From 033ac3315fb3c8fa3173145863294774c8b46898 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Tue, 10 Sep 2013 16:02:58 +0100
Subject: [PATCH] Add "safe type cast" warnings

---
 webservices/compbio/ws/server/RNAalifoldWS.java |   19 ++++++-------------
 1 file changed, 6 insertions(+), 13 deletions(-)

diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index 33208a0..ed94c23 100644
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -20,9 +20,7 @@ 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);
 	
@@ -32,18 +30,19 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 	
 	// 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,
@@ -51,12 +50,9 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 			WrongParameterException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);
-		
-		List<String> params = WSUtil.getCommands(options,
-				RNAalifold.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(""));
 	}
 	
 	
@@ -69,9 +65,6 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 			Preset<RNAalifold> preset) throws UnsupportedRuntimeException,
 			LimitExceededException, JobSubmissionException,
 			WrongParameterException {
-
 		return analize(sequences);
 	}
 }
-	
-	
-- 
1.7.10.2