From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 6 Sep 2013 16:23:22 +0000 (+0100)
Subject: Merge branch 'JABAWS_Release_2_5' into develop
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4b647613e686c4edffd44702d86662c6facb2d5a;p=jabaws.git

Merge branch 'JABAWS_Release_2_5' into develop

Conflicts:
	.project
	WEB-INF/sun-jaxws.xml
	conf/Executable.properties
	testsrc/compbio/data/sequence/SequenceUtilTester.java
	webservices/compbio/data/msa/Category.java
	webservices/compbio/ws/client/Jws2Client.java
	webservices/compbio/ws/client/Services.java
	webservices/compbio/ws/client/WSTester.java
	webservices/compbio/ws/server/WSUtil.java
	webservices/compbio/ws/server/resource/AAConWS.wsdl
	webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
	webservices/compbio/ws/server/resource/ClustalWS.wsdl
	webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
	webservices/compbio/ws/server/resource/DisemblWS.wsdl
	webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
	webservices/compbio/ws/server/resource/GlobPlotWS.wsdl
	webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
	webservices/compbio/ws/server/resource/IUPredWS.wsdl
	webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd
	webservices/compbio/ws/server/resource/JronnWS.wsdl
	webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
	webservices/compbio/ws/server/resource/MafftWS.wsdl
	webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
	webservices/compbio/ws/server/resource/MuscleWS.wsdl
	webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
	webservices/compbio/ws/server/resource/RegistryWS.wsdl
	webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd
	webservices/compbio/ws/server/resource/TcoffeeWS.wsdl
	webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
	wsbuild.xml
---

