/*
 * 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.Color;
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.Locale;
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.SwingUtilities;
import javax.swing.UIManager;
import javax.swing.UIManager.LookAndFeelInfo;

import com.formdev.flatlaf.FlatLightLaf;
import com.formdev.flatlaf.util.SystemInfo;
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.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.ChannelProperties;
import jalview.util.HttpUtils;
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
{
  static
  {
    Platform.getURLCommandArguments();
  }

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

  private Desktop desktop;

  public static AlignFrame 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<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)
  {
    // setLogging(); // BH - for event debugging in JavaScript
    instance = new Jalview();
    instance.doMain(args);
  }

  private static void logClass(String name)
  {
    // BH - for event debugging in JavaScript
    ConsoleHandler consoleHandler = new ConsoleHandler();
    consoleHandler.setLevel(Level.ALL);
    Logger logger = Logger.getLogger(name);
    logger.setLevel(Level.ALL);
    logger.addHandler(consoleHandler);
  }

  @SuppressWarnings("unused")
  private static void setLogging()
  {

    /**
     * @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)
  {

    if (!Platform.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.loadBuildProperties(true);

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

    String usrPropsFile = aparser.getValue("props");
    Cache.loadProperties(usrPropsFile); // must do this before
    if (usrPropsFile != null)
    {
      System.out.println(
              "CMD [-props " + usrPropsFile + "] executed successfully!");
    }

    if (!Platform.isJS())
    /**
     * Java only
     * 
     * @j2sIgnore
     */
    {
      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;
      }
      // anything else!

      // allow https handshakes to download intermediate certs if necessary
      System.setProperty("com.sun.security.enableAIAcaIssuers", "true");

      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);
        if (Platform.isJS())
        {
          Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
        }
        // 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 (full SO)
     * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
     */
    boolean soDefault = !Platform.isJS();
    if (Cache.getDefault("USE_FULL_SO", soDefault))
    {
      SequenceOntologyFactory.setInstance(new SequenceOntology());
    }

    if (!headless)
    {
      Desktop.nosplash = aparser.contains("nosplash");
      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();
      }

      // set Proxy settings before all the internet calls
      Cache.setProxyPropertiesFromPreferences();

      desktop.setVisible(true);

      if (!Platform.isJS())
      /**
       * Java only
       * 
       * @j2sIgnore
       */
      {
        if (!aparser.contains("nowebservicediscovery"))
        {
          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 = "https://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 (!Platform.isJS())
      /**
       * ignore in JavaScript -- can't just file existence - could load it?
       * 
       * @j2sIgnore
       */
      {
        if (!HttpUtils.startsWithHttpOrHttps(file))
        {
          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;
          }
          FileFormatI outFormat = null;
          try
          {
            outFormat = FileFormats.getInstance().forName(outputFormat);
          } catch (Exception formatP)
          {
            System.out.println("Couldn't parse " + outFormat
                    + " as a valid Jalview format string.");
          }
          if (outFormat != null)
          {
            if (!outFormat.isWritable())
            {
              System.out.println(
                      "This version of Jalview does not support alignment export as "
                              + outputFormat);
            }
            else
            {
              af.saveAlignment(file, outFormat);
              if (af.isSaveAlignmentSuccessful())
              {
                System.out.println("Written alignment in "
                        + outFormat.getName() + " format to " + file);
              }
              else
              {
                System.out.println("Error writing file " + file + " in "
                        + outFormat.getName() + " 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 (!Platform.isJS() && !headless && file == null
            && Cache.getDefault("SHOW_STARTUP_FILE", true))
    /**
     * Java only
     * 
     * @j2sIgnore
     */
    {
      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
              jalview.bin.Cache.getDefault("www.jalview.org",
                      "https://www.jalview.org")
                      + "/examples/exampleFile_2_7.jvp");
      if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
              || file.equals(
                      "http://www.jalview.org/examples/exampleFile_2_7.jar"))
      {
        file.replace("http:", "https:");
        // hardwire upgrade of the startup file
        file.replace("_2_3", "_2_7");
        file.replace("2_7.jar", "2_7.jvp");
        // and remove the stale setting
        Cache.removeProperty("STARTUP_FILE");
      }

      protocol = AppletFormatAdapter.checkProtocol(file);

      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",
    // "mac" or "flat"
    // 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 "flat":
      lafSet = setFlatLookAndFeel();
      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())
      {
        setFlatLookAndFeel();
      }
      if (Platform.isMac())
      {
        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(Locale.ROOT)
                        .startsWith(name.toLowerCase(Locale.ROOT))
                : info.getName().toLowerCase(Locale.ROOT)
                        .equals(name.toLowerCase(Locale.ROOT)))
        {
          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 setFlatLookAndFeel()
  {
    boolean set = setSpecificLookAndFeel("flatlaf light",
            "com.formdev.flatlaf.FlatLightLaf", false);
    if (set)
    {
      if (Platform.isMac())
      {
        System.setProperty("apple.laf.useScreenMenuBar", "true");
        System.setProperty("apple.awt.application.name",
                ChannelProperties.getProperty("app_name"));
        System.setProperty("apple.awt.application.appearance", "system");
        if (SystemInfo.isMacFullWindowContentSupported
                && Desktop.desktop != null)
        {
          Desktop.desktop.getRootPane()
                  .putClientProperty("apple.awt.fullWindowContent", true);
          Desktop.desktop.getRootPane()
                  .putClientProperty("apple.awt.transparentTitleBar", true);
        }

        SwingUtilities.invokeLater(() -> {
          FlatLightLaf.setup();
        });
      }

      UIManager.put("TabbedPane.showTabSeparators", true);
      UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
      UIManager.put("TabbedPane.tabsOverlapBorder", true);
      // UIManager.put("TabbedPane.hasFullBorder", true);
      UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
      UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
      UIManager.put("TabbedPane.smoothScrolling", true);
      UIManager.put("TabbedPane.tabWidthMode", "compact");
      UIManager.put("TabbedPane.selectedBackground", Color.white);
    }
    return set;
  }

  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",
            ChannelProperties.getProperty("app_name"));
    System.setProperty("apple.laf.useScreenMenuBar", "true");
    set = setQuaquaLookAndFeel();
    if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
            .toLowerCase(Locale.ROOT).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"
                    + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
                    + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
                    + "\n~Read documentation in Application or visit https://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;
  }
}