/*
 * 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.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.UIManager;
import javax.swing.UIManager.LookAndFeelInfo;

import com.threerings.getdown.util.LaunchUtil;

import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
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;

/**
 * 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
{
  /*
   * singleton instance of this class
   */
  private static Jalview instance;

  private Desktop desktop;

  public static AlignFrame currentAlignFrame;

  static
  {
    // grab all the rights we can 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;
    }

  }

  public static Jalview getInstance()
  {
    return instance;
  }

  /**
   * main class for Jalview application
   * 
   * @param args
   *          open <em>filename</em>
   */
  public static void main(String[] args)
  {
    instance = new Jalview();
    instance.doMain(args);
  }

  /**
   * @param args
   */
  void doMain(String[] args)
  {
    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;

    if (aparser.contains("help") || aparser.contains("h"))
    {
      showUsage();
      System.exit(0);
    }
    if (aparser.contains("nodisplay") || aparser.contains("nogui")
            || aparser.contains("headless"))
    {
      System.setProperty("java.awt.headless", "true");
      headless = true;
    }
    String usrPropsFile = aparser.getValue("props");
    Cache.loadProperties(usrPropsFile); // must do this before
    if (usrPropsFile != null)
    {
      System.out.println(
              "CMD [-props " + usrPropsFile + "] executed successfully!");
    }

    // anything else!

    final String jabawsUrl = aparser.getValue("jabaws");
    if (jabawsUrl != null)
    {
      try
      {
        Jws2Discoverer.getDiscoverer().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("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);
        // DISABLED FOR SECURITY REASONS
        // TODO: add a property to allow properties to be overriden by cli args
        // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
      }
      defs = aparser.getValue("setprop");
    }
    if (System.getProperty("java.awt.headless") != null
            && System.getProperty("java.awt.headless").equals("true"))
    {
      headless = true;
    }
    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);
    }

    desktop = null;

    setLookAndFeel();

    /*
     * configure 'full' SO model if preferences say to, else use the default (SO
     * Lite)
     */
    if (Cache.getDefault("USE_FULL_SO", true))
    {
      SequenceOntologyFactory.setInstance(new SequenceOntology());
    }

    if (!headless)
    {

      desktop = new Desktop();
      desktop.setInBatchMode(true); // indicate we are starting up

      try
      {
        JalviewTaskbar.setTaskbar(this);
      } catch (Exception e)
      {
        Cache.log.info("Cannot set Taskbar");
        Cache.log.error(e.getMessage());
        // e.printStackTrace();
      } catch (Throwable t)
      {
        Cache.log.info("Cannot set Taskbar");
        Cache.log.error(t.getMessage());
        // t.printStackTrace();
      }

      desktop.setVisible(true);
      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();
    }

    // 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();
    }

    String file = null, data = null;
    FileFormatI format = null;
    DataSourceType protocol = null;
    FileLoader fileLoader = new FileLoader(!headless);

    String groovyscript = null; // script to execute after all loading is
    // completed one way or another
    // extract groovy argument and execute if necessary
    groovyscript = aparser.getValue("groovy", true);
    file = aparser.getValue("open", true);

    if (file == null && desktop == null)
    {
      System.out.println("No files to open!");
      System.exit(1);
    }
    long progress = -1;
    // Finally, deal with the remaining input data.
    if (file != null)
    {
      if (!headless)
      {
        desktop.setProgressBar(
                MessageManager
                        .getString("status.processing_commandline_args"),
                progress = System.currentTimeMillis());
      }
      System.out.println("CMD [-open " + file + "] executed successfully!");

      if (!file.startsWith("http://"))
      {
        if (!(new File(file)).exists())
        {
          System.out.println("Can't find " + file);
          if (headless)
          {
            System.exit(1);
          }
        }
      }

      protocol = AppletFormatAdapter.checkProtocol(file);

      try
      {
        format = new IdentifyFile().identify(file, protocol);
      } catch (FileFormatException e1)
      {
        // TODO ?
      }

      AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
              format);
      if (af == null)
      {
        System.out.println("error");
      }
      else
      {
        setCurrentAlignFrame(af);
        data = aparser.getValue("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("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("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("annotations", true);
        if (data != null)
        {
          af.loadJalviewDataFile(data, null, null, null);
          // System.out.println("Added " + data);
          System.out.println(
                  "CMD [-annotations " + data + "] executed successfully!");
        }
        // set or clear the sortbytree flag.
        if (aparser.contains("sortbytree"))
        {
          af.getViewport().setSortByTree(true);
          if (af.getViewport().getSortByTree())
          {
            System.out.println("CMD [-sortbytree] executed successfully!");
          }
        }
        if (aparser.contains("no-annotation"))
        {
          af.getViewport().setShowAnnotation(false);
          if (!af.getViewport().isShowAnnotation())
          {
            System.out.println("CMD no-annotation executed successfully!");
          }
        }
        if (aparser.contains("nosortbytree"))
        {
          af.getViewport().setSortByTree(false);
          if (!af.getViewport().getSortByTree())
          {
            System.out
                    .println("CMD [-nosortbytree] executed successfully!");
          }
        }
        data = aparser.getValue("tree", true);
        if (data != null)
        {
          try
          {
            System.out.println(
                    "CMD [-tree " + data + "] executed successfully!");
            NewickFile nf = new NewickFile(data,
                    AppletFormatAdapter.checkProtocol(data));
            af.getViewport()
                    .setCurrentTree(af.showNewickTree(nf, data).getTree());
          } 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)
        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;
        }
        String imageName = "unnamed.png";
        while (aparser.getSize() > 1)
        {
          String outputFormat = aparser.nextValue();
          file = aparser.nextValue();

          if (outputFormat.equalsIgnoreCase("png"))
          {
            af.createPNG(new File(file));
            imageName = (new File(file)).getName();
            System.out.println("Creating PNG image: " + file);
            continue;
          }
          else if (outputFormat.equalsIgnoreCase("svg"))
          {
            File imageFile = new File(file);
            imageName = imageFile.getName();
            af.createSVG(imageFile);
            System.out.println("Creating SVG image: " + file);
            continue;
          }
          else if (outputFormat.equalsIgnoreCase("html"))
          {
            File imageFile = new File(file);
            imageName = imageFile.getName();
            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
            htmlSVG.exportHTML(file);

            System.out.println("Creating HTML image: " + file);
            continue;
          }
          else if (outputFormat.equalsIgnoreCase("biojsmsa"))
          {
            if (file == null)
            {
              System.err.println("The output html file must not be null");
              return;
            }
            try
            {
              BioJsHTMLOutput.refreshVersionInfo(
                      BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
            } catch (URISyntaxException e)
            {
              e.printStackTrace();
            }
            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
            bjs.exportHTML(file);
            System.out
                    .println("Creating BioJS MSA Viwer HTML file: " + file);
            continue;
          }
          else if (outputFormat.equalsIgnoreCase("imgMap"))
          {
            af.createImageMap(new File(file), imageName);
            System.out.println("Creating image map: " + file);
            continue;
          }
          else if (outputFormat.equalsIgnoreCase("eps"))
          {
            File outputFile = new File(file);
            System.out.println(
                    "Creating EPS file: " + outputFile.getAbsolutePath());
            af.createEPS(outputFile);
            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());
        }
      }
    }
    AlignFrame startUpAlframe = null;
    // We'll only open the default file if the desktop is visible.
    // And the user
    // ////////////////////

    if (!headless && file == null
            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
    {
      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
              jalview.bin.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
        jalview.bin.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?
        }
      }

      startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
              format);
      // extract groovy arguments before anything else.
    }

    // Once all other stuff is done, execute any groovy scripts (in order)
    if (groovyscript != null)
    {
      if (Cache.groovyJarsPresent())
      {
        System.out.println("Executing script " + groovyscript);
        executeGroovyScript(groovyscript, startUpAlframe);
      }
      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);
    }
  }

