package org.bioxsd.workflows;




import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.rmi.RemoteException;

import org.apache.axis2.AxisFault;
import org.apache.xmlbeans.XmlException;

import org.bioxsd.bioxsd_0_4.AnnotatedSequence;
import org.bioxsd.bioxsd_0_4.AminoacidSequenceRecord;
import org.bioxsd.bioxsd_0_4.GeneralAminoacidSequenceRecord;
import org.bioxsd.bioxsd_0_4.BiosequenceRecord;
import org.bioxsd.bioxsd_0_4.SequenceReference;

import fr.ibcp.gbio.clustalw.CancelClustalwDocument;
import fr.ibcp.gbio.clustalw.CheckStatusClustalwDocument;
import fr.ibcp.gbio.clustalw.ClustalWStub;
import fr.ibcp.gbio.clustalw.GetResultsClustalwDocument;
import fr.ibcp.gbio.clustalw.GetResultsClustalwResponseDocument;
import fr.ibcp.gbio.clustalw.SubmitClustalwDocument;
import fr.ibcp.gbio.goriv.CancelGorIVDocument;
import fr.ibcp.gbio.goriv.CheckStatusGorIVDocument;
import fr.ibcp.gbio.goriv.GetResultsGorIVDocument;
import fr.ibcp.gbio.goriv.GorIVStub;
import fr.ibcp.gbio.goriv.SubmitGorIVDocument;
import no.uni.bccs.esysbio.schema.blastparameterschema.MatrixType;
import no.uni.bccs.www.service.blast.BlastServiceStub;
import no.uni.bccs.www.service.blast.BlastJobServiceStub;
import no.uni.bccs.www.service.blast.BlastDbServiceStub;
import no.uni.bccs.www.service.blast.GetResultDocument;
import no.uni.bccs.www.service.blast.GetResultFaultException0;
import no.uni.bccs.www.service.blast.GetResultResponseDocument;
import no.uni.bccs.www.service.blast.GetSequencesDocument;
import no.uni.bccs.www.service.blast.GetSequencesFaultException0;
import no.uni.bccs.www.service.blast.GetStatusDocument;
import no.uni.bccs.www.service.blast.GetStatusFaultException2;
import no.uni.bccs.www.service.blast.RunBlastpDocument;
import no.uni.bccs.www.service.blast.RunBlastpFaultException3;
import dk.dtu.cbs.www.ws.ws_common.Jobstatus.Enum;
import dk.dtu.cbs.www.ws.ws_common.PollQueue.Job;
import dk.dtu.cbs.www.ws.wsmaxalign_1_1_ws1.MaxalignDocument;
import dk.dtu.cbs.www.ws.wsmaxalign_1_1_ws1.MaxalignResponseDocument;
import dk.dtu.cbs.www.ws.wsmaxalign_1_1_ws1.WSMaxAlign_1_1_ws1Stub;
import dk.dtu.cbs.www.ws.wsprop_1_0_ws0.WSProP_1_0_ws0Stub;
import dk.dtu.cbs.www.ws.wsnetnes_1_1_ws0.WSNetNES_1_1_ws0Stub;




public class WorkflowNr1
{

	public class ResultException extends Exception
	{
		private static final long serialVersionUID = -5651350712038788788L;
		public String service, detail;
		public ResultException(String service, String detail)
		{
			this.service = service;
			this.detail = detail;
		}
	}//ResultException

	public class JobException extends Exception
	{
		private static final long serialVersionUID = 6981789948985964011L;
	}//JobException


	public static void main(String[] args)
	{
		PrintStream out = null;