4b647613e686c4edffd44702d86662c6facb2d5a
diff --cc WEB-INF/sun-jaxws.xml
index 1aade67,e39eaed..e8b759b
--- a/WEB-INF/sun-jaxws.xml
+++ b/WEB-INF/sun-jaxws.xml
@@@ -1,55 -1,42 +1,45 @@@
  <?xml version="1.0" encoding="UTF-8"?>
  <endpoints xmlns='http://java.sun.com/xml/ns/jax-ws/ri/runtime' version='2.0'>
-     <endpoint
-         name='RegistryWS'
-         implementation='compbio.ws.server.RegistryWS'
-         url-pattern='/RegistryWS'/>
-     <endpoint
-         name='ClustalWS'
-         implementation='compbio.ws.server.ClustalWS'
-         url-pattern='/ClustalWS'/>
-     <endpoint
-         name='ClustalOWS'
-         implementation='compbio.ws.server.ClustalOWS'
-         url-pattern='/ClustalOWS'/>
-     <endpoint
-         name='MuscleWS'
-         implementation='compbio.ws.server.MuscleWS'
-         url-pattern='/MuscleWS'/>
-     <endpoint
-         name='TcoffeeWS'
-         implementation='compbio.ws.server.TcoffeeWS'
-         url-pattern='/TcoffeeWS'/>
-     <endpoint
-         name='MafftWS'
-         implementation='compbio.ws.server.MafftWS'
-         url-pattern='/MafftWS'/>
-     <endpoint
-         name='ProbconsWS'
-         implementation='compbio.ws.server.ProbconsWS'
-         url-pattern='/ProbconsWS'/>
-     <endpoint
-         name='AAConWS'
-         implementation='compbio.ws.server.AAConWS'
-         url-pattern='/AAConWS'/>
-     <endpoint
-         name='JronnWS'
-         implementation='compbio.ws.server.JronnWS'
-         url-pattern='/JronnWS'/>
-     <endpoint
-         name='DisemblWS'
-         implementation='compbio.ws.server.DisemblWS'
-         url-pattern='/DisemblWS'/>
-     <endpoint
-         name='GlobPlotWS'
-         implementation='compbio.ws.server.GlobPlotWS'
-         url-pattern='/GlobPlotWS'/>
-     <endpoint
-         name='IUPredWS'
-         implementation='compbio.ws.server.IUPredWS'
-         url-pattern='/IUPredWS'/>
-     <endpoint
-     	name='RNAalifoldWS'
-     	implementation='compbio.ws.server.RNAalifoldWS'
-     	url-pattern='/RNAalifoldWS'/>
+ 	<endpoint name='RegistryWS'
+ 		implementation='compbio.ws.server.RegistryWS'
+ 		url-pattern='/RegistryWS'/>
+ 	<endpoint name='ClustalWS'
+ 		implementation='compbio.ws.server.ClustalWS'
+ 		url-pattern='/ClustalWS'/>
+ 	<endpoint name='ClustalOWS'
+ 		implementation='compbio.ws.server.ClustalOWS'
+ 		url-pattern='/ClustalOWS'/>
+ 	<endpoint name='MuscleWS'
+ 		implementation='compbio.ws.server.MuscleWS'
+ 		url-pattern='/MuscleWS'/>
+ 	<endpoint name='TcoffeeWS'
+ 		implementation='compbio.ws.server.TcoffeeWS'
+ 		url-pattern='/TcoffeeWS'/>
+ 	<endpoint name='MafftWS'
+ 		implementation='compbio.ws.server.MafftWS'
+ 		url-pattern='/MafftWS'/>
+ 	<endpoint name='ProbconsWS'
+ 		implementation='compbio.ws.server.ProbconsWS'
+ 		url-pattern='/ProbconsWS'/>
+ 	<endpoint name='AAConWS'
+ 		implementation='compbio.ws.server.AAConWS'
+ 		url-pattern='/AAConWS'/>
+ 	<endpoint name='JronnWS'
+ 		implementation='compbio.ws.server.JronnWS'
+ 		url-pattern='/JronnWS'/>
+ 	<endpoint name='DisemblWS'
+ 		implementation='compbio.ws.server.DisemblWS'
+ 		url-pattern='/DisemblWS'/>
+ 	<endpoint name='GlobPlotWS'
+ 		implementation='compbio.ws.server.GlobPlotWS'
+ 		url-pattern='/GlobPlotWS'/>
+ 	<endpoint name='IUPredWS'
+ 		implementation='compbio.ws.server.IUPredWS'
+ 		url-pattern='/IUPredWS'/>
+ 	<endpoint name='JpredWS'
+ 		implementation='compbio.ws.server.JpredWS'
+ 		url-pattern='/JpredWS'/>
++	<endpoint name='RNAalifoldWS'
++		implementation='compbio.ws.server.RNAalifoldWS'
++		url-pattern='/RNAalifoldWS'/>
  </endpoints>
diff --cc WEB-INF/web.xml
index 7fd7ea2,bf30cbf..6a3cea7
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@@ -160,24 -161,13 +160,30 @@@
  		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
  		<load-on-startup>1</load-on-startup>
  	</servlet>
 +	
 +	<servlet>
 +		<servlet-name>RNAalifoldWS</servlet-name>
 +		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
 +		<load-on-startup>1</load-on-startup>
 +	</servlet>
 +	<servlet>
 +		<display-name>Apache-Axis Servlet</display-name>
 +		<servlet-name>AxisServlet</servlet-name>
 +		<servlet-class>org.apache.axis.transport.http.AxisServlet</servlet-class>
 +	</servlet>
 +	<servlet>
 +		<display-name>Axis Admin Servlet</display-name>
 +		<servlet-name>AdminServlet</servlet-name>
 +		<servlet-class>org.apache.axis.transport.http.AdminServlet</servlet-class>
 +		<load-on-startup>100</load-on-startup>
 +	</servlet>
  
+ 	<servlet>
+ 		<servlet-name>JpredWS</servlet-name>
+ 		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+ 		<load-on-startup>1</load-on-startup>
+ 	</servlet>
+ 
  	<!-- JABAWS servlet mappings -->
  	<servlet-mapping>
  		<servlet-name>listings</servlet-name>
@@@ -278,28 -268,11 +284,32 @@@
  		<servlet-name>IUPredWS</servlet-name>
  		<url-pattern>/IUPredWS</url-pattern>
  	</servlet-mapping>
 +	
 +	<servlet-mapping>
 +		<servlet-name>RNAalifoldWS</servlet-name>
 +		<url-pattern>/RNAalifoldWS</url-pattern>
 +	</servlet-mapping>
 +	<servlet-mapping>
 +		<servlet-name>AxisServlet</servlet-name>
 +		<url-pattern>/servlet/AxisServlet</url-pattern>
 +	</servlet-mapping>
 +	<servlet-mapping>
 +		<servlet-name>AxisServlet</servlet-name>
 +		<url-pattern>*.jws</url-pattern>
 +	</servlet-mapping>
 +	<servlet-mapping>
 +		<servlet-name>AxisServlet</servlet-name>
 +		<url-pattern>/services/*</url-pattern>
 +	</servlet-mapping>
 +	<servlet-mapping>
 +		<servlet-name>AdminServlet</servlet-name>
 +		<url-pattern>/servlet/AdminServlet</url-pattern>
 +	</servlet-mapping>
  
