package jalview.bin;

import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import java.util.Map;

import jalview.analysis.AlignmentUtils;
import jalview.api.AlignmentViewPanel;
import jalview.bin.ArgParser.Arg;
import jalview.bin.ArgParser.ArgValues;
import jalview.datamodel.AlignmentAnnotation;
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;
import jalview.ws.dbsources.EBIAlfaFold;

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;
    if (argParser != null && argParser.linkedIds() != null)
    {
      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);

    /*
    // 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;

        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)
        {
          // get kind of temperature factor annotation
          AlignmentAnnotation.TFType tempfacType = null;
          if ((m.get(Arg.NOTEMPFAC) == null
                  || !m.get(Arg.NOTEMPFAC).getBoolean())
                  && m.get(Arg.TEMPFAC) != null)
          {
            try
            {
              tempfacType = AlignmentAnnotation.TFType
                      .valueOf(m.get(Arg.TEMPFAC).getValue()
                              .toUpperCase(Locale.ROOT));
              Console.debug("Obtained Temperature Factor type of '"
                      + tempfacType + "'");
            } catch (IllegalArgumentException e)
            {
              StringBuilder sb = new StringBuilder().append("Cannot set --")
                      .append(Arg.TEMPFAC.getName()).append(" to '")
                      .append(tempfacType)
                      .append("', ignoring.  Valid values are: ");
              Iterator<AlignmentAnnotation.TFType> it = Arrays
                      .stream(AlignmentAnnotation.TFType.values())
                      .iterator();
              while (it.hasNext())
              {
                sb.append(it.next().toString().toLowerCase(Locale.ROOT));
                if (it.hasNext())
                  sb.append(", ");
              }
              Console.warn(sb.toString());
            }
          }

          Console.debug(
                  "Opening '" + openFile + "' in new alignment frame");
          FileLoader fileLoader = new FileLoader(!headless);
          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format,
                  tempfacType);

          // wrap alignment?
          if (m.get(Arg.WRAP) != null && m.get(Arg.WRAP).getBoolean())
          {
            af.getCurrentView().setWrapAlignment(true);
          }

          // change alignment frame title
          if (m.get(Arg.TITLE) != null)
            af.setTitle(m.get(Arg.TITLE).getValue());

          // show secondary structure annotations?
          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);
          }

          // show temperature factor annotations?
          if (m.get(Arg.NOTEMPFAC) != null
                  && m.get(Arg.NOTEMPFAC).getBoolean())
          {
            // do this better (annotation types?)
            List<String> hideThese = new ArrayList<>();
            hideThese.add("Temperature Factor");
            hideThese.add(MessageManager
                    .getString("label.alphafold_reliability"));
            AlignmentUtils.showOrHideSequenceAnnotations(
                    af.getCurrentView().getAlignment(), hideThese, null,
                    false, false);
          }
          else
          {
            if (m.get(Arg.TEMPFAC_LABEL) != null)
            {
              AlignmentAnnotation aa = AlignmentUtils
                      .getFirstSequenceAnnotationOfType(
                              af.getCurrentView().getAlignment(),
                              AlignmentAnnotation.LINE_GRAPH);
              if (aa != null)
              {
                aa.label = m.get(Arg.TEMPFAC_LABEL).getValue();
              }
            }
          }

          // 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);
      }

    }

    // load a pAE file if given
    if (m.get(Arg.PAEMATRIX) != null)
    {
      AlignFrame af = afMap.get(id);
      if (af != null)
      {
        for (String val : m.get(Arg.PAEMATRIX).getValues())
        {
          SubId subId = new SubId(val);
          File paeFile = new File(subId.content);
          EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
                  paeFile, subId.index,
                  "id".equals(subId.keyName) ? subId.keyValue : null);
          // required to readjust the height and position of the pAE
          // annotation
          for (AlignmentViewPanel ap : af.getAlignPanels())
          {
            ap.adjustAnnotationHeight();
          }
        }
      }
    }
  }

  /**
   * A helper class to parse a string of the possible forms "content"
   * "[index]content", "[keyName=keyValue]content" and return the integer index,
   * the strings keyName and keyValue, and the content after the square brackets
   * (if present). Values not set will be -1 or null.
   */
  protected class SubId
  {
    protected int index = 0;

    protected String keyName = null;

    protected String keyValue = null;

    protected String content = null;

    protected SubId(String item)
    {
      if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
      {
        int openBracket = item.indexOf('[');
        int closeBracket = item.indexOf(']');
        String indexString = item.substring(openBracket + 1, closeBracket);
        this.content = item.substring(closeBracket + 1);
        int equals = indexString.indexOf('=');
        if (equals > -1)
        {
          this.keyName = indexString.substring(0, equals);
          this.keyValue = indexString.substring(equals + 1);
          this.index = -1;
        }
        else
        {
          try
          {
            this.index = Integer.parseInt(indexString);
          } catch (NumberFormatException e)
          {
            Console.warn("Failed to obtain sequenced id or index from '"
                    + item + "'. Setting index=0 and using content='"
                    + content + "'.");
          }
        }
      }
      else
      {
        this.content = item;
      }
    }
  }
}