
          protocol = DataSourceType.URL;
        }

        if (file.endsWith(".jar"))
        {
          format = FileFormat.Jalview;
        }
        else
        {
          try
          {
            format = new IdentifyFile().identify(file, protocol);
          } catch (FileFormatException e)
          {
            // TODO what?
          }
        }
        af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
      }
    }
    else
    {
      if (!headless)
      {
        desktop.setProgressBar(
                MessageManager
                        .getString("status.processing_commandline_args"),
                progress = System.currentTimeMillis());
      }
      System.out.println("CMD [-open " + file + "] executed successfully!");

      if (!Platform.isJS())
      /**
       * ignore in JavaScript -- can't just file existence - could load it?
       * 
       * @j2sIgnore
       */
      {
        if (!file.startsWith("http://") && !file.startsWith("https://"))
        // BH 2019 added https check for Java
        {
          if (!(new File(file)).exists())
          {
            System.out.println("Can't find " + file);
            if (headless)
            {
              System.exit(1);
            }
          }
        }
      }
      
      String fileFormat = (isJS
              ? (String) aparser.getAppletValue("format", null, true)
              : null);
      protocol = AppletFormatAdapter.checkProtocol(file);
      try
      {
        format = (fileFormat != null
                ? FileFormats.getInstance().forName(fileFormat)
                : null);
        if (format == null)
        {
          format = new IdentifyFile().identify(file, protocol);
        }
      } catch (FileFormatException e1)
      {
        // TODO ?
      }

      af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, protocol,
              format);
      if (af == null)
      {
        System.out.println("jalview error - AlignFrame was not created");
      }
      else
      {

        // JalviewLite interface for JavaScript allows second file open
        String file2 = aparser.getValue(ArgsParser.OPEN2, true);
        if (file2 != null)
        {
          protocol = AppletFormatAdapter.checkProtocol(file2);
          try
          {
            format = new IdentifyFile().identify(file2, protocol);
          } catch (FileFormatException e1)
          {
            // TODO ?
          }
          AlignFrame af2 = new FileLoader(!headless)
                  .LoadFileWaitTillLoaded(file2, protocol, format);
          if (af2 == null)
          {
            System.out.println("error");
          }
          else
          {
            AlignViewport.openLinkedAlignmentAs(af,
                    af.getViewport().getAlignment(),
                    af2.getViewport().getAlignment(), "",
                    AlignViewport.SPLIT_FRAME);
            System.out.println(
                    "CMD [-open2 " + file2 + "] executed successfully!");
          }
        }
        setCurrentAlignFrame(af);

        setFrameDependentProperties(aparser, af);
        
        if (isJS)
        {
          jsApp.initFromParams(af);
        }
        else
        /**
         * Java only
         * 
         * @j2sIgnore
         */
        {
          if (groovyscript != null)
          {
            // Execute the groovy script after we've done all the rendering
            // stuff
            // and before any images or figures are generated.
            System.out.println("Executing script " + groovyscript);
            executeGroovyScript(groovyscript, af);
            System.out.println("CMD groovy[" + groovyscript
                    + "] executed successfully!");
            groovyscript = null;
          }
        }
        if (!isJS || !isStartup) {
          createOutputFiles(aparser, format);
        }
      }
    }
    // extract groovy arguments before anything else.
    // Once all other stuff is done, execute any groovy scripts (in order)
    if (!isJS && groovyscript != null)
    {
      if (Cache.groovyJarsPresent())
      {
        System.out.println("Executing script " + groovyscript);
        executeGroovyScript(groovyscript, af);
      }
      else
      {
        System.err.println(
                "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
                        + groovyscript);
      }
    }

    // and finally, turn off batch mode indicator - if the desktop still exists
    if (desktop != null)
    {
      if (progress != -1)
      {
        desktop.setProgressBar(null, progress);
      }
      desktop.setInBatchMode(false);
    }
    
    if (jsApp != null) {
      jsApp.callInitCallback();
    }
  }
  
  /**
   * Set general display parameters irrespective of file loading or headlessness.
   * 
   * @param aparser
   */
  private void setDisplayParameters(ArgsParser aparser)
  {
    if (aparser.contains(ArgsParser.NOMENUBAR))
    {
      noMenuBar = true;
      System.out.println("CMD [nomenu] executed successfully!");
    }

    if (aparser.contains(ArgsParser.NOSTATUS))
    {
      noStatus = true;
      System.out.println("CMD [nostatus] executed successfully!");
    }

    if (aparser.contains(ArgsParser.NOANNOTATION)
            || aparser.contains(ArgsParser.NOANNOTATION2))
    {
      noAnnotation = true;
      System.out.println("CMD no-annotation executed successfully!");
    }
    if (aparser.contains(ArgsParser.NOCALCULATION))
    {
      noCalculation = true;
      System.out.println("CMD [nocalculation] executed successfully!");
    }
  }


  private void setFrameDependentProperties(ArgsParser aparser,
          AlignFrame af)
  {
    String data = aparser.getValue(ArgsParser.COLOUR, true);
    if (data != null)
    {
      data.replaceAll("%20", " ");

      ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
              af.getViewport(), af.getViewport().getAlignment(), data);

      if (cs != null)
      {
        System.out.println(
                "CMD [-color " + data + "] executed successfully!");
      }
      af.changeColour(cs);
    }

    // Must maintain ability to use the groups flag
    data = aparser.getValue(ArgsParser.GROUPS, true);
    if (data != null)
    {
      af.parseFeaturesFile(data,
              AppletFormatAdapter.checkProtocol(data));
      // System.out.println("Added " + data);
      System.out.println(
              "CMD groups[-" + data + "]  executed successfully!");
    }
    data = aparser.getValue(ArgsParser.FEATURES, true);
    if (data != null)
    {
      af.parseFeaturesFile(data,
              AppletFormatAdapter.checkProtocol(data));
      // System.out.println("Added " + data);
      System.out.println(
              "CMD [-features " + data + "]  executed successfully!");
    }
    data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
    if (data != null)
    {
      af.loadJalviewDataFile(data, null, null, null);
      // System.out.println("Added " + data);
      System.out.println(
              "CMD [-annotations " + data + "] executed successfully!");
    }

    // JavaScript feature

    if (aparser.contains(ArgsParser.SHOWOVERVIEW))
    {
      af.overviewMenuItem_actionPerformed(null);
      System.out.println("CMD [showoverview] executed successfully!");
    }

    // set or clear the sortbytree flag.
    if (aparser.contains(ArgsParser.SORTBYTREE))
    {
      af.getViewport().setSortByTree(true);
      if (af.getViewport().getSortByTree())
      {
        System.out.println("CMD [-sortbytree] executed successfully!");
      }
    }

    boolean doUpdateAnnotation = false;
    /**
     * we do this earlier in JalviewJS because of a complication with
     * SHOWOVERVIEW
     * 
     * For now, just fixing this in JalviewJS.
     *
     * 
     * @j2sIgnore
     * 
     */
    {
      if (noAnnotation)
      {
        af.getViewport().setShowAnnotation(false);
        if (!af.getViewport().isShowAnnotation())
        {
          doUpdateAnnotation = true;
        }
      }
    }

    if (aparser.contains(ArgsParser.NOSORTBYTREE))
    {
      af.getViewport().setSortByTree(false);
      if (!af.getViewport().getSortByTree())
      {
        doUpdateAnnotation = true;
        System.out
                .println("CMD [-nosortbytree] executed successfully!");
      }
    }
    if (doUpdateAnnotation)
    { // BH 2019.07.24
      af.setMenusForViewport();
      af.alignPanel.updateLayout();
    }

    data = aparser.getValue(ArgsParser.TREE, true);
    if (data != null)
    {
      try
      {
        NewickFile nf = new NewickFile(data,
                AppletFormatAdapter.checkProtocol(data));
        af.getViewport()
                .setCurrentTree(af.showNewickTree(nf, data).getTree());
        System.out.println(
                "CMD [-tree " + data + "] executed successfully!");
      } catch (IOException ex)
      {
        System.err.println("Couldn't add tree " + data);
        ex.printStackTrace(System.err);
      }
    }
    // TODO - load PDB structure(s) to alignment JAL-629
    // (associate with identical sequence in alignment, or a specified
    // sequence)

