/**
 *  Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases
 *  Internet robot, InterPro, that uses form, located in page
 *  http://www.ebi.ac.uk/interpro/scan.html.
 *  It is your responsibility to find and cite appropriate references
 *  from this page.
 *  Generated 2002.5.18  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 InterPro 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.
   /** default=q@q.q */
   public String Emaddr="q@q.q"; // text
       /** 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://srs.ebi.ac.uk/srs6bin/cgi-bin/subiprscan"); // connect
    map.add("connect:action", "POST"); // connect
    map.add("connect:master", "http://www.ebi.ac.uk/interpro/scan.html"); // connect
    map.add("qstr", "goaway"); // hidden
    map.add("sequence", request.Sequence); // textarea
    map.add("runtype", "interactive"); // radio
    map.add("sndmail", "0"); // hidden
    map.add("emaddr", request.Emaddr); // 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

  /** Form URL to connect. http://srs.ebi.ac.uk/srs6bin/cgi-bin/subiprscan.*/
  public String getFormURL() {
     return "http://srs.ebi.ac.uk/srs6bin/cgi-bin/subiprscan"; }

  /** URL to refer. http://www.ebi.ac.uk/interpro/scan.html.*/
  public String getMasterURL() {
     return "http://www.ebi.ac.uk/interpro/scan.html"; }

    /** Type definitions for Request. */
   public dStructure getRequestDds() {
    return new Sight.dds.Records(false,
     new dField[] {
        new dField("Sequence","CharSequence",null,""),
        new dField("Emaddr","CharSequence",null,"q@q.q")                 }
    );
   }
 /* 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 Hit;
        public CharSequence Url;
      };
      /** 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 ""+" <a href=\""+r.Url+"\"> "+r.Hit+"</a>" ;
              case 1:  return ""+" <a href=\""+r.Url+"\"> "+r.Hit+"</a>" ;
              default: return ""+" :" +" <a href=\""+r.Url+"\"> "+r.Hit+"</a> ";
            }
          };
      }

    /** Type definitions for Result. */
   public dStructure getResultDds() {
    return new Sight.dds.Records(true,
     new dField[] {
        new dField("Hit",null,null,""),
        new dField("Url","URL","Hit url ","")                 }
    );
   }

  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.Hit=noHtml(fields[0]);
        r.Url=getURL(fields[0]);
        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 InterPro() { ignoreFirstLine=false;
   ignoreLastLine =false;
   table_position ="3.2.1";
   setDescription("Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases");
   // define pre scan section.
   preScan = new preScan();
   addRedirector(new RedirWaitLonger());
   };
  /** Public instance of agent for user. */
  public static InterPro Public = new InterPro();
  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();
         };
   };

   static class RedirWaitLonger extends Sight.Agents.Redirectors.RedirectionSystem implements RedirectionProvider, Cloneable
    {
       public Redirection getRedirection(String text)
        {
          Redirection R = super.getRedirection(text);
          if (R!=null)
           {
            if (R.waitFor<55) R.waitFor = 55;
            R.explain="Wait longer (55s). "+R.explain;
           };
          return R;
        };

       public RedirectionProvider getCopy()
        {
          return this;
        }
  }

}