X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=webservices%2Fcompbio%2Fws%2Fserver%2FRNAalifoldWS.java;h=33208a0c265060c0d9801496e03c328042863652;hb=6ccf6e7acc4d35484ae6ad0f03d22c19b8ce63fc;hp=d640e273ebee5696590b3510ec719798cd61179c;hpb=d182b2d2b6ede7c952c6ca5a24b1576c6a194eed;p=jabaws.git

diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index d640e27..33208a0 100644
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -9,13 +9,11 @@ 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;
@@ -31,17 +29,8 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 	public RNAalifoldWS() {
 		super (new RNAalifold(), log);
 	}
-
-	
-//	// for testing
-//	@Override
-//	public RNAStructScoreManager getAnnotation(String jobId) 
-//			throws ResultNotAvailableException {
-//		return WSUtil.getAnnotation(jobId, log);
-//	}
 	
-	
-	// Only purpose of Overrides is to replace "analize" with "fold" method 
+	// Only purpose is to replace "analize" with "fold" method 
 	// so that a clustal input file and not fasta will be generated
 	@Override
 	public String analize(List<FastaSequence> sequences)
@@ -53,8 +42,8 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 				getLimit(""));
 	}
 
-	// Only purpose of Overrides is to replace "analize" with "fold" method 
-		// so that a clustal input file and not fasta will be generated
+	// Only purpose is to replace "analize" with "fold" method 
+	// so that a clustal input file and not fasta will be generated
 	@Override
 	public String customAnalize(List<FastaSequence> sequences,
 			List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,
@@ -64,7 +53,7 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 		ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);
 		
 		List<String> params = WSUtil.getCommands(options,
-				AACon.KEY_VALUE_SEPARATOR);
+				RNAalifold.KEY_VALUE_SEPARATOR);
 		confRNAalifold.addParameters(params);
 		return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",
 				getLimit(""));