  }

  /**
   * Writes an output file for each format (if any) specified in the
   * command-line arguments. Supported formats are currently
   * <ul>
   * <li>png</li>
   * <li>svg</li>
   * <li>html</li>
   * <li>biojsmsa</li>
   * <li>imgMap</li>
   * <li>eps</li>
   * </ul>
   * A format parameter should be followed by a parameter specifying the output
   * file name. {@code imgMap} parameters should follow those for the
   * corresponding alignment image output.
   * 
   * @param aparser
   * @param format
   */
  private void createOutputFiles(ArgsParser aparser,
          FileFormatI format)
  {
    AlignFrame af = currentAlignFrame;
    while (aparser.getSize() >= 2)
    {
      String outputFormat = aparser.nextValue();
      File imageFile;
      String fname;
      switch (outputFormat.toLowerCase())
      {
      case "png":
        imageFile = new File(aparser.nextValue());
        af.createPNG(imageFile);
        System.out.println(
                "Creating PNG image: " + imageFile.getAbsolutePath());
        continue;
      case "svg":
        imageFile = new File(aparser.nextValue());
        af.createSVG(imageFile);
        System.out.println(
                "Creating SVG image: " + imageFile.getAbsolutePath());
        continue;
      case "eps":
        imageFile = new File(aparser.nextValue());
        System.out.println(
                "Creating EPS file: " + imageFile.getAbsolutePath());
        af.createEPS(imageFile);
        continue;
      case "biojsmsa":
        fname = new File(aparser.nextValue()).getAbsolutePath();
        try
        {
          BioJsHTMLOutput.refreshVersionInfo(
                  BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
        } catch (URISyntaxException e)
        {
          e.printStackTrace();
        }
        BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
        bjs.exportHTML(fname);
        System.out.println("Creating BioJS MSA Viwer HTML file: " + fname);
        continue;
      case "html":
        fname = new File(aparser.nextValue()).getAbsolutePath();
        HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
        htmlSVG.exportHTML(fname);
        System.out.println("Creating HTML image: " + fname);
        continue;
      case "imgmap":
        imageFile = new File(aparser.nextValue());
        af.alignPanel.makePNGImageMap(imageFile, "unnamed.png");
        System.out.println(
                "Creating image map: " + imageFile.getAbsolutePath());
        continue;
      default:
	  // fall through - try to parse as an alignment data export format
          FileFormatI outFormat=null;
          try {
            outFormat = FileFormats.getInstance().forName(outputFormat);
          } catch (Exception formatP) {
          }
          if (outFormat==null) {
            System.out.println("Couldn't parse "+outputFormat+" as a valid Jalview format string.");
	    continue;
	  }
          if (!outFormat.isWritable())
          {
            System.out.println(
                    "This version of Jalview does not support alignment export as "
                            + outputFormat);
	    continue;
          }
          // record file as it was passed to Jalview so it is recognisable to the CLI caller
          String file;
	  fname = new File(file=aparser.nextValue()).getAbsolutePath();
	  // JBPNote - yuck - really wish we did have a bean returned from this which gave success/fail like before !
	  af.saveAlignment(fname, outFormat);
	  if (!af.isSaveAlignmentSuccessful())
          {
              System.out.println("Written alignment in " + outputFormat
                      + " format to " + file);
	      continue;
          } else {
                System.out.println("Error writing file " + file + " in "
                        + outputFormat + " format!!");
          }
      }
    }
    // ??? Should report - 'ignoring' extra args here...
    while (aparser.getSize() > 0)
    {
      System.out.println("Ignoring extra argument: " + aparser.nextValue());
    }
  }

  private static void showUsage()
  {
    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"
                    + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
                    + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
                    + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
                    + "-features FILE\tUse the given file to mark features on the alignment.\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"
                    + "-json FILE\tCreate alignment file FILE in JSON format.\n"
                    + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
                    + "-png FILE\tCreate PNG image FILE from alignment.\n"
                    + "-svg FILE\tCreate SVG image FILE from alignment.\n"
                    + "-html FILE\tCreate HTML file from alignment.\n"
                    + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML 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.\n"
                    + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
                    + "-noquestionnaire\tTurn off questionnaire check.\n"
                    + "-nonews\tTurn off check for Jalview news.\n"
                    + "-nousagestats\tTurn off google analytics tracking for this session.\n"
                    + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
                    // +
                    // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
                    // after all other properties files have been read\n\t
                    // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
                    // passed in correctly)"
                    + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
                    + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
                    + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
                    + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
  }

  private static void startUsageStats(final Desktop desktop)
  {
    /**
     * start a User Config prompt asking if we can log usage statistics.
     */
    PromptUserConfig prompter = new PromptUserConfig(Desktop.getDesktopPane(),
            "USAGESTATS", "Jalview Usage Statistics",
            "Do you want to help make Jalview better by enabling "
                    + "the collection of usage statistics with Google Analytics ?"
                    + "\n\n(you can enable or disable usage tracking in the preferences)",
            new Runnable()
            {
              @Override
              public void run()
              {
                Cache.log.debug(
                        "Initialising googletracker for usage stats.");
                Cache.initGoogleTracker();
                Cache.log.debug("Tracking enabled.");
              }
            }, new Runnable()
            {
              @Override
              public void run()
              {
                Cache.log.debug("Not enabling Google Tracking.");
              }
            }, null, true);
    desktop.addDialogThread(prompter);
  }

