package jalview.hmmer;

import jalview.bin.Cache;
import jalview.gui.Preferences;
import jalview.util.MessageManager;
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.IntegerParameter;
import jalview.ws.params.simple.LogarithmicParameter;
import jalview.ws.params.simple.Option;
import jalview.ws.params.simple.StringParameter;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Scanner;

public class HMMERParamStore implements ParamDatastoreI
{

  String name;

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

  public HMMERParamStore(String name)
  {
    this.name = name;
  }

  @Override
  public List<WsParamSetI> getPresets()
  {
    // TODO Auto-generated method stub
    return presets;
  }

  @Override
  public WsParamSetI getPreset(String name)
  {
    // TODO Auto-generated method stub
    return null;
  }

  @Override
  public List<ArgumentI> getServiceParameters()
  {
    List<ArgumentI> args = new ArrayList<>();
    if ("hmmsearch".equals(name))
    {
      getHMMSearchParams(args);
    }
    if ("hmmalign".equals(name))
    {
      getHMMAlignParams(args);

    }
    if ("hmmbuild".equals(name))
    {
      getHMMBuildParams(args);

    }
    return args;
  }

  private void getHMMSearchParams(List<ArgumentI> args)
  {
    args.add(new IntegerParameter(
            MessageManager.getString("label.number_of_results"),
            MessageManager.getString("label.number_of_results_desc"), true,
            100, 0, 100000));
    String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
    if (names != null && !names.isEmpty())
    {
      Collection<String> databases = new ArrayList<>();
      databases.add(MessageManager.getString("label.this_alignment"));
      Scanner nameScanner = new Scanner(names);

      if (nameScanner.hasNext())
      {
        while (nameScanner.hasNext())
        {
          String next = nameScanner.next();
          if (next == "null")
          {
            Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
            Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
          }
          else
          {
            databases.add(next);
          }
        }
      }
      nameScanner.close();
      args.add(new Option(MessageManager.getString("label.database"),
              MessageManager.getString("label.database_for_hmmsearch"),
              true, MessageManager.getString("label.this_alignment"),
              MessageManager.getString("label.this_alignment"), databases,
              null));
    }
    args.add(new BooleanOption(
            MessageManager.getString("label.auto_align_seqs"),
            MessageManager.getString("label.auto_align_seqs_desc"), false,
            false, true, null));
    args.add(new BooleanOption(
            MessageManager.getString("label.use_accessions"),
            MessageManager.getString("label.use_accessions_desc"), false,
            false, true, null));
    args.add(new BooleanOption(
            MessageManager.getString("label.trim_termini"),
            MessageManager.getString("label.trim_termini_desc"), false,
            false, true, null));
    args.add(new LogarithmicParameter(
            MessageManager.getString("label.seq_e_value"),
            MessageManager.getString("label.seq_e_value_desc"), false, -3d,
            -37.92977945, 1d, 10d));
    /*
    args.add(new DoubleParameter(
            MessageManager.getString("label.seq_score"),
            MessageManager.getString("label.seq_score_desc"), false,
            0d, 0d, 10000d));
       */
    args.add(new LogarithmicParameter(
            MessageManager.getString("label.dom_e_value_desc"),
            MessageManager.getString("label.dom_e_value_desc"), false, -3d,
            -37.92977945, 1d, 10d));
    /*
    args.add(new DoubleParameter(
            MessageManager.getString("label.dom_score"),
            MessageManager.getString("label.dom_score_desc"), false, 0d,
            0d,
            10000d));
            */
  }

  private void getHMMAlignParams(List<ArgumentI> args)
  {
    args.add(new BooleanOption(
            MessageManager.getString("label.trim_termini"),
            MessageManager.getString(
                    "label.trim_termini = Trim Non-Matching Termini_desc"),
            false, false, true, null));
  }

  private void getHMMBuildParams(List<ArgumentI> args)
  {
    args.add(new StringParameter(MessageManager.getString("label.hmm_name"),
            MessageManager.getString("label.hmm_name_desc"), true, ""));
    args.add(new BooleanOption(
            MessageManager.getString("label.use_reference"),
            MessageManager.getString("label.use_reference_desc"), true,
            true, true, null));

    Collection<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 name)
  {
    // TODO Auto-generated method stub
    return false;
  }

  @Override
  public void deletePreset(String name)
  {
    // TODO Auto-generated method stub

  }

  @Override
  public void storePreset(String presetName, String text,
          List<ArgumentI> jobParams)
  {
    // TODO Auto-generated method stub

  }

  @Override
  public void updatePreset(String oldName, String presetName, String text,
          List<ArgumentI> jobParams)
  {
    // TODO Auto-generated method stub

  }

  @Override
  public WsParamSetI parseServiceParameterFile(String name,
          String description, String[] serviceURL, String parameters)
          throws IOException
  {
    // TODO Auto-generated method stub
    return null;
  }

  @Override
  public String generateServiceParameterFile(WsParamSetI pset)
          throws IOException
  {
    // TODO Auto-generated method stub
    return null;
  }

}