package jalview.hmmer;

import jalview.bin.Cache;
import jalview.datamodel.SequenceI;
import jalview.gui.Preferences;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.ParamDatastoreI;
import jalview.ws.params.WsParamSetI;
import jalview.ws.params.simple.BooleanOption;
import jalview.ws.params.simple.DoubleParameter;
import jalview.ws.params.simple.FileParameter;
import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.LogarithmicParameter;
import jalview.ws.params.simple.Option;
import jalview.ws.params.simple.RadioChoiceParameter;
import jalview.ws.params.simple.StringParameter;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Scanner;

public final class HMMERParamStore implements ParamDatastoreI
{
  private static final String HMMBUILD = "hmmbuild";

  private static final String HMMALIGN = "hmmalign";

  private static final String HMMSEARCH = "hmmsearch";

  private static final String JACKHMMER = "jackhmmer";

  private String name;

  private List<WsParamSetI> presets = new ArrayList<>();

  private AlignmentViewport viewport;

  private HMMERParamStore(String nam, AlignmentViewport av)
  {
    this.viewport = av;
    this.name = nam;
  }

  public static HMMERParamStore forBuild(AlignmentViewport viewport)
  {
    return new HMMERParamStore(HMMBUILD, viewport);
  }

  public static HMMERParamStore forAlign(AlignmentViewport viewport)
  {
    return new HMMERParamStore(HMMALIGN, viewport);
  }

  public static HMMERParamStore forSearch(AlignmentViewport viewport)
  {
    return new HMMERParamStore(HMMSEARCH, viewport);
  }

  public static HMMERParamStore forJackhmmer(AlignmentViewport viewport)
  {
    return new HMMERParamStore(JACKHMMER, viewport);
  }

  @Override
  public List<WsParamSetI> getPresets()
  {
    return presets;
  }

  @Override
  public WsParamSetI getPreset(String nam)
  {
    return null;
  }

  @Override
  public List<ArgumentI> getServiceParameters()
  {
    List<ArgumentI> args = new ArrayList<>();
    switch (name)
    {
    case HMMSEARCH:
      getHMMSearchParams(args);
      break;
    case HMMALIGN:
      getHMMAlignParams(args);
      break;
    case HMMBUILD:
      getHMMBuildParams(args);
      break;
    case JACKHMMER:
      getJackhmmerParams(args);
    default:
    }

    return args;
  }

  /**
   * Answers default parameters for hmmsearch, taking into account any
   * configured as user preferences
   * 
   * @param args
   */
  private void getHMMSearchParams(List<ArgumentI> args)
  {
    /*
     * 'Options'
     */
    args.add(new BooleanOption(
            MessageManager.getString(HMMSearch.AUTO_ALIGN_SEQS_KEY),
            MessageManager.getString("label.auto_align_seqs_desc"), false,
            false, false, null));
    args.add(new BooleanOption(
            MessageManager.getString(HMMSearch.USE_ACCESSIONS_KEY),
            MessageManager.getString("label.use_accessions_desc"), false,
            false, true, null));
    args.add(new BooleanOption(
            MessageManager.getString(HMMSearch.TRIM_TERMINI_KEY),
            MessageManager.getString("label.trim_termini_desc"), false,
            false, true, null));
    args.add(new BooleanOption(
            MessageManager.getString(HMMSearch.RETURN_N_NEW_SEQ),
            MessageManager.getString("label.check_for_new_sequences_desc"),
            false, false, false, null));

    /*
     * 'Parameters'
     */
    addChoiceOfHmm(args);

    // addChoiceOfDatabase(args);

