/**
 *  New Genscan web server at MIT
 *  Internet robot, GenScan, that uses form, located in page
 *  http://genes.mit.edu/oldGENSCAN.html.
 *  It is your responsibility to find and cite appropriate references
 *  from this page.
 *  Generated 2002.6.25  by Sight 2.0, Ulm university.
 */
package impl.dna_analysers.geneScanners;

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

public class GenScan extends Sight.Agents.Prototypes.preformattedResponseAgent implements Serializable {
 /* Data structure to pass query to this robot. */
  public class Request extends Sight.Request implements java.io.Serializable {
   /** Choices for -o:
    * Vertebrate=Vertebrate default Arabidopsis=Arabidopsis Maize=Maize , default=Vertebrate. */
   public String _o="Vertebrate"; // select
     /** Choices for -e:
    * 1.00=1.00 default 0.50=0.50 0.25=0.25 0.10=0.10 0.05=0.05 0.02=0.02 0.01=0.01 , default=1.00. */
   public String _e="1.00"; // select
   /** default=Sight_200 */
   public String _n="Sight_200"; // text
   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://genes.mit.edu/cgi-bin/oldgenscanw.cgi"); // connect
    map.add("connect:action", "POST"); // connect
    map.add("connect:master", "http://genes.mit.edu/oldGENSCAN.html"); // connect
    map.add("-o", request._o); // select
    map.add("-e", request._e); // select
    map.add("-n", request._n); // text
    map.add("-p", "Predicted peptides only"); // select
    map.add("-s", request.Sequence); // textarea
    map.add("-a", ""); // text
    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("_o","CharSequence","Organism","Vertebrate",new String[] {"Vertebrate","Arabidopsis","Maize"},new String[] {"Vertebrate default","Arabidopsis","Maize"}),
        new dField("_e","CharSequence","Suboptimal exon cutoff ","1.00",new String[] {"1.00","0.50","0.25","0.10","0.05","0.02","0.01"},new String[] {"1.00 default","0.50","0.25","0.10","0.05","0.02","0.01"}),
        new dField("_n","CharSequence","Sequence name, will be placed in header","Sight_200"),
        new dField("Sequence","CharSequence","Sequence","")                 }
    );
   }
 /* 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 Header;
        public CharSequence Sequence;
      };
      /** 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.Header+" "+r.Sequence+" ";
              case 1:  return ""+r.Header+" "+r.Sequence+" ";
              default: return ""+" : "+r.Header+" "+" : "+r.Sequence+" ";
            }
          };
      }

    /** Type definitions for Result. */
   public dStructure getResultDds() {
    return new Sight.dds.Records(true,
     new dField[] {
        new dField("Header","CharSequence",null,""),
        new dField("Sequence","CharSequence",null,"")                 }
    );
   }

  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.Header=fields[0];
        r.Sequence=fields[1];
        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 GenScan() { signatures = new Sight.tools.xPlain.fastaSignatures();
   signatures.far_start=null;
   signatures.top="</STRONG><b>Predicted peptide sequence(s):\n</b>";
   signatures.bottom="<b>Explanation</b>";
   signatures.Columns = 2;
   setDescription("New Genscan web server at MIT");
   setFormURL("http://genes.mit.edu/cgi-bin/oldgenscanw.cgi");
   setMasterURL("http://genes.mit.edu/oldGENSCAN.html");
   // define pre scan section.
   preScan = new preScan();
   };
  /** Public instance of agent for user. */
  public static GenScan Public = new GenScan();
  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="";
        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();
         };
   }
;
  }