Main.java

package uk.co.flax.biosolr.pdbe.fasta;

import java.rmi.RemoteException;

import javax.xml.rpc.ServiceException;

import uk.ac.ebi.webservices.axis1.stubs.fasta.InputParameters;
import uk.ac.ebi.webservices.axis1.stubs.fasta.JDispatcherService_PortType;
import uk.ac.ebi.webservices.axis1.stubs.fasta.JDispatcherService_Service;
import uk.ac.ebi.webservices.axis1.stubs.fasta.JDispatcherService_ServiceLocator;

public class Main {

  private static final String EMAIL = "sameer@ebi.ac.uk";

  public static void main(String[] args) {
    if (args.length < 4) {
      System.err.println("Arguments: [sequence] [e value] [n scores] [n alignments]");
      return;
    }
    try {
      JDispatcherService_Service service = new JDispatcherService_ServiceLocator();
      JDispatcherService_PortType fasta = service.getJDispatcherServiceHttpPort();

      String sequence = args[0];
      double eVal = new Double(args[1]);
      int nScores = new Integer(args[2]);
      int nAlignments = new Integer(args[3]);

      InputParameters params = new InputParameters();
      params.setProgram("ssearch");
      params.setDatabase(new String[] { "pdb" });
      params.setStype("protein");
      params.setSequence(sequence);
      params.setExplowlim(0.0d);
      params.setExpupperlim(eVal);
      params.setScores(nScores);
      params.setAlignments(nAlignments);

      FastaJob job = new FastaJob(fasta, EMAIL, params);
      job.run();

      if (job.getException() != null) {
        System.err.println("Error during run()");
        job.getException().printStackTrace(System.err);
      }

      System.out.println(new String(job.getRawResults()));
    } catch (NumberFormatException e) {
      System.err.println("Cannot parse command line arguments");
      e.printStackTrace(System.err);
    } catch (ServiceException e) {
      System.err.println("Cannot create FASTA service");
      e.printStackTrace(System.err);
    } catch (RemoteException e) {
      System.err.println("Cannot retrieve FASTA results");
      e.printStackTrace(System.err);
    }
  }

}