  private static void setLookAndFeel()
  {
    // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
    // "mac"
    // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
    // try Quaqua/Vaqua.
    String lafProp = System.getProperty("laf");
    String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
    String laf = "none";
    if (lafProp != null)
    {
      laf = lafProp;
    }
    else if (lafSetting != null)
    {
      laf = lafSetting;
    }
    boolean lafSet = false;
    switch (laf)
    {
    case "crossplatform":
      lafSet = setCrossPlatformLookAndFeel();
      if (!lafSet)
      {
        Cache.log.error("Could not set requested laf=" + laf);
      }
      break;
    case "system":
      lafSet = setSystemLookAndFeel();
      if (!lafSet)
      {
        Cache.log.error("Could not set requested laf=" + laf);
      }
      break;
    case "gtk":
      lafSet = setGtkLookAndFeel();
      if (!lafSet)
      {
        Cache.log.error("Could not set requested laf=" + laf);
      }
      break;
    case "metal":
      lafSet = setMetalLookAndFeel();
      if (!lafSet)
      {
        Cache.log.error("Could not set requested laf=" + laf);
      }
      break;
    case "nimbus":
      lafSet = setNimbusLookAndFeel();
      if (!lafSet)
      {
        Cache.log.error("Could not set requested laf=" + laf);
      }
      break;
    case "quaqua":
      lafSet = setQuaquaLookAndFeel();
      if (!lafSet)
      {
        Cache.log.error("Could not set requested laf=" + laf);
      }
      break;
    case "vaqua":
      lafSet = setVaquaLookAndFeel();
      if (!lafSet)
      {
        Cache.log.error("Could not set requested laf=" + laf);
      }
      break;
    case "mac":
      lafSet = setMacLookAndFeel();
      if (!lafSet)
      {
        Cache.log.error("Could not set requested laf=" + laf);
      }
      break;
    case "none":
      break;
    default:
      Cache.log.error("Requested laf=" + laf + " not implemented");
    }
    if (!lafSet)
    {
      setSystemLookAndFeel();
      if (Platform.isLinux())
      {
        setMetalLookAndFeel();
      }
      if (Platform.isAMac())
      {
        setMacLookAndFeel();
      }
    }
  }

  private static boolean setCrossPlatformLookAndFeel()
  {
    boolean set = false;
    try
    {
      UIManager.setLookAndFeel(
              UIManager.getCrossPlatformLookAndFeelClassName());
      set = true;
    } catch (Exception ex)
    {
      Cache.log.error("Unexpected Look and Feel Exception");
      Cache.log.error(ex.getMessage());
      Cache.log.debug(Cache.getStackTraceString(ex));
    }
    return set;
  }

  private static boolean setSystemLookAndFeel()
  {
    boolean set = false;
    try
    {
      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
      set = true;
    } catch (Exception ex)
    {
      Cache.log.error("Unexpected Look and Feel Exception");
      Cache.log.error(ex.getMessage());
      Cache.log.debug(Cache.getStackTraceString(ex));
    }
    return set;
  }

  private static boolean setSpecificLookAndFeel(String name,
          String className, boolean nameStartsWith)
  {
    boolean set = false;
    try
    {
      for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
      {
        if (info.getName() != null && nameStartsWith
                ? info.getName().toLowerCase()
                        .startsWith(name.toLowerCase())
                : info.getName().toLowerCase().equals(name.toLowerCase()))
        {
          className = info.getClassName();
          break;
        }
      }
      UIManager.setLookAndFeel(className);
      set = true;
    } catch (Exception ex)
    {
      Cache.log.error("Unexpected Look and Feel Exception");
      Cache.log.error(ex.getMessage());
      Cache.log.debug(Cache.getStackTraceString(ex));
    }
    return set;
  }

  private static boolean setGtkLookAndFeel()
  {
    return setSpecificLookAndFeel("gtk",
            "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
  }

  private static boolean setMetalLookAndFeel()
  {
    return setSpecificLookAndFeel("metal",
            "javax.swing.plaf.metal.MetalLookAndFeel", false);
  }

  private static boolean setNimbusLookAndFeel()
  {
    return setSpecificLookAndFeel("nimbus",
            "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
  }

  private static boolean setQuaquaLookAndFeel()
  {
    return setSpecificLookAndFeel("quaqua",
            ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
                    .getName(),
            false);
  }

  private static boolean setVaquaLookAndFeel()
  {
    return setSpecificLookAndFeel("vaqua",
            "org.violetlib.aqua.AquaLookAndFeel", false);
  }

  private static boolean setMacLookAndFeel()
  {
    boolean set = false;
    System.setProperty("com.apple.mrj.application.apple.menu.about.name",
            "Jalview");
    System.setProperty("apple.laf.useScreenMenuBar", "true");
    set = setQuaquaLookAndFeel();
    if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
            .toLowerCase().contains("quaqua"))
    {
      set = setVaquaLookAndFeel();
    }
    return set;
  }

  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.desktop,
            "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.currentAlignFrame;
  }

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