package jalview.ws2.client.ebi;

import jalview.ws.params.ArgumentI;
import jalview.ws.params.ParamDatastoreI;
import jalview.ws.params.ParamManager;
import jalview.ws.params.simple.*;
import jalview.ws2.params.SimpleParamDatastore;

import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

class ParamStores
{
  static final List<ArgumentI> phmmerParameters;

  /**
   * Set up phmmer parameters list.
   */
  static
  {
    var parameters = new ArrayList<ArgumentI>();
    URL baseURL;
    try
    {
      baseURL = new URL( "https://www.ebi.ac.uk/Tools/services/rest/hmmer3_phmmer/");
    } catch (MalformedURLException e)
    {
      throw new ExceptionInInitializerError(e);
    }
    {
      var builder = StringParameter.newBuilder();
      builder.setName("cut-offs");
      builder.setLabel("Cut-offs");
      builder.setDescription("Set the method of controlling which target sequences match your query.");
      builder.setRequired(true);
      builder.setValue("E");
      builder.setDefaultValue("E");
      builder.setPossibleValues(List.of("E", "T"));
      builder.setDisplayValues(List.of("E-values", "Bit scores"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("incE");
      builder.setLabel("Significance E-values[Sequence]");
      builder.setDescription("Significance E-values[Sequence]");
      builder.setRequired(false);
      builder.setValue(0.01);
      builder.setDefaultValue(0.01);
      builder.setMin(0.);
      builder.setMax(10.);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incE"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("incdomE");
      builder.setLabel("Significance E-values[Hit]");
      builder.setDescription("Significance E-values[Hit]");
      builder.setRequired(false);
      builder.setValue(0.03);
      builder.setDefaultValue(0.03);
      builder.setMin(0.);
      builder.setMax(10.);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incdomE"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("E");
      builder.setLabel("Report E-values[Sequence]");
      builder.setDescription("Report E-values[Sequence]");
      builder.setRequired(false);
      builder.setValue(1.0);
      builder.setDefaultValue(1.0);
      builder.setMin(0.);
      builder.setMax(10.);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/E"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("domE");
      builder.setLabel("Report E-values[Hit]");
      builder.setDescription("Report E-values[Hit]");
      builder.setRequired(false);
      builder.setValue(1.0);
      builder.setDefaultValue(1.0);
      builder.setMin(0.);
      builder.setMax(10.);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/domE"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("incT");
      builder.setLabel("Significance bit scores[Sequence]");
      builder.setDescription("Significance bit scores[Sequence]");
      builder.setRequired(false);
      builder.setValue(25.0);
      builder.setDefaultValue(25.0);
      builder.setMin(0.);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incT"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("incdomT");
      builder.setLabel("Significance bit scores[Hit]");
      builder.setDescription("Significance bit scores[Hit]");
      builder.setRequired(false);
      builder.setValue(22.0);
      builder.setDefaultValue(22.0);
      builder.setMin(0.);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incdomT"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("T");
      builder.setLabel("Report bit scores[Sequence]");
      builder.setDescription("Report bit scores[Sequence]");
      builder.setRequired(false);
      builder.setValue(7.0);
      builder.setDefaultValue(7.0);
      builder.setMin(0.);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/T"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("domT");
      builder.setLabel("Report bit scores[Hit]");
      builder.setDescription("Report bit scores[Hit]");
      builder.setRequired(false);
      builder.setValue(5.0);
      builder.setDefaultValue(5.0);
      builder.setMin(0.);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/domT"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("popen");
      builder.setLabel("Gap Penalties[open]");
      builder.setDescription("Gap Penalties[open]");
      builder.setRequired(false);
      builder.setValue(0.02);
      builder.setDefaultValue(0.02);
      builder.setMin(0.);
      builder.setMax(0.5);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/popen"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("pextend");
      builder.setLabel("Gap Penalties[extend]");
      builder.setDescription("Gap Penalties[extend]");
      builder.setRequired(false);
      builder.setValue(0.4);
      builder.setDefaultValue(0.4);
      builder.setMin(0.);
      builder.setMax(1.);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/pextend"));
