package jalview.ws.rest.clientdefs;

import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
import jalview.ws.rest.InputType;
import jalview.ws.rest.RestClient;
import jalview.ws.rest.RestServiceDescription;
import jalview.ws.rest.params.Alignment;
import jalview.ws.rest.params.JobConstant;
import jalview.ws.rest.params.SeqGroupIndexVector;

import java.util.Hashtable;

public class ShmrRestClient
{

  public static RestClient makeShmmrRestClient()
  {
    String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
            .getString("label.multiharmony");
    Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
    jalview.ws.rest.params.JobConstant toolp;
    // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
    // iparams.put(toolp.token, toolp);
    // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
    // iparams.put(toolp.token, toolp);
    // toolp = new
    // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
    // iparams.put(toolp.token, toolp);
    // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
    // iparams.put(toolp.token, toolp);
    // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
    // iparams.put(toolp.token, toolp);
  
    jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
    // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
    // so we always upload our files.
    aliinput.token = "ali_file";
    aliinput.writeAsFile = true;
    iparams.put(aliinput.token, aliinput);
    jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
    sgroups.setMinsize(2);
    sgroups.min = 2;// need at least two group defined to make a partition
    iparams.put("groups", sgroups);
    sgroups.token = "groups";
    sgroups.sep = " ";
    RestServiceDescription shmrService = new RestServiceDescription(
            action,
            description,
            name,
            "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
            "?tool=jalview", iparams, true, false, '-');
    // a priori knowledge of the data returned from the service
    shmrService.addResultDatatype(JvDataType.ANNOTATION);
    return new RestClient(shmrService);
  }

}