		try
		{

		// Read input sequence record & output target
			String in = "<xml-fragment xmlns:bx=\"http://bioxsd.org/BioXSD-0.4\"><bx:sequence>MSSSGTPDLPVLLTDLKIQYTKIFINNEWHDSVSGKKFPVFNPATEEELCQVEEGDKEDVDKAVKAARQAFQIGSPWRTMDASERGRLLYKLADLIERDRLLLATMESMNGGKLYSNAYLNDLAGCIKTLRYCAGWADKIQGRTIPIDGNFFTYTRHEPIGVCGQIIPWNFPLVMLIWKIGPALSCGNTVVVKPAEQTPLTALHVASLIKEAGFPPGVVNIVPGYGPTAGAAISSHMDIDKVAFTGSTEVGKLIKEAAGKSNLKRVTLELGGKSPCIVLADADLDNAVEFAHHGVFYHQGQCCIAASRIFVEESIYDEFVRRSVERAKKYILGNPLTPGVTQGPQIDKEQYDKILDLIESGKKEGAKLECGGGPWGNKGYFVQPTVFSNVTDEMRIAKEEIFGPVQQIMKFKSLDDVIKRANNTFYGLSAGVFTKDIDKAITISSALQAGTVW</bx:sequence><bx:formalReference><bx:accession>XP_001143065</bx:accession></bx:formalReference></xml-fragment>";
			AminoacidSequenceRecord mySeq = AminoacidSequenceRecord.Factory.parse(args.length == 0 ? in : args[0]);
			String outName = args.length < 2 ? "out" + /*System.currentTimeMillis() +*/ ".xml" : args[1];
			System.out.println("Input sequence record:\n" + mySeq + "\n\nOutput file: " + outName + "\n\nWorkflow started");
			out = new PrintStream(outName);
			out.println("<workflowNr1>\n<input>\n" + mySeq + "\n</input>\n\n<!--==============================================================================================-->\n\n");

		// Submit CBU BLAST and get result
			BlastServiceStub blast1a = new BlastServiceStub();
			blast1a._getServiceClient().getOptions().setProperty(org.apache.axis2.transport.http.HTTPConstants.HTTP_PROTOCOL_VERSION, org.apache.axis2.transport.http.HTTPConstants.HEADER_PROTOCOL_10);
			RunBlastpDocument blast1In = RunBlastpDocument.Factory.newInstance();
			blast1In.addNewRunBlastp().addNewQuerySequence();
			blast1In.getRunBlastp().setQuerySequenceArray(0, mySeq);
			blast1In.getRunBlastp().setDatabaseURI("Swiss-Prot");
			blast1In.getRunBlastp().setAlignmentNumber(5);
			blast1In.getRunBlastp().setExpectValue(10);
			blast1In.getRunBlastp().setWordSize(0);
			blast1In.getRunBlastp().setMatrix(MatrixType.Factory.newInstance().BLOSUM_62);
			blast1In.getRunBlastp().setGapOpenPenalty(-1);
			blast1In.getRunBlastp().setGapExtensionPenalty(-1);
			String jobId = blast1a.RunBlastp(blast1In).getRunBlastpResponse().getJobId();
			System.out.println("\nBLAST submitted. Job id: " + jobId);
			BlastJobServiceStub blast1b = new BlastJobServiceStub();
			GetStatusDocument blast1Job = GetStatusDocument.Factory.newInstance();
			blast1Job.addNewGetStatus().setJobId(jobId);
			long t0 = System.currentTimeMillis(), t1, t = t0, wait = 2000, limit = 120000;
			String status;
			while (!(status = blast1b.GetStatus(blast1Job).getGetStatusResponse().getStatus()).equalsIgnoreCase("COMPLETE"))
			{
				System.out.println("BLAST status: " + status);
				if (t - t0 > limit)
				{
					System.out.println("WARNING: BLAST@CBU JOB IS TAKING TOO LONG [Status = \"" + status + "\"] ABORTED");
					throw (new WorkflowNr1()).new JobException();
				}//fi
				if (status.equalsIgnoreCase("INQUEUE") || status.equalsIgnoreCase("INPROGRESS"))
				{
					t1 = System.currentTimeMillis();
					while (t - t1 < wait)
						t = System.currentTimeMillis();
				}
				else // Abort in other cases
				{
					System.out.println("WARNING: BLAST@CBU JOB ABORTED [Status = \"" + status + "\"]");
					throw (new WorkflowNr1()).new JobException();
				}//fi(else)
			}//while
			System.out.println("BLAST finished. Status: " + status);
			GetResultDocument blast1JobRes = GetResultDocument.Factory.newInstance();
			blast1JobRes.addNewGetResult().setJobId(jobId);
			GetResultResponseDocument blast1Out = blast1b.GetResult(blast1JobRes);
			if (blast1Out.getGetResultResponse().getBlastOutput().getBlastOutputIterations().getIterationArray().length == 0)
				throw (new WorkflowNr1()).new ResultException("BLAST@CBU", "NO ITERATIONS");
			int n = blast1Out.getGetResultResponse().getBlastOutput().getBlastOutputIterations().getIterationArray(0).getIterationHits().sizeOfHitArray();
			if (n == 0)
				throw (new WorkflowNr1()).new ResultException("BLAST@CBU", "NO HITS");
			String[] ids = new String[n];
			for (int i = 0; i < n; i++)
				ids[i] = blast1Out.getGetResultResponse().getBlastOutput().getBlastOutputIterations().getIterationArray(0).getIterationHits().getHitArray(i).getHitId();
			BlastDbServiceStub blast1c = new BlastDbServiceStub();
			GetSequencesDocument idsIn = GetSequencesDocument.Factory.newInstance();
			idsIn.addNewGetSequences().setSequenceIdentifierArray(ids);
			idsIn.getGetSequences().setDatabaseURI("Swiss-Prot");
			BiosequenceRecord[] similarSeqs = blast1c.GetSequences(idsIn).getGetSequencesResponse().getSequenceArray();