    String thisAlignment = MessageManager
            .getString(HMMSearch.THIS_ALIGNMENT_KEY);
    String database = MessageManager.getString("label.database");
    args.add(new FileParameter(database, "", false, "", ""));
    args.add(new IntegerParameter(
            MessageManager.getString(HMMSearch.NUMBER_OF_RESULTS_KEY),
            MessageManager.getString("label.number_of_results_desc"), true,
            100, 0, 100000));
    args.add(new RadioChoiceParameter(
            MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
            Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
                    MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
            MessageManager.getString(HMMSearch.CUTOFF_EVALUE)));
    args.add(new LogarithmicParameter(
            MessageManager.getString(HMMSearch.REPORTING_SEQ_EVALUE_KEY),
            MessageManager.getString("label.reporting_seq_e_value_desc"),
            false, 1D,
            1E-100, 10D));
    args.add(new LogarithmicParameter(
            MessageManager.getString(HMMSearch.REPORTING_DOM_EVALUE_KEY),
            MessageManager.getString("label.reporting_dom_e_value_desc"),
            false, 1D,
            1E-100, 10D));
    args.add(
            new DoubleParameter(
                    MessageManager
                            .getString(HMMSearch.REPORTING_SEQ_SCORE_KEY),
                    MessageManager.getString(
                            "label.reporting_seq_score_desc"),
                    false,
                    0d, 0d, 1000d));
    args.add(
            new DoubleParameter(
                    MessageManager
                            .getString(HMMSearch.REPORTING_DOM_SCORE_KEY),
                    MessageManager.getString(
                            "label.reporting_dom_score_desc"),
                    false,
                    0d, 0d, 1000d));
    args.add(new RadioChoiceParameter(
            MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
            null,
            Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
                    MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
            MessageManager.getString(HMMSearch.CUTOFF_EVALUE)));
    args.add(new LogarithmicParameter(
            MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
            MessageManager.getString("label.inclusion_seq_e_value_desc"),
            false, 1D,
            1E-100, 10D));
    args.add(new LogarithmicParameter(
            MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
            MessageManager.getString("label.inclusion_dom_e_value_desc"),
            false, 1D,
            1E-100, 10D));
    args.add(new DoubleParameter(
            MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
            MessageManager.getString("label.inclusion_seq_score_desc"),
            false, 0d, 0d,
            1000d));
    args.add(new DoubleParameter(
            MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
            MessageManager.getString("label.inclusion_dom_score_desc"),
            false, 0d, 0d,
            1000d));
  }

  /**
   * Answers default parameters for jackhmmer, taking into account any configured
   * as user preferences
   * 
   * @param args
   */
  private void getJackhmmerParams(List<ArgumentI> args)
  {

    /*
     * 'Parameters'
     */
    addChoiceOfSequence(args);

    // addChoiceOfDatabase(args);

    String database = MessageManager.getString("label.database");
    args.add(new FileParameter(database, "", false, "", ""));
    args.add(new IntegerParameter(
            MessageManager.getString(HMMSearch.NUMBER_OF_ITERATIONS),
            MessageManager.getString("label.number_of_iterations_desc"),
            true, 5, 1, 20));
    args.add(new RadioChoiceParameter(
            MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
            Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
                    MessageManager.getString(JackHMMER.CUTOFF_EVALUE),
                    MessageManager.getString(JackHMMER.CUTOFF_SCORE)),
            MessageManager.getString(JackHMMER.CUTOFF_EVALUE)));
    args.add(new LogarithmicParameter(
            MessageManager.getString(JackHMMER.REPORTING_SEQ_EVALUE_KEY),
            MessageManager.getString("label.reporting_seq_e_value_desc"),
            false, 1D,
            1E-38, 10D));
    args.add(new LogarithmicParameter(
            MessageManager.getString(JackHMMER.REPORTING_DOM_EVALUE_KEY),
            MessageManager.getString(
                    "label.reporting_dom_e_value_desc"),
            false, 1D,
            1E-38, 10D));
    args.add(new DoubleParameter(
            MessageManager.getString(JackHMMER.REPORTING_SEQ_SCORE_KEY),
            MessageManager.getString("label.reporting_seq_score_desc"),
            false, 0d, 0d,
            1000d));
    args.add(new DoubleParameter(
            MessageManager.getString(JackHMMER.REPORTING_DOM_SCORE_KEY),
            MessageManager.getString("label.reporting_dom_score_desc"),
            false, 0d, 0d,
            1000d));
    args.add(new RadioChoiceParameter(
            MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
            null,
            Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
                    MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
            MessageManager.getString(HmmerCommand.CUTOFF_EVALUE)));
    args.add(new LogarithmicParameter(
            MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
            MessageManager.getString("label.inclusion_seq_e_value_desc"),
            false, 1D, 1E-100, 10D));
    args.add(new LogarithmicParameter(
            MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
            MessageManager.getString("label.inclusion_dom_e_value_desc"),
            false, 1D, 1E-100, 10D));
    args.add(new DoubleParameter(
            MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
            MessageManager.getString("label.inclusion_seq_score_desc"),
            false, 0d, 0d, 1000d));
    args.add(new DoubleParameter(
            MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
            MessageManager.getString("label.inclusion_dom_score_desc"),
            false, 0d, 0d, 1000d));
  }

  /**
   * Constructs a choice parameter for database to search; always includes 'this
   * alignment', and also includes any databases held under user preferences key
   * "HMMSEARCH_DBS" as a comma-delimited list
   * 
   * @param args
   */
  protected void addChoiceOfDatabase(List<ArgumentI> args)
  {
    String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
    if (names == null || names.isEmpty())
    {
      return;
    }

    List<String> filePaths = new ArrayList<>();
    List<String> fileNames = new ArrayList<>();

    String thisAlignment = MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY);
    filePaths.add(thisAlignment);
    fileNames.add(thisAlignment);