      parameters.add(builder.build());
    }
    {
      var builder = StringParameter.newBuilder();
      builder.setName("mx");
      builder.setLabel("Gap Penalties[Substitution scoring matrix]");
      builder.setDescription("Gap Penalties[Substitution scoring matrix]");
      builder.setRequired(false);
      builder.setValue("BLOSUM62");
      builder.setDefaultValue("BLOSUM62");
      builder.setPossibleValues(List.of("BLOSUM45", "BLOSUM62", "BLOSUM90", "PAM30", "PAM70"));
      builder.setDisplayValues(List.of("BLOSUM45", "BLOSUM62", "BLOSUM90", "PAM30", "PAM70"));
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/mx"));
      parameters.add(builder.build());
    }
    {
      var builder = BooleanOption.newBuilder();
      builder.setName("nobias");
      builder.setLabel("No bias filter");
      builder.setDescription(
              "The '--nobias' option turns off (bypasses) the biased composition filter which is on by default.");
      builder.setRequired(false);
      builder.setValue(false);
      builder.setDefaultValue(false);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/nobias"));
      parameters.add(builder.build());
    }
    {
      var builder = BooleanOption.newBuilder();
      builder.setName("compressedout");
      builder.setLabel("Compressed Output");
      builder.setDescription(
              "By default it runs hmm2c plus post-processing (default output), whereas with compressedout, it gets compressed output only.");
      builder.setRequired(false);
      builder.setValue(false);
      builder.setDefaultValue(false);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/compressedout"));
      parameters.add(builder.build());
    }
    {
      var builder = BooleanOption.newBuilder();
      builder.setName("alignView");
      builder.setLabel("Output Alignment");
      builder.setDescription("Output alignment in result");
      builder.setRequired(false);
      builder.setValue(true);
      builder.setDefaultValue(true);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/alignView"));
      parameters.add(builder.build());
    }
    {
      var builder = StringParameter.newBuilder();
      builder.setName("database");
      builder.setLabel("Sequence Database");
      builder.setDescription("Sequence Database Selection");
      builder.setRequired(true);
      builder.setValue("uniprotkb");
      builder.setDefaultValue("uniprotkb");
      builder.setPossibleValues(List.of("swissprot", "uniprotrefprot", "uniprotkb", "pdb", "rp75", "rp55", "rp35", "rp15", "ensembl", "merops", "qfo", "chembl"));
      builder.setDisplayValues(List.of("SwissProt", "Reference Proteomes", "UniProtKB", "PDB", "rp75", "rp55", "rp35", "rp15", "Ensembl", "MEROPS", "Quest for Orthologs", "ChEMBL"));
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/database"));
      parameters.add(builder.build());
    }
    {
      var builder = DoubleParameter.newBuilder();
      builder.setName("evalue");
      builder.setLabel("Expectation Value Threshold");
      builder.setDescription(
              "Expectation value cut-off for reporting target profiles in the per-target output.");
      builder.setRequired(false);
      builder.setValue(0.01);
      builder.setDefaultValue(0.01);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/evalue"));
      parameters.add(builder.build());
    }
//    {
//      var builder = StringParameter.newBuilder();
//      builder.setName("sequence");
//      builder.setLabel("Input Sequence");
//      builder.setDescription(
//              "The input sequence can be entered directly into this form. The sequence can be be in FASTA or UniProtKB/Swiss-Prot format. A partially formatted sequence is not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.");
//      builder.setRequired(false);
//
//      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/sequence"));
//      parameters.add(builder.build());
//    }
    {
      var builder = IntegerParameter.newBuilder();
      builder.setName("nhits");
      builder.setLabel("Number of Hits Displayed");
      builder.setDescription("Number of hits to be displayed.");
      builder.setRequired(false);
      builder.setValue(100);
      builder.setDefaultValue(100);
      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/nhits"));
      parameters.add(builder.build());
    }
    phmmerParameters = Collections.unmodifiableList(parameters);
  }

  private static URL resolveURL(URL base, String spec)
  {
    try
    {
      return new URL(base, spec);
    } catch (MalformedURLException e)
    {
      throw new ExceptionInInitializerError(e);
    }
  }
  
  public static ParamDatastoreI newPhmmerDatastore(URL url, ParamManager manager)
  {
    return new SimpleParamDatastore(url, phmmerParameters,
            Collections.emptyList(), manager);
  }
}