		// Submit ClustalW and get result
			ClustalWStub clustalw = new ClustalWStub();
			SubmitClustalwDocument clustalwIn = SubmitClustalwDocument.Factory.newInstance();
			clustalwIn.addNewSubmitClustalw().addNewSequenceRecord();
			clustalwIn.getSubmitClustalw().setSequenceRecordArray(0, mySeq);
			if (!clustalwIn.getSubmitClustalw().getSequenceRecordArray(0).isSetCustomName())
				clustalwIn.getSubmitClustalw().getSequenceRecordArray(0).setCustomName("My sequence");
			for (int i = 0; (i < n); i++)
			{
				clustalwIn.getSubmitClustalw().addNewSequenceRecord();
				clustalwIn.getSubmitClustalw().setSequenceRecordArray(i + 1, similarSeqs[i]);
				if (!clustalwIn.getSubmitClustalw().getSequenceRecordArray(i + 1).isSetCustomName())
					clustalwIn.getSubmitClustalw().getSequenceRecordArray(i + 1).setCustomName("Similar sequence " + (i + 1));
			}//for
			jobId = clustalw.submitClustalw(clustalwIn).getSubmitClustalwResponse().getJobId();
			System.out.println("\nClustalW submitted. Job id: " + jobId);
			CheckStatusClustalwDocument clustalwJob = CheckStatusClustalwDocument.Factory.newInstance();
			clustalwJob.addNewCheckStatusClustalw().setJobId(jobId);
			t0 = System.currentTimeMillis();
			wait = 3000;
			limit = 60000;
			while (!(status = clustalw.checkStatusClustalw(clustalwJob).getCheckStatusClustalwResponse().getStatus()).equalsIgnoreCase("done"))
			{
				System.out.println("ClustalW status: " + status);
				if (t - t0 > limit)
				{
					System.out.println("WARNING: ClustalW JOB IS TAKING TOO LONG [Status = \"" + status + "\"] ABORTED");
					CancelClustalwDocument cancelJob = CancelClustalwDocument.Factory.newInstance();
					cancelJob.addNewCancelClustalw().setJobId(jobId);
					clustalw.cancelClustalw(cancelJob);
					throw (new WorkflowNr1()).new JobException();
				}//fi
				if (status.equalsIgnoreCase("running") || status.equalsIgnoreCase("waiting"))
				{
					t1 = System.currentTimeMillis();
					while (t - t1 < wait)
						t = System.currentTimeMillis();
				}
				else // Abort in other cases
				{
					System.out.println("WARNING: ClustalW JOB ABORTED [Status = \"" + status + "\"]");
					throw (new WorkflowNr1()).new JobException();
				}//fi(else)
			}//while
			System.out.println("ClustalW finished. Status: " + status);
			GetResultsClustalwDocument clustalwJobRes = GetResultsClustalwDocument.Factory.newInstance();
			clustalwJobRes.addNewGetResultsClustalw().setJobId(jobId);
			GetResultsClustalwResponseDocument clustalwOut = clustalw.getResultsClustalw(clustalwJobRes);
			n = clustalwOut.getGetResultsClustalwResponse().getAlignment().sizeOfAlignedSequenceArray();
			for (int i = 0; (i < n); i++)
				if (!clustalwOut.getGetResultsClustalwResponse().getAlignment().getAlignedSequenceArray(i).getSequenceRecord().isSetFormalReference() || !clustalwOut.getGetResultsClustalwResponse().getAlignment().getAlignedSequenceArray(i).getSequenceRecord().getFormalReference().isSetAccession())
				{
					SequenceReference r;
					if (clustalwOut.getGetResultsClustalwResponse().getAlignment().getAlignedSequenceArray(i).getSequenceRecord().isSetFormalReference())
						r = clustalwOut.getGetResultsClustalwResponse().getAlignment().getAlignedSequenceArray(i).getSequenceRecord().getFormalReference();
					else
						r = SequenceReference.Factory.newInstance();
					String nm = clustalwOut.getGetResultsClustalwResponse().getAlignment().getAlignedSequenceArray(i).getSequenceRecord().getCustomName();
					String ac = "";
					for (int j = 0; j < nm.length(); j++)
						ac = ac.concat(nm.charAt(j) == ' ' ? "" : nm.substring(j, j + 1)); 
					r.setAccession(ac);
					clustalwOut.getGetResultsClustalwResponse().getAlignment().getAlignedSequenceArray(i).getSequenceRecord().setFormalReference(r);
				}//fi
			//for

