package jalview.bin;

import java.io.File;
import java.io.IOException;
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.ArgValue;
import jalview.bin.ArgParser.ArgValuesMap;
import jalview.bin.ArgParser.SubVals;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
import jalview.gui.AssociatePdbFileWithSeq;
import jalview.gui.Desktop;
import jalview.gui.Preferences;
import jalview.gui.StructureChooser;
import jalview.gui.StructureViewer;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.schemes.AnnotationColourGradient;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.EBIAlfaFold;
import mc_view.PDBChain;

public class Commands
{
  Desktop desktop;

  private boolean headless;

  private ArgParser argParser;

  private Map<String, AlignFrame> afMap;

  private boolean commandArgsProvided = false;

  private boolean argsWereParsed = false;

  public Commands(ArgParser argparser, boolean headless)
  {
    this(Desktop.instance, argparser, headless);
  }

  public Commands(Desktop d, ArgParser argparser, boolean h)
  {
    argParser = argparser;
    headless = h;
    desktop = d;
    afMap = new HashMap<String, AlignFrame>();
    if (argparser != null)
    {
      processArgs(argparser, headless);
    }
  }

  private boolean processArgs(ArgParser argparser, boolean h)
  {
    argParser = argparser;
    headless = h;
    boolean theseArgsWereParsed = false;

    if (argParser != null && argParser.linkedIds() != null)
    {
      for (String id : argParser.linkedIds())
      {
        ArgValuesMap avm = argParser.linkedArgs(id);
        theseArgsWereParsed = true;
        if (id == null)
        {
          theseArgsWereParsed &= processUnlinked(id);
        }
        else
        {
          theseArgsWereParsed &= processLinked(id);
        }
        theseArgsWereParsed &= processImages(id);

        // close ap
        if (avm.getBoolean(Arg.CLOSE))
        {
          AlignFrame af = afMap.get(id);
          if (af != null)
          {
            af.closeMenuItem_actionPerformed(true);
          }
        }

      }

    }
    if (argParser.getBool(Arg.QUIT))
    {
      Jalview.getInstance().quit();
      return true;
    }
    // carry on with jalview.bin.Jalview
    argsWereParsed = theseArgsWereParsed;
    return argsWereParsed;
  }

  public boolean commandArgsProvided()
  {
    return commandArgsProvided;
  }

  public boolean argsWereParsed()
  {
    return argsWereParsed;
  }

  protected boolean processUnlinked(String id)
  {
    return processLinked(id);
  }

  protected boolean processLinked(String id)
  {
    boolean theseArgsWereParsed = false;
    ArgValuesMap avm = argParser.linkedArgs(id);
    if (avm == null)
      return true;

    /*
    // 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 (avm.containsArg(Arg.OPEN))
    {
      commandArgsProvided = true;
      long progress = -1;

      boolean first = true;
      boolean progressBarSet = false;
      AlignFrame af;
      for (ArgValue av : avm.getArgValueList(Arg.OPEN))
      {
        String openFile = av.getValue();
        if (openFile == null)
          continue;

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

        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 + "'");
            }
          }
        }

        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)
        {
          /*
           * this approach isn't working yet
          // get default annotations before opening AlignFrame
          if (m.get(Arg.SSANNOTATION) != null)
          {
            Console.debug("***** SSANNOTATION="
                    + m.get(Arg.SSANNOTATION).getBoolean());
          }
          if (m.get(Arg.NOTEMPFAC) != null)
          {
            Console.debug(
                    "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
          }
          boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
                  ? m.get(Arg.SSANNOTATION).getBoolean()
                  : false;
          boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null)
                  ? !m.get(Arg.NOTEMPFAC).getBoolean()
                  : false;
          Console.debug("***** tempfac=" + showTemperatureFactor
                  + ", showSS=" + showSecondaryStructure);
          StructureSelectionManager ssm = StructureSelectionManager
                  .getStructureSelectionManager(Desktop.instance);
          if (ssm != null)
          {
            ssm.setAddTempFacAnnot(showTemperatureFactor);
            ssm.setProcessSecondaryStructure(showSecondaryStructure);
          }
           */

          // get kind of temperature factor annotation
          StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
          if ((!avm.getBoolean(Arg.NOTEMPFAC))
                  && avm.containsArg(Arg.TEMPFAC))
          {
            try
            {
              tempfacType = StructureImportSettings.TFType
                      .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
                              .toUpperCase(Locale.ROOT));
              Console.debug("Obtained Temperature Factor type of '"
                      + tempfacType + "'");
            } catch (IllegalArgumentException e)
            {
              // Just an error message!
              StringBuilder sb = new StringBuilder().append("Cannot set --")
                      .append(Arg.TEMPFAC.getName()).append(" to '")
                      .append(tempfacType)
                      .append("', ignoring.  Valid values are: ");
              Iterator<StructureImportSettings.TFType> it = Arrays
                      .stream(StructureImportSettings.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);