  /**
   * Locate the given string as a file and pass it to the groovy interpreter.
   * 
   * @param groovyscript
   *          the script to execute
   * @param jalviewContext
   *          the Jalview Desktop object passed in to the groovy binding as the
   *          'Jalview' object.
   */
  private void executeGroovyScript(String groovyscript, AlignFrame af)
  {
    /**
     * for scripts contained in files
     */
    File tfile = null;
    /**
     * script's URI
     */
    URL sfile = null;
    if (groovyscript.trim().equals("STDIN"))
    {
      // read from stdin into a tempfile and execute it
      try
      {
        tfile = File.createTempFile("jalview", "groovy");
        PrintWriter outfile = new PrintWriter(
                new OutputStreamWriter(new FileOutputStream(tfile)));
        BufferedReader br = new BufferedReader(
                new InputStreamReader(System.in));
        String line = null;
        while ((line = br.readLine()) != null)
        {
          outfile.write(line + "\n");
        }
        br.close();
        outfile.flush();
        outfile.close();

      } catch (Exception ex)
      {
        System.err.println("Failed to read from STDIN into tempfile "
                + ((tfile == null) ? "(tempfile wasn't created)"
                        : tfile.toString()));
        ex.printStackTrace();
        return;
      }
      try
      {
        sfile = tfile.toURI().toURL();
      } catch (Exception x)
      {
        System.err.println(
                "Unexpected Malformed URL Exception for temporary file created from STDIN: "
                        + tfile.toURI());
        x.printStackTrace();
        return;
      }
    }
    else
    {
      try
      {
        sfile = new URI(groovyscript).toURL();
      } catch (Exception x)
      {
        tfile = new File(groovyscript);
        if (!tfile.exists())
        {
          System.err.println("File '" + groovyscript + "' does not exist.");
          return;
        }
        if (!tfile.canRead())
        {
          System.err.println("File '" + groovyscript + "' cannot be read.");
          return;
        }
        if (tfile.length() < 1)
        {
          System.err.println("File '" + groovyscript + "' is empty.");
          return;
        }
        try
        {
          sfile = tfile.getAbsoluteFile().toURI().toURL();
        } catch (Exception ex)
        {
          System.err.println("Failed to create a file URL for "
                  + tfile.getAbsoluteFile());
          return;
        }
      }
    }
    try
    {
      Map<String, java.lang.Object> vbinding = new HashMap<>();
      vbinding.put("Jalview", this);
      if (af != null)
      {
        vbinding.put("currentAlFrame", af);
      }
      Binding gbinding = new Binding(vbinding);
      GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
      gse.run(sfile.toString(), gbinding);
      if ("STDIN".equals(groovyscript))
      {
        // delete temp file that we made -
        // only if it was successfully executed
        tfile.delete();
      }
    } catch (Exception e)
    {
      System.err.println("Exception Whilst trying to execute file " + sfile
              + " as a groovy script.");
      e.printStackTrace(System.err);

    }
  }

  public static boolean isHeadlessMode()
  {
    String isheadless = System.getProperty("java.awt.headless");
    if (isheadless != null && isheadless.equalsIgnoreCase("true"))
    {
      return true;
    }
    return false;
  }

  public AlignFrame[] getAlignFrames()
  {
    return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
            : Desktop.getAlignFrames();

  }

  /**
   * Quit method delegates to Desktop.quit - unless running in headless mode
   * when it just ends the JVM
   */
  public void quit()
  {
    if (desktop != null)
    {
      desktop.quit();
    }
    else
    {
      System.exit(0);
    }
  }

  public static AlignFrame getCurrentAlignFrame()
  {
    return Jalview.getInstance().currentAlignFrame;
  }

  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
  {
    Jalview.getInstance().currentAlignFrame = currentAlignFrame;
  }

  
  public void notifyWorker(AlignCalcWorkerI worker, String status)
  {
    // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
    // + " " + status);
  }


  private static boolean isInteractive = true;

  public static boolean isInteractive()
  {
    return isInteractive;
  }

  public static void setInteractive(boolean tf)
  {
    isInteractive = tf;
  }

}