		// Call MaxAlign and prepare inputs for feature predictions
			WSMaxAlign_1_1_ws1Stub maxalign = new WSMaxAlign_1_1_ws1Stub();
			MaxalignDocument maxalignIn = MaxalignDocument.Factory.newInstance();
			maxalignIn.addNewMaxalign().addNewParameters().addNewOriginalAlignment();
			maxalignIn.getMaxalign().getParameters().setOriginalAlignment(clustalwOut.getGetResultsClustalwResponse().getAlignment());
			MaxalignResponseDocument maxalignOut = maxalign.maxalign(maxalignIn);
			System.out.println("\nMaxAlign finished");
			n = maxalignOut.getMaxalignResponse().getResultAlignment().sizeOfAlignedSequenceArray();
			GeneralAminoacidSequenceRecord[] seq = new GeneralAminoacidSequenceRecord[n];
			dk.dtu.cbs.www.ws.wsprop_1_0_ws0.RunServiceDocument propIn = dk.dtu.cbs.www.ws.wsprop_1_0_ws0.RunServiceDocument.Factory.newInstance();
			propIn.addNewRunService().addNewParameters();
			dk.dtu.cbs.www.ws.wsnetnes_1_1_ws0.RunServiceDocument netnesIn = dk.dtu.cbs.www.ws.wsnetnes_1_1_ws0.RunServiceDocument.Factory.newInstance();
			netnesIn.addNewRunService().addNewParameters();
			for (int i = 0; i < n; i++)
			{
				seq[i] = GeneralAminoacidSequenceRecord.Factory.parse(maxalignOut.getMaxalignResponse().getResultAlignment().getAlignedSequenceArray(i).getSequenceRecord().toString());
				propIn.getRunService().getParameters().addNewSequenceRecord();
				propIn.getRunService().getParameters().setSequenceRecordArray(i, seq[i]);
				netnesIn.getRunService().getParameters().addNewSequenceRecord();
				netnesIn.getRunService().getParameters().setSequenceRecordArray(i, seq[i]);
			}//for