+ 	<servlet-mapping>
+ 		<servlet-name>JpredWS</servlet-name>
+ 		<url-pattern>/JpredWS</url-pattern>
+ 	</servlet-mapping>
  
  
  	<!-- JABAWS security constraints -->
diff --cc datamodel/compbio/data/sequence/SequenceUtil.java
index 3a84873,d1140cf..376193f
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@@ -30,8 -32,8 +32,9 @@@ import java.io.InputStreamReader
  import java.io.OutputStream;
  import java.io.OutputStreamWriter;
  import java.util.ArrayList;
 +import java.util.Arrays;
  import java.util.HashMap;
+ import java.util.Collections;
  import java.util.HashSet;
  import java.util.List;
  import java.util.Map;
diff --cc testsrc/compbio/data/sequence/SequenceUtilTester.java
index 25c81a1,7f98180..9468cda
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@@ -140,42 -133,9 +133,38 @@@ public class SequenceUtilTester 
  		}
  	}
  
 -	// This method tests the loading of horizontally formatted Jronn output file
 +	// Potential Bug :- Sequence names are shortened to 2-3 letters
 +	@Test
 +	public void testReadFastaWriteClustal() {
 +		
 +		try {
 +			FileInputStream fio = new FileInputStream(
 +					AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");
 +			assertNotNull(fio);
 +			List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);
 +			assertNotNull(fseqs);
 +			fio.close();
 +			
 +			char gapChar = '-';
 +			FileOutputStream fou = new FileOutputStream(
 +					AllTestSuit.TEST_DATA_PATH + "TO1381.aln.written");
 +			SequenceUtil.writeClustal(fou, fseqs, gapChar);
 +			fou.close();
 +			
 +		} catch (FileNotFoundException e) {
 +			e.printStackTrace();
 +			fail(e.getLocalizedMessage());
 +		} catch (IOException e) {
 +			e.printStackTrace();
 +			fail(e.getLocalizedMessage());
 +		}
- 	}		
- 		
- 			
++	}
 +
- 			
- 	
 +	/**
 +	 * This test tests the loading of horizontally formatted Jronn output file
 +	 */
  	@Test
- 	public void loadJronnFile() {
+ 	public void LoadJronnFile() {
  
  		FileInputStream fio;
  		try {
@@@ -439,5 -380,17 +409,18 @@@
  			fail(e.getMessage());
  		}
  	}
+ 	@Test
+ 	public void ReadJpredResults() {
+ 		try {
+ 			InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "Jpred.test1.out");
+ 			List<FastaSequence> result = SequenceUtil.readJpredFile(inStream);
+ 			inStream.close();
+ 			assertNotNull(result);
+ 			assertEquals(result.size(), 19);
+ 		} catch (IOException e) {
+ 			e.printStackTrace();
+ 			fail(e.getMessage());
+ 		}
+ 	}
  }
 +
diff --cc testsrc/compbio/metadata/AllTestSuit.java
index bbb7fbd,f60075b..8e9d9aa
--- a/testsrc/compbio/metadata/AllTestSuit.java
+++ b/testsrc/compbio/metadata/AllTestSuit.java
@@@ -64,15 -43,9 +43,11 @@@ public class AllTestSuit 
  	public static final String RUNNER_TEST_LOGGER = "RunnerLogger";
  
  	public static final String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "TO1381.fasta";
- 
  	public static final String test_alignment_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "TO1381.fasta.aln";
- 
  	public static final String test_input_real = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "50x500Protein.fasta";
- 
  	public static final String test_input_dna = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "3dnaseqs.fasta";
- 
  	public static final String test_input_large = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "1000x3000Dna.fasta";
 +	
 +	public static final String test_input_aln = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "unfolded_RF00031.aln";
  
