/**
 *  Prediction of mitochondrial targeting sequences
 *  Internet robot, Predotar, that uses form, located in page
 *  http://www.inra.fr/predotar/.
 *  It is your responsibility to find and cite appropriate references
 *  from this page.
 *  Generated 2002.5.27  by Sight 2.0, Ulm university.
 */
package impl.protein_analysers;

import Sight.Agents.*;
import Sight.Agents.Redirectors.*;
import Sight.Structures.*;
import Sight.dds.*;
import java.io.*;
import Sight.Agents.util.*;

public class Predotar extends Sight.Agents.Prototypes.tableBasedAgent implements Serializable {
 /* Data structure to pass query to this robot. */
  public class Request extends Sight.Request implements java.io.Serializable {
   public String Sequence; // required.
       /** Submit request, compute key by SHA digesting algorithm. */
       public Sight.Agents.Request submit() { return Sight.Agents.Request.submit(Public, this, getKey()); };
       /** Submit request with the known key. */
       public Sight.Agents.Request submit(String key)
        { return Sight.Agents.Request.submit(Public, this, key); };
       };

   /** Get the AMap data structure, required by post method. */
  protected AMap getFormParameters(Object req) {
    Request request = (Request) req;
    AMap map = new AMap();
    map.add("connect:url", "http://www.inra.fr/servlets/WebPredotar"); // connect
    map.add("connect:action", "post"); // connect
    map.add("connect:master", "http://www.inra.fr/predotar/"); // connect
    map.add("name", ""); // text
    map.add("sequence", request.Sequence); // textarea
    return map; };
  /** Get default request for this robot. */
  public static Request getDefaultRequest() {
     return Public.getRequest(); }
  private Request getRequest() { return new Request(); }; // must be non static

    /** Type definitions for Request. */
   public dStructure getRequestDds() {
    return new Sight.dds.Records(false,
     new dField[] {
        new dField("Sequence","CharSequence",null,"")                 }
    );
   }
 /* Record type, used in results for this robot. */
 /* The result of this robot is an array of records. */
  public static class Record extends Sight.Record implements Serializable {
        public CharSequence plastid;
        /** Plastid score */
        public CharSequence mitochondria;
        /** prediction */
        public CharSequence prediction;
      };
      /** The result of this robot. */
      public static class Result extends Sight.Result implements Serializable {
         public Record[] a; // array of results.
         /** Create report for one record. */
         public CharSequence getReportForRecord(Object ro, int level)
          { Record r = (Record) ro;
           switch (level) {
              case 0:  return ""+r.prediction+" ";
              case 1:  return ""+r.plastid+" "+r.mitochondria+" "+r.prediction+" ";
              default: return ""+" :" +r.plastid+" "+" Plastid score:" +r.mitochondria+" "+" prediction:" +r.prediction+" ";
            }
          };
      }

    /** Type definitions for Result. */
   public dStructure getResultDds() {
    return new Sight.dds.Records(true,
     new dField[] {
        new dField("plastid",null,null,""),
        new dField("mitochondria",null,"Plastid score",""),
        new dField("prediction",null,"prediction","")                 }
    );
   }

  public Sight.Record createRecord(String[] row) throws Exception
    { return fillRecord(row); };
  public Class getRecordClass() { return Record.class; };
   Record fillRecord(String[] fields) throws Exception {
        Record r = new Record();
        r.plastid=fields[1];
        r.mitochondria=fields[2];
        r.prediction=fields[3];
        return r;
   };

   /** Get result from the given html content. */
  public Sight.Result resultFromString(String html) throws Exception {
     Result r = new Result();
     r.a = (Record[]) createResultArray(html);
     return r;
   };
  public Predotar() { ignoreFirstLine=true;
   ignoreLastLine =false;
   table_position ="2";
   setDescription("Prediction of mitochondrial targeting sequences");
   setFormURL("http://www.inra.fr/servlets/WebPredotar");
   setMasterURL("http://www.inra.fr/predotar/");
   // define pre scan section.
   preScan = new preScan();
   };
  /** Public instance of agent for user. */
  public static Predotar Public = new Predotar();
  public static Agent getAvailableAgent() { return Public; };
  /** main(..) method provided to check robot, launching it
   * as standalone program. */
  public static void main(String[] args) {
  Sight.Agents.util.Pind.showConsoles();
      try {
        Request request = getDefaultRequest();
        // Now modify and assign request fields in accordance with task:
        request. Sequence="MPSSGRALLDSPLDSGSLTSLDSSVFCSEGEGEPLALGDCFTVNVGGSRFVLSQQALSCFPHTRLGKLAVVVASYRRPGALAAVPSPLELCDDANPVDNEYFFDRSSQAFRYVLHYYRTGRLHVMEQLCALSFLQEIQYWGIDELSIDSCCRDRYFRRKELSETLDFKKDTEDQESQHESEQDFSQGPCPTVRQKLWNILEKPGSSTAARIFGVISIIFVVVSIINMALMSAELSWLDLQLLEILEYVCISWFTGEFVLRFLCVRDRCRFLRKVPNIIDLLAILPFYITLLVESLSGSQTTQELENVGRIVQVLRLLRALRMLKLGRHSTGLRSLGMTITQCYEEVGLLLLFLSVGISIFSTVEYFAEQSIPDTTFTSVPCAWWWATTSMTTVGYGDIRPDTTTGKIVAFMCILSGILVLALPIAIINDRFSACYFTLKLKEAAVRQREALKKLTKNIATDSYISVNLRDVYARSIMEMLRLKGRERASTRSSGGDDFWF";
        Sight.Agents.Request submission = request.submit();
        // processing now started in separate thread:
        Result response = (Result) submission.getResult();
        // print report, verbosity level 2:
        System.out.println(response.getReport(2));
      } catch (Exception exc)
         { if (exc!=null) System.out.println(exc.getMessage());
           exc.printStackTrace();
         };
   }
;
  }