		// Submit ProP
			WSProP_1_0_ws0Stub prop = new WSProP_1_0_ws0Stub();
			String propJobId = prop.runService(propIn).getRunServiceResponse().getQueueentry().getJobid();
			System.out.println("\nProP submitted. Job id: " + propJobId);

		// Submit NetNES
			WSNetNES_1_1_ws0Stub netnes = new WSNetNES_1_1_ws0Stub();
			String netnesJobId = netnes.runService(netnesIn).getRunServiceResponse().getQueueentry().getJobid();
			System.out.println("NetNES submitted. Job id: " + netnesJobId);

		// Submit GorIV
			GorIVStub gor4 = new GorIVStub();
			String[] gorJobId = new String[n];
			for (int i = 0; i < n; i++)
			{
				SubmitGorIVDocument gor4In = SubmitGorIVDocument.Factory.newInstance();
				gor4In.setSubmitGorIV(seq[i]);
				gorJobId[i] = gor4.submitGorIV(gor4In).getSubmitGorIVResponse().getJobId();
				System.out.println("GorIV(" + i + ") submitted. Job id: " + gorJobId[i]);
				t0 = System.currentTimeMillis();
				wait = 1000;
				while (t - t0 < wait)
					t = System.currentTimeMillis();
			}//for

		// Get results ProP
			dk.dtu.cbs.www.ws.wsprop_1_0_ws0.PollQueueDocument propJob = dk.dtu.cbs.www.ws.wsprop_1_0_ws0.PollQueueDocument.Factory.newInstance();
			Job insideJob = Job.Factory.newInstance();
			insideJob.setJobid(propJobId);
			propJob.addNewPollQueue().setJob(insideJob);
			t0 = System.currentTimeMillis();
			wait = 1500;
			limit = 30000;
			Enum enumStatus;
			while (!(enumStatus = prop.pollQueue(propJob).getPollQueueResponse().getQueueentry().getStatus()).toString().equalsIgnoreCase("FINISHED"))
			{
				System.out.println("ProP status: " + enumStatus);
				if (t - t0 > limit)
				{
					System.out.println("WARNING: ProP JOB IS TAKING TOO LONG [Status = \"" + enumStatus + "\"] ABORTED");
					throw (new WorkflowNr1()).new JobException();
				}//fi
				if (enumStatus.toString().equalsIgnoreCase("QUEUED") || enumStatus.toString().equalsIgnoreCase("PENDING") || enumStatus.toString().equalsIgnoreCase("ACTIVE") || enumStatus.toString().equalsIgnoreCase("WAITING"))
				{
					t1 = System.currentTimeMillis();
					while (t - t1 < wait)
						t = System.currentTimeMillis();
				}
				else // Abort in other cases: "UNKNOWN JOBID", "REJECTED", "QUEUE DOWN", "DATABASE DOWN", "FAILED"
				{
					System.out.println("WARNING: ProP JOB ABORTED [Status = \"" + enumStatus + "\"]");
					throw (new WorkflowNr1()).new JobException();
				}//fi(else)
			}//while
			System.out.println("ProP finished. Status: " + enumStatus);
			dk.dtu.cbs.www.ws.wsprop_1_0_ws0.FetchResultDocument propJobRes = dk.dtu.cbs.www.ws.wsprop_1_0_ws0.FetchResultDocument.Factory.newInstance();
			propJobRes.addNewFetchResult().addNewJob().setJobid(propJobId);
			AnnotatedSequence[] propResult = prop.fetchResult(propJobRes).getFetchResultResponse().getAnnotatedSequenceArray();