    Scanner nameScanner = new Scanner(names);
    nameScanner.useDelimiter(Preferences.COMMA);

    while (nameScanner.hasNext())
    {
      String next = nameScanner.next();
      if ("null".equals(next))
      {
        Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
      }
      else
      {
        filePaths.add(next);
        int pos = next.lastIndexOf(File.separator);
        String fileName = next.substring(pos + 1);
        fileNames.add(fileName);
      }
    }
    nameScanner.close();
    ArgumentI databasesOption = new StringParameter(
            MessageManager.getString(HMMSearch.DATABASE_KEY),
            MessageManager.getString("label.database_for_hmmsearch"), true,
            thisAlignment,
            thisAlignment,
            filePaths, fileNames);
    args.add(databasesOption);
  }

  /**
   * Answers default parameters for hmmalign, taking into account any configured
   * as user preferences
   * 
   * @param args
   */
  private void getHMMAlignParams(List<ArgumentI> args)
  {
    addChoiceOfHmm(args);

    boolean def = Cache.getDefault(Preferences.HMMALIGN_TRIM_TERMINI,
            false);
    args.add(new BooleanOption(
            MessageManager.getString("label.trim_termini"),
            MessageManager.getString("label.trim_termini_desc"),
            false, false, def, null));
  }

  /**
   * Adds an argument representing the choice of HMM sequences (profiles)
   * against which to perform align or search, provided at least one is found
   * 
   * @param args
   */
  protected void addChoiceOfHmm(List<ArgumentI> args)
  {
    List<SequenceI> hmms = viewport.getAlignment().getHmmSequences();
    if (!hmms.isEmpty())
    {
      List<String> options = new ArrayList<>();
      for (SequenceI hmmSeq : hmms)
      {
        options.add(hmmSeq.getName());
      }
      String defseq = options.get(0);
      ArgumentI arg = new StringParameter(
              MessageManager.getString("label.use_hmm"), null, true, defseq,
              defseq, options, null);
      args.add(arg);
    }
  }

  /**
   * Adds an argument representing the choice of sequence against which to perform
   * jackhmmer
   * 
   * @param args
   */
  protected void addChoiceOfSequence(List<ArgumentI> args)
  {
    List<SequenceI> sequences = viewport.getAlignment().getSequences();

    List<String> options = new ArrayList<>();

    for (SequenceI seq : sequences)
    {
      options.add(seq.getName());
    }

    String defseq = options.get(0);
    ArgumentI arg = new StringParameter(
            MessageManager.getString("label.use_sequence"), null, true,
            defseq,
            defseq, options, null);
    args.add(arg);
  }

  /**
   * Answers default parameters for hmmbuild, taking into account any configured
   * as user preferences
   * 
   * @param args
   */
  private void getHMMBuildParams(List<ArgumentI> args)
  {
    /*
     * name to give the computed alignment HMM consensus sequence
     * (Jalview constructs group HMM consensus sequence names)
     */
    String defValue = "Alignment_HMM";
    StringParameter nameParam = new StringParameter(MessageManager.getString("label.hmm_name"),
            MessageManager.getString("label.hmm_name_desc"), true, defValue,
            defValue);
    args.add(nameParam);

    /*
     * only enable Use Reference Annotation if RF is present
     */
    if (viewport.hasReferenceAnnotation())
    {
      args.add(new BooleanOption(
              MessageManager.getString("label.use_reference"),
              MessageManager.getString("label.use_reference_desc"), true,
              true, true, null));
    }

    /*
     * choice of whether to compute HMM for alignment and/or group(s)
     * - only if there are any groups
     */
    if (!viewport.getAlignment().getGroups().isEmpty())
    {
      List<String> options = new ArrayList<>();
      options.add(MessageManager.getString("label.alignment"));
      options.add(MessageManager.getString("label.groups_and_alignment"));
      options.add(MessageManager.getString("label.groups"));
      options.add(MessageManager.getString("label.selected_group"));
      args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
              MessageManager.getString("label.hmmbuild_for_desc"), true,
              MessageManager.getString("label.alignment"),
              MessageManager.getString("label.alignment"), options, null));
    }
  }

  @Override
  public boolean presetExists(String forName)
  {
    return false;
  }

  @Override
  public void deletePreset(String forName)
  {
  }

  @Override
  public void storePreset(String presetName, String text,
          List<ArgumentI> jobParams)
  {
  }

  @Override
  public void updatePreset(String oldName, String presetName, String text,
          List<ArgumentI> jobParams)
  {
  }

  @Override
  public WsParamSetI parseServiceParameterFile(String forName,
          String description, String[] serviceURL, String parameters)
          throws IOException
  {
    return null;
  }

  @Override
  public String generateServiceParameterFile(WsParamSetI pset)
          throws IOException
  {
    return null;
  }

}