package jalview.bin;

import java.io.File;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;

import jalview.analysis.AlignmentUtils;
import jalview.bin.ArgParser.Arg;
import jalview.bin.ArgParser.ArgValues;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
import jalview.io.FileLoader;
import jalview.io.IdentifyFile;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;

public class Commands
{
  Desktop desktop;

  private static boolean headless;

  private static ArgParser argParser;

  private Map<String, AlignFrame> afMap;

  public static void processArgs(ArgParser ap, boolean h)
  {
    argParser = ap;
    headless = h;
    for (String id : argParser.linkedIds())
    {
      Commands cmds = new Commands();
      if (id == null)
      {
        cmds.processUnlinked(id);
      }
      else
      {
        cmds.processLinked(id);
      }
    }
  }

  public Commands()
  {
    this(Desktop.instance);
  }

  public Commands(Desktop d)
  {
    this.desktop = d;
    afMap = new HashMap<String, AlignFrame>();
  }

  protected void processUnlinked(String id)
  {
    processLinked(id);
  }

  protected void processLinked(String id)
  {
    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
    FileLoader fileLoader = new FileLoader(!headless);

    /*
    // script to execute after all loading is completed one way or another
    String groovyscript = m.get(Arg.GROOVY) == null ? null
            : m.get(Arg.GROOVY).getValue();
    String file = m.get(Arg.OPEN) == null ? null
            : m.get(Arg.OPEN).getValue();
    String data = null;
    FileFormatI format = null;
    DataSourceType protocol = null;
    */

    if (m.get(Arg.OPEN) != null)
    {
      long progress = -1;

      boolean first = true;
      AlignFrame af;
      OPEN: for (String openFile : m.get(Arg.OPEN).getValues())
      {
        if (openFile == null)
          continue OPEN;
        Console.debug("********** id = " + id + ", openFile = " + openFile);

        if (first)
        {
          first = false;
          if (!headless)
          {
            desktop.setProgressBar(
                    MessageManager.getString(
                            "status.processing_commandline_args"),
                    progress = System.currentTimeMillis());
          }
        }

        if (!Platform.isJS())
        /**
         * ignore in JavaScript -- can't just file existence - could load it?
         * 
         * @j2sIgnore
         */
        {
          if (!HttpUtils.startsWithHttpOrHttps(openFile))
          {
            if (!(new File(openFile)).exists())
            {
              Console.warn("Can't find file '" + openFile + "'");
              continue OPEN;
            }
          }
        }

        DataSourceType protocol = AppletFormatAdapter
                .checkProtocol(openFile);

        FileFormatI format = null;
        try
        {
          format = new IdentifyFile().identify(openFile, protocol);
        } catch (FileFormatException e1)
        {
          Console.error("Unknown file format for '" + openFile + "'");
        }

        af = afMap.get(id);
        if (af == null)
        {
          Console.debug(
                  "Opening '" + openFile + "' in new alignment frame");
          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
                  format);
          if (m.get(Arg.TITLE) != null)
            af.setTitle(m.get(Arg.TITLE).getValue());
          if (m.get(Arg.SSANNOTATION) != null
                  && !m.get(Arg.SSANNOTATION).getBoolean())
          {
            // do this better (annotation types?)
            AlignmentUtils.showOrHideSequenceAnnotations(
                    af.getCurrentView().getAlignment(),
                    Collections.singleton("Secondary Structure"), null,
                    false, false);
          }
          if (m.get(Arg.NOTEMPFAC) != null
                  && m.get(Arg.NOTEMPFAC).getBoolean())
          {
            // do this better (annotation types?)
            AlignmentUtils.showOrHideSequenceAnnotations(
                    af.getCurrentView().getAlignment(),
                    Collections.singleton("Temperature Factor"), null,
                    false, false);
            AlignmentUtils.showOrHideSequenceAnnotations(
                    af.getCurrentView().getAlignment(),
                    Collections.singleton("Alphafold Reliability"), null,
                    false, false);
          }

          // store the AlignFrame for this id
          afMap.put(id, af);
        }
        else
        {
          Console.debug(
                  "Opening '" + openFile + "' in existing alignment frame");
          af.getCurrentView().addFile(new File(openFile), format);
        }

        System.out
                .println("Command " + Arg.OPEN + " executed successfully!");

      }
      if (first) // first=true means nothing opened
      {
        if (headless)
        {
          Console.error("Could not open any files in headless mode");
          System.exit(1);
        }
      }
      else
      {
        Console.warn("No more files to open");
        if (desktop != null)
          desktop.setProgressBar(null, progress);
      }

    }
  }

}