          StructureImportSettings.setTemperatureFactorType(tempfacType);

          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
                  format);

          // wrap alignment?
          if (avm.getBoolean(Arg.WRAP))
          {
            af.getCurrentView().setWrapAlignment(true);
          }

          // colour aligment?
          if (avm.containsArg(Arg.COLOUR))
          {
            af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
          }

          // change alignment frame title
          if (avm.containsArg(Arg.TITLE))
            af.setTitle(avm.getValue(Arg.TITLE));

          /* hacky approach to hiding the annotations */
          // show secondary structure annotations?
          if (avm.getBoolean(Arg.SSANNOTATION))
          {
            // do this better (annotation types?)
            AlignmentUtils.showOrHideSequenceAnnotations(
                    af.getCurrentView().getAlignment(),
                    Collections.singleton("Secondary Structure"), null,
                    false, false);
          }

          // show temperature factor annotations?
          if (avm.getBoolean(Arg.NOTEMPFAC))
          {
            // do this better (annotation types?)
            List<String> hideThese = new ArrayList<>();
            hideThese.add("Temperature Factor");
            hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
            AlignmentUtils.showOrHideSequenceAnnotations(
                    af.getCurrentView().getAlignment(), hideThese, null,
                    false, false);
          }
          else
          /* comment out hacky approach up to here and add this line:
           if (showTemperatureFactor)
             */
          {
            if (avm.containsArg(Arg.TEMPFAC_LABEL))
            {
              AlignmentAnnotation aa = AlignmentUtils
                      .getFirstSequenceAnnotationOfType(
                              af.getCurrentView().getAlignment(),
                              AlignmentAnnotation.LINE_GRAPH);
              String label = avm.getValue(Arg.TEMPFAC_LABEL);
              if (aa != null)
              {
                aa.label = label;
              }
              else
              {
                Console.info(
                        "Could not find annotation to apply tempfac_label '"
                                + label);
              }
            }
          }

          // store the AlignFrame for this id
          afMap.put(id, af);

          // is it its own structure file?
          if (format.isStructureFile())
          {
            StructureSelectionManager ssm = StructureSelectionManager
                    .getStructureSelectionManager(Desktop.instance);
            SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
            ssm.computeMapping(false, new SequenceI[] { seq }, null,
                    openFile, DataSourceType.FILE, null, null, null);
          }
        }
        else
        {
          Console.debug(
                  "Opening '" + openFile + "' in existing alignment frame");
          af.getCurrentView().addFile(new File(openFile), format, false);
        }

        Console.debug("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 (progressBarSet && desktop != null)
        desktop.setProgressBar(null, progress);

    }

    // open the structure (from same PDB file or given PDBfile)
    if (!avm.getBoolean(Arg.NOSTRUCTURE))
    {
      AlignFrame af = afMap.get(id);
      if (avm.containsArg(Arg.STRUCTURE))
      {
        commandArgsProvided = true;
        for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
        {
          String val = av.getValue();
          SubVals subId = new SubVals(val);
          SequenceI seq = getSpecifiedSequence(af, subId);
          if (seq == null)
          {
            Console.warn("Could not find sequence for argument --"
                    + Arg.STRUCTURE + "=" + val);
            // you probably want to continue here, not break
            // break;
            continue;
          }
          File structureFile = null;
          if (subId.getContent() != null
                  && subId.getContent().length() != 0)
          {
            structureFile = new File(subId.getContent());
            Console.debug("Using structure file (from argument) '"
                    + structureFile.getAbsolutePath() + "'");
          }

          // TRY THIS
          /*
           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
                  .associatePdbWithSeq(selectedPdbFileName,
                          DataSourceType.FILE, selectedSequence, true,
                          Desktop.instance);
                          
           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
                  ap, new SequenceI[]
                  { selectedSequence });
          
           */

          /* THIS DOESN'T WORK */
          else if (seq.getAllPDBEntries() != null
                  && seq.getAllPDBEntries().size() > 0)
          {
            structureFile = new File(
                    seq.getAllPDBEntries().elementAt(0).getFile());
            Console.debug("Using structure file (from sequence) '"
                    + structureFile.getAbsolutePath() + "'");
          }

          if (structureFile == null)
          {
            Console.warn("Not provided structure file with '" + val + "'");
            continue;
          }

          if (!structureFile.exists())
          {
            Console.warn("Structure file '"
                    + structureFile.getAbsoluteFile() + "' not found.");
            continue;
          }