		// Get results NetNES
			dk.dtu.cbs.www.ws.wsnetnes_1_1_ws0.PollQueueDocument netnesJob = dk.dtu.cbs.www.ws.wsnetnes_1_1_ws0.PollQueueDocument.Factory.newInstance();
			insideJob.setJobid(netnesJobId);
			netnesJob.addNewPollQueue().setJob(insideJob);
			t0 = System.currentTimeMillis();
			t = t0;
			wait = 1500;
			limit = 20000;
			while (!(enumStatus = netnes.pollQueue(netnesJob).getPollQueueResponse().getQueueentry().getStatus()).toString().equalsIgnoreCase("FINISHED"))
			{
				System.out.println("NetNES status: " + enumStatus);
				if (t - t0 > limit)
				{
					System.out.println("WARNING: NetNES JOB IS TAKING TOO LONG [Status = \"" + enumStatus + "\"] ABORTED");
					throw (new WorkflowNr1()).new JobException();
				}//fi
				if (enumStatus.toString().equalsIgnoreCase("QUEUED") || enumStatus.toString().equalsIgnoreCase("PENDING") || enumStatus.toString().equalsIgnoreCase("ACTIVE") || enumStatus.toString().equalsIgnoreCase("WAITING"))
				{
					t1 = System.currentTimeMillis();
					while (t - t1 < wait)
						t = System.currentTimeMillis();
				}
				else // Abort in other cases: "UNKNOWN JOBID", "REJECTED", "QUEUE DOWN", "DATABASE DOWN", "FAILED"
				{
					System.out.println("WARNING: NetNES JOB ABORTED [Status = \"" + enumStatus + "\"]");
					throw (new WorkflowNr1()).new JobException();
				}//fi(else)
			}//while
			System.out.println("NetNES finished. Status: " + enumStatus);
			dk.dtu.cbs.www.ws.wsnetnes_1_1_ws0.FetchResultDocument netnesJobRes = dk.dtu.cbs.www.ws.wsnetnes_1_1_ws0.FetchResultDocument.Factory.newInstance();
			netnesJobRes.addNewFetchResult().addNewJob().setJobid(netnesJobId);
			AnnotatedSequence[] netnesResult = netnes.fetchResult(netnesJobRes).getFetchResultResponse().getAnnotatedSequenceArray();