  }
diff --cc webservices/compbio/data/msa/Category.java
index 3de1b31,59bcf30..fa9968b
--- a/webservices/compbio/data/msa/Category.java
+++ b/webservices/compbio/data/msa/Category.java
@@@ -34,8 -35,8 +35,8 @@@ public class Category 
  	public static final String CATEGORY_ALIGNMENT = "Alignment";
  	public static final String CATEGORY_DISORDER = "Protein Disorder";
  	public static final String CATEGORY_CONSERVATION = "Conservation";
- 	public static final String CATEGORY_RNASTRUCT = "RNA Structure Prediction";
+ 	public static final String CATEGORY_PREDICTION = "Prediction";
 -	
 +
  	public String name;
  	Set<Services> services;
  
@@@ -71,20 -72,16 +72,17 @@@
  		disorder_services.add(Services.GlobPlotWS);
  		disorder_services.add(Services.IUPredWS);
  		disorder_services.add(Services.JronnWS);
- 
  		Category disorder = new Category(CATEGORY_DISORDER, disorder_services);
+ 
  		Set<Services> conservation_services = new HashSet<Services>();
  		conservation_services.add(Services.AAConWS);
+ 		Category conservation = new Category(CATEGORY_CONSERVATION, conservation_services);
  
- 		Category conservation = new Category(CATEGORY_CONSERVATION,
- 				conservation_services);
+ 		Set<Services> prediction_services = new HashSet<Services>();
+ 		prediction_services.add(Services.JpredWS);
++		prediction_services.add(Services.RNAalifoldWS);
+ 		Category prediction = new Category(CATEGORY_PREDICTION, prediction_services);
  
- 		Set<Services> rnastruct_services = new HashSet<Services>();
- 		rnastruct_services.add(Services.RNAalifoldWS);
- 		
- 		Category rnastruct = new Category(CATEGORY_RNASTRUCT,
- 				rnastruct_services);
- 		
  		Set<Category> categories = new HashSet<Category>();
  		categories.add(alignment);
  		categories.add(disorder);
diff --cc webservices/compbio/ws/client/Jws2Client.java
index 5a72802,94854d4..96343db
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@@ -509,18 -459,8 +460,8 @@@ public class Jws2Client 
  		}
  		return alignment;
  	}
 -
 +	
  	/**
- 	 * Prints Jws2Client usage information to standard out
- 	 * 
- 	 * @param exitStatus
- 	 */
- 	static void printUsage(int exitStatus) {
- 		System.out.println(Constraints.help_text);
- 		System.exit(exitStatus);
- 	}
- 
- 	/**
  	 * Starts command line client, if no parameter are supported print help. Two
  	 * parameters are required for successful call the JWS2 host name and a
  	 * service name.
diff --cc webservices/compbio/ws/client/Services.java
index 2d2cdc8,2720eb7..a4e101d
--- a/webservices/compbio/ws/client/Services.java
+++ b/webservices/compbio/ws/client/Services.java
@@@ -39,8 -39,7 +39,7 @@@ public enum Services 
  	 * Make sure this class has NO references to runners or engines as it is a
  	 * part of minimal client package. Such things should go into ServicesUtil
  	 */
- 	MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS,
- 	JronnWS, DisemblWS, GlobPlotWS, IUPredWS, RNAalifoldWS;
 -	MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS, JpredWS;
++	MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS, JpredWS, RNAalifoldWS;
  
  	public static Services getService(String servName) {
  		servName = servName.trim().toLowerCase();
@@@ -78,10 -76,8 +76,9 @@@
  			case DisemblWS :
  			case GlobPlotWS :
  			case IUPredWS :
 +			case RNAalifoldWS :
  				return SequenceAnnotation.class;
- 
- 				// deliberate leaking
+ 			case JpredWS :
  			case ClustalWS :
  			case ClustalOWS :
  			case MafftWS :
@@@ -89,13 -85,33 +86,35 @@@
  			case ProbconsWS :
  			case TcoffeeWS :
  				return MsaWS.class;
- 				
++
  			default :
- 				throw new RuntimeException("Unrecognised Web Service Type "
- 						+ this + " - Should never happened!");
+ 				throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");
  		}
  	}
  
