X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FRNAalifoldWS.java;h=ed94c23cdc071f3617cf1910dd5f87bdc8a0b3e5;hb=184bf3dce9500c599b5257140ec49edd80f8cea1;hp=a6ed826f25dc1b1562032cfd113a5f9f2fb6f8e7;hpb=778c188406bfee47be3cdc76fb95a36bbb8ea737;p=jabaws.git

diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index a6ed826..ed94c23 100644
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -14,23 +14,48 @@ 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);
 	}
+	
+	// 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(""));
+	}
 
+	// 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,
+			LimitExceededException, JobSubmissionException,
+			WrongParameterException {
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);
+		List<String> params = WSUtil.getCommands(options, RNAalifold.KEY_VALUE_SEPARATOR);
+		confRNAalifold.addParameters(params);
+		return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize", getLimit(""));
+	}
+	
+	
 	/*
 	 * No presets are supported, thus the result of this call will be as simple
 	 * call to analize without parameters
@@ -40,9 +65,6 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 			Preset<RNAalifold> preset) throws UnsupportedRuntimeException,
 			LimitExceededException, JobSubmissionException,
 			WrongParameterException {
-
 		return analize(sequences);
 	}
 }
-	
-