		// Get results GorIV and merge with other predictions
			AnnotatedSequence[] result = new AnnotatedSequence[n];
			for (int i = 0; i < n; i++)
			{
				CheckStatusGorIVDocument gor4Job = CheckStatusGorIVDocument.Factory.newInstance();
				gor4Job.addNewCheckStatusGorIV().setJobId(gorJobId[i]);
				t0 = System.currentTimeMillis();
				wait = 2000;
				limit = 30000;
				while (!(status = gor4.checkStatusGorIV(gor4Job).getCheckStatusGorIVResponse().getStatus()).equalsIgnoreCase("done"))
				{
					System.out.println("GorIV(" + i + ") status: " + status);
					if (t - t0 > limit)
					{
						System.out.println("WARNING: GorIV(" + i + ") JOB IS TAKING TOO LONG [Status = \"" + status + "\"] ABORTED");
						CancelGorIVDocument cancelJob = CancelGorIVDocument.Factory.newInstance();
						cancelJob.addNewCancelGorIV().setJobId(gorJobId[i]);
						gor4.cancelGorIV(cancelJob);
						throw (new WorkflowNr1()).new JobException();
					}//fi
					if (status.equalsIgnoreCase("running") || status.equalsIgnoreCase("waiting"))
					{
						t1 = System.currentTimeMillis();
						while (t - t1 < wait)
							t = System.currentTimeMillis();
					}
					else // Abort in other cases
					{
						System.out.println("WARNING: GorIV(" + i + ") JOB ABORTED [Status = \"" + status + "\"]");
						throw (new WorkflowNr1()).new JobException();
					}//fi(else)
				}//while
				System.out.println("GorIV(" + i + ") finished. Status: " + status);
				GetResultsGorIVDocument gor4JobRes = GetResultsGorIVDocument.Factory.newInstance();
				gor4JobRes.addNewGetResultsGorIV().setJobId(gorJobId[i]);
				AnnotatedSequence goriResult = gor4.getResultsGorIV(gor4JobRes).getGetResultsGorIVResponse().getSecondaryStructure();
				int propiAnnsM = propResult[i].sizeOfAnnotationArray();
				int nesiAnnsM = netnesResult[i].sizeOfAnnotationArray();
				int goriAnnsM = goriResult.sizeOfAnnotationArray();
				result[i] = propResult[i];
				for (int j = 0; j < nesiAnnsM; j++)
				{
					result[i].addNewAnnotation();
					result[i].setAnnotationArray(j + propiAnnsM, netnesResult[i].getAnnotationArray(j));
				}//for
				for (int j = 0; j < goriAnnsM; j++)
				{
					result[i].addNewAnnotation();
					result[i].setAnnotationArray(j + propiAnnsM + nesiAnnsM, goriResult.getAnnotationArray(j));
				}//for
				int j = -1;
				if (propResult[i].sizeOfMethodArray() > 0)
				{
					result[i].addNewMethod();
					j++;
					result[i].setMethodArray(j, propResult[i].getMethodArray(0));
				}//fi
				if (netnesResult[i].sizeOfMethodArray() > 0)
				{
					result[i].addNewMethod();
					j++;
					result[i].setMethodArray(j, netnesResult[i].getMethodArray(0));
				}//fi
				if (goriResult.sizeOfMethodArray() > 0)
				{
					result[i].addNewMethod();
					j++;
					result[i].setMethodArray(j, goriResult.getMethodArray(0));
				}//fi
				out.println("\n<annotation sequenceNr=\"" + i + "\">\n" + result[i] + "\n</annotation>\n");
			}//for
			out.println("\n<alignment>\n" + maxalignOut + "\n</alignment>\n</workflowNr1>");
			System.out.println("\nWorkflow completed. Output in \"" + outName + "\"");


		}//try
		catch (FileNotFoundException e)
		{
			System.out.println("-=Workflow1: FileNotFoundException=-");
			e.printStackTrace();
		}
		catch (XmlException e)
		{
			System.out.println("-=Workflow1: XMLException=-");
			e.printStackTrace();
		}//catch
		catch (AxisFault e)
		{
			System.out.println("-=Workflow1: AxisFault=-");
			e.printStackTrace();
		}//catch
		catch (RemoteException e)
		{
			System.out.println("-=Workflow1: RemoteException=-");
			e.printStackTrace();
		}//catch
		catch (JobException e)
		{
			System.out.println("-=Workflow1: JobException=-");
		}//catch
		catch (ResultException e)
		{
			System.out.println(e.service + ": EMPTY OR INVALID RESULT [" + e.detail + "]\n");
		}//catch
		catch (RunBlastpFaultException3 e)
		{
			System.out.println("-=BLAST@CBU: RunBlastp Fault=-");
			e.printStackTrace();
		}//catch
		catch (GetStatusFaultException2 e)
		{
			System.out.println("-=BLAST@CBU: GetStatus Fault=-");
			e.printStackTrace();
		}//catch
		catch (GetResultFaultException0 e)
		{
			System.out.println("-=BLAST@CBU: GetResult Fault=-");
			e.printStackTrace();
		}//catch
		catch (GetSequencesFaultException0 e)
		{
			System.out.println("-=BLAST@CBU: GetSequences Fault=-");
			e.printStackTrace();
		}//catch

		
		if (out != null)
			out.close();

	}//main

}//Workflow1