+ 	
+ 	String getServiceNamespace() {
+ 		switch (this) {
 -			case JpredWS :
++			case RNAalifoldWS :
+ 			case AAConWS :
+ 			case JronnWS :
+ 			case DisemblWS :
+ 			case GlobPlotWS :
+ 			case IUPredWS :
 -			case ClustalOWS :
+ 				return JABAService.V2_SERVICE_NAMESPACE;
++			case ClustalOWS :
++			case JpredWS :
+ 			case ClustalWS :
+ 			case MafftWS :
+ 			case MuscleWS :
+ 			case ProbconsWS :
+ 			case TcoffeeWS :
+ 				return JABAService.SERVICE_NAMESPACE;
+ 			default :
+ 				throw new RuntimeException("Unrecognised JABAWS Namespace for service " + this +"!");
+ 		}
+ 	}
+ 	
  	JABAService getInterface(Service service) {
  		assert service != null;
  
@@@ -128,11 -145,8 +148,10 @@@
  				return PROBCONS_INFO;
  			case TcoffeeWS :
  				return TCOFFEE_INFO;
 +			case RNAalifoldWS :
 +				return RNAALIFOLD_INFO;
  			default :
- 				throw new RuntimeException("Unrecognised Web Service Type "
- 						+ this + " - Should never happened!");
+ 				throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");
  		}
  	}
  
@@@ -191,17 -216,8 +221,16 @@@
  			MafftWS,
  			"Katoh, Toh 2010 (Bioinformatics 26:1899-1900)\r\n"
  					+ "Parallelization of the MAFFT multiple sequence alignment program. ",
- 			"6.8.57", "http://mafft.cbrc.jp/alignment/software/").toString();;
+ 			"6.8.57", "http://mafft.cbrc.jp/alignment/software/").toString();
  
- 	// TODO reference
 +	public static final String RNAALIFOLD_INFO = new ServiceInfo(
 +			RNAalifoldWS,
 +			"Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler 'Secondary Structure Prediction"
 +			+ " for Aligned RNA Sequences'. J.Mol.Biol. 319: 1059-1066, 2002. Stephan H. Bernhart,"
 +			+ " Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler. "
 +			+ "'RNAalifold: Improved consensus structure prediction for RNA alignments'. BMC Bioinformatics, 9:474, 2008.\r\n",
- 			"2.1.2", "http://www.tbi.univie.ac.at/RNA/").toString();;
- 			
++			"2.1.2", "http://www.tbi.univie.ac.at/RNA/").toString();
++
  	@XmlAccessorType(XmlAccessType.FIELD)
  	static class ServiceInfo {
  		Services service;
@@@ -236,4 -251,4 +264,4 @@@
  	public static void main(String[] args) {
  		System.out.println(MUSCLE_INFO);
  	}
--}
++}
diff --cc webservices/compbio/ws/client/ServicesUtil.java
index 9873875,26f1467..7084028
--- a/webservices/compbio/ws/client/ServicesUtil.java
+++ b/webservices/compbio/ws/client/ServicesUtil.java
@@@ -54,12 -56,8 +57,10 @@@ public class ServicesUtil 
  				return Jronn.class;
  			case IUPredWS :
  				return IUPred.class;
 +			case RNAalifoldWS :
 +				return RNAalifold.class;
  			default :
- 				throw new RuntimeException(
- 						"Unknown web service implementation class for service: "
- 								+ service);
+ 				throw new RuntimeException("Unknown web service implementation class for service: " + service);
  		}
  	}
  
diff --cc webservices/compbio/ws/client/WSTester.java
index 483c162,bae843b..226af80
--- a/webservices/compbio/ws/client/WSTester.java
+++ b/webservices/compbio/ws/client/WSTester.java
@@@ -61,27 -62,22 +62,25 @@@ import compbio.util.Util
  public class WSTester {
  
