X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FRNAalifoldWS.java;h=ed94c23cdc071f3617cf1910dd5f87bdc8a0b3e5;hb=68fe46f278b4ec408d6c68677bd56199aac749b3;hp=beca1dc1a6786e02a63b556d0c8cce60d6571f8d;hpb=191ed00f52901ed7ee6d1137637e66c999913be8;p=jabaws.git

diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index beca1dc..ed94c23 100644
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -9,47 +9,40 @@ import org.apache.log4j.Logger;
 import compbio.data.msa.JABAService;
 import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.RNAStructScoreManager;
 import compbio.engine.client.ConfiguredExecutable;
 import compbio.metadata.JobSubmissionException;
 import compbio.metadata.LimitExceededException;
 import compbio.metadata.Option;
 import compbio.metadata.Preset;
-import compbio.metadata.ResultNotAvailableException;
 import compbio.metadata.UnsupportedRuntimeException;
 import compbio.metadata.WrongParameterException;
 import compbio.runner.conservation.AACon;
 import compbio.runner.structure.RNAalifold;
 
 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")
-public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold> 
-		implements
-			SequenceAnnotation<RNAalifold> {
+public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold> implements SequenceAnnotation<RNAalifold> {
 
 	private static Logger log = Logger.getLogger(RNAalifoldWS.class);
 	
 	public RNAalifoldWS() {
 		super (new RNAalifold(), log);
 	}
-
-	
-	// for testing
-	@Override
-	public RNAStructScoreManager getAnnotation(String jobId) 
-			throws ResultNotAvailableException {
-		return WSUtil.getAnnotation(jobId, log);
-	}
 	
+	// Only purpose is to replace "analize" with "fold" method 
+	// so that a clustal input file and not fasta will be generated
+	@SuppressWarnings("unchecked")
 	@Override
 	public String analize(List<FastaSequence> sequences)
 			throws UnsupportedRuntimeException, LimitExceededException,
 			JobSubmissionException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);
-		return WSUtil.fold(sequences, confRNAalifold, log, "analize",
-				getLimit(""));
+		return WSUtil.fold(sequences, confRNAalifold, log, "analize", getLimit(""));
 	}
 
+	// Only purpose is to replace "analize" with "fold" method 
+	// so that a clustal input file and not fasta will be generated
+	@SuppressWarnings("unchecked")
 	@Override
 	public String customAnalize(List<FastaSequence> sequences,
 			List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,
@@ -57,12 +50,9 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 			WrongParameterException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);
-		
-		List<String> params = WSUtil.getCommands(options,
-				AACon.KEY_VALUE_SEPARATOR);
+		List<String> params = WSUtil.getCommands(options, RNAalifold.KEY_VALUE_SEPARATOR);
 		confRNAalifold.addParameters(params);
-		return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",
-				getLimit(""));
+		return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize", getLimit(""));
 	}
 	
 	
@@ -75,9 +65,6 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 			Preset<RNAalifold> preset) throws UnsupportedRuntimeException,
 			LimitExceededException, JobSubmissionException,
 			WrongParameterException {
-
 		return analize(sequences);
 	}
 }
-	
-