          Console.debug("Using structure file "
                  + structureFile.getAbsolutePath());

          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
                  .associatePdbWithSeq(structureFile.getAbsolutePath(),
                          DataSourceType.FILE, seq, true, Desktop.instance);

          // open structure view
          AlignmentPanel ap = af.alignPanel;
          if (headless)
          {
            Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
                    StructureViewer.ViewerType.JMOL.toString());
          }

          // get tft, paeFilename, label?
          /*
          ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
                  Arg.TEMPFAC);
           */
          StructureChooser.openStructureFileForSequence(null, null, ap, seq,
                  false, structureFile.getAbsolutePath(), null, null); // tft,
                                                                       // paeFilename);
        }
      }
    }

    // load a pAE file if given
    if (avm.containsArg(Arg.PAEMATRIX))
    {
      AlignFrame af = afMap.get(id);
      if (af != null)
      {
        for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
        {
          String val = av.getValue();
          SubVals subVals = ArgParser.getSubVals(val);
          File paeFile = new File(subVals.getContent());
          String paePath = null;
          try
          {
            paePath = paeFile.getCanonicalPath();
          } catch (IOException e)
          {
            paePath = paeFile.getAbsolutePath();
            Console.warn(
                    "Problem with the PAE file path: '" + paePath + "'");
          }
          String structId = subVals.get("structid");
          if (subVals.notSet())
          {
            // take structid from pdbfilename
          }
          if (subVals.has("structfile"))
          {
            Console.info("***** Attaching paeFile '" + paePath + "' to "
                    + "structfile=" + subVals.get("structfile"));
            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
                    paeFile, subVals.getIndex(), subVals.get("structfile"),
                    true, false);
          }
          else if (subVals.has("structid"))
          {
            Console.info("***** Attaching paeFile '" + paePath + "' to "
                    + "structid=" + subVals.get("structid"));
            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
                    paeFile, subVals.getIndex(), subVals.get("structid"),
                    true, true);
          }
          else
          {
            Console.debug("***** Attaching paeFile '" + paePath
                    + "' to sequence index " + subVals.getIndex());
            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
                    paeFile, subVals.getIndex(), null, false, false);
            // required to readjust the height and position of the pAE
            // annotation
          }
          for (AlignmentViewPanel ap : af.getAlignPanels())
          {
            ap.adjustAnnotationHeight();
          }
        }
      }
    }

    boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
    if (doShading)
    {
      AlignFrame af = afMap.get(id);
      for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
              .findAnnotation(PDBChain.class.getName().toString()))
      {
        AnnotationColourGradient acg = new AnnotationColourGradient(aa,
                af.alignPanel.av.getGlobalColourScheme(), 0);
        acg.setSeqAssociated(true);
        af.changeColour(acg);
        Console.info("Changed colour " + acg.toString());
      }
    }

    return theseArgsWereParsed;
  }

  protected boolean processImages(String id)
  {
    ArgValuesMap avm = argParser.linkedArgs(id);
    AlignFrame af = afMap.get(id);

    if (af == null)
    {
      Console.warn("Did not have an alignment window for id=" + id);
      return false;
    }

    if (avm.containsArg(Arg.IMAGE))
    {
      for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
      {
        String val = av.getValue();
        SubVals subVal = new SubVals(val);
        String type = "png"; // default
        String fileName = subVal.getContent();
        File file = new File(fileName);
        if (subVal.has("type"))
        {
          type = subVal.get("type");
        }
        else if (fileName != null)
        {
          for (String ext : new String[] { "svg", "png", "html" })
          {
            if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
            {
              type = ext;
            }
          }
        }
        // for moment we disable JSON export
        Cache.setPropsAreReadOnly(true);
        Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");

        switch (type)
        {
        case "svg":
          Console.debug("Outputting type '" + type + "' to " + fileName);
          af.createSVG(file);
          break;
        case "png":
          Console.debug("Outputting type '" + type + "' to " + fileName);
          af.createPNG(file);
          break;
        case "html":
          Console.debug("Outputting type '" + type + "' to " + fileName);
          HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
          htmlSVG.exportHTML(fileName);
          break;
        default:
          Console.warn("--image type '" + type + "' not known. Ignoring");
          break;
        }
      }
    }
    return true;
  }

  private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
  {
    AlignmentI al = af.getCurrentView().getAlignment();
    if (-1 < subId.getIndex()
            && subId.getIndex() < al.getSequences().size())
    {
      return al.getSequenceAt(subId.getIndex());
    }
    else if (subId.has("seqid"))
    {
      return al.findName(subId.get("seqid"));
    }
    return null;
  }
}