  	/**
- 	 * Sequences to be used as input for all WS
+ 	 * Test sequences to be used as input for WS
  	 */
- 	public static final String fastaInput = ">Foo\n"
- 			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"
- 			+ "\n>Bar\n"
- 			+ "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";
- 
- 	public static final String fastaAlignment = ">Foo\n"
- 			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"
- 			+ ">Bar\n"
- 			+ "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"
- 			+ "";
- 
- 	public static final String fastaRNAAlignment = ">Foo\n"
- 			+ "C-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGAUGGUUG----GCAAC\n"
- 			+ ">Bar\n"
- 			+ "G-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGAU-UACGAUUAACCAC\n";
+ 	public static final String fastaInput2records = 
+ 			">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n"
+ 		+   ">Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";
+ 	public static final String fastaInput1record = 
+ 			">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n";
+ 	public static final String fastaAlignment = 
+ 			">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"
+ 		+   ">Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n";
++	public static final String fastaRNAAlignment = 
++			">Foo\nC-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGAUGGUUG----GCAAC\n"
++		+   ">Bar\nG-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGAU-UACGAUUAACCAC\n";
  
+ 	/**
+ 	 * Status strings
+ 	 */
  	private static final String FAILED = "FAILED";
  	private static final String OK = "OK";
- 
  	private static final String UNSUPPORTED = "UNSUPPORTED";
  
  	/**
@@@ -262,11 -241,9 +258,11 @@@
  			SequenceAnnotation<T> wservice, Services service) throws Exception {
  		writer.print("Calling analyse.........");
  
- 		List<FastaSequence> input = loadSeqs();
+ 		List<FastaSequence> input = loadSeqs(2);
 -		if (service == Services.AAConWS) {
 +		if (service == Services.AAConWS ) {
  			input = loadAlignment();
 +		} else if (service == Services.RNAalifoldWS) {
 +			input = loadRNAAlignment();
  		}
  		boolean success = testDefaultAnalyse(input, wservice, null, null);
  
diff --cc webservices/compbio/ws/server/WSUtil.java
index da4182c,e6dd02d..07d005d
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@@ -190,11 -189,8 +208,9 @@@ public final class WSUtil 
  			throws ResultNotAvailableException {
  		WSUtil.validateJobId(jobId);
  		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
- 		ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine
- 				.getResults(jobId);
- 		
+ 		ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine.getResults(jobId);
  		ScoreManager mas = aacon.getResults();
 +		
  		log.trace(jobId + " getConservation : " + mas);
  		return mas;
  	}
diff --cc wsbuild.xml
index c614ba6,485ad24..9408d8e
--- a/wsbuild.xml
+++ b/wsbuild.xml
@@@ -28,7 -29,7 +29,8 @@@
  	<property name="iupred.wsdl" location="${wsdl.dir}/IUPredWS.wsdl" />
  	<property name="jronn.wsdl" location="${wsdl.dir}/JronnWS.wsdl" />
  	<property name="registry.wsdl" location="${wsdl.dir}/RegistryWS.wsdl" />
 +	<property name="rnaalifold.wsdl" location="${wsdl.dir}/RNAalifold.wsdl" />  
+ 
  	<taskdef name="wsgen" onerror="report" classname="com.sun.tools.ws.ant.WsGen">
  		<classpath refid="project.classpath" />
  	</taskdef>
@@@ -160,21 -172,7 +173,20 @@@
  				<classpath refid="classes.path" />
  				<classpath refid="project.classpath" />
  		</wsgen>
- 		
 +		<wsgen sei="compbio.ws.server.RNAalifoldWS"
 +				sourcedestdir="${basedir}/webservices"
 +				destdir="${classes}"
 +				resourcedestdir="${wsdl.dir}"
 +				keep="true" genwsdl="true"
 +				extension="false"
 +				xendorsed="true"
 +				verbose="true">
 +				<classpath refid="classes.path" />
 +				<classpath refid="project.classpath" />
 +		</wsgen>
 +		
  	</target>
 +		
  
  	<taskdef name="wsimport" classname="com.sun.tools.ws.ant.WsImport">
  		<classpath refid="project.classpath" />
@@@ -231,15 -229,6 +243,14 @@@
  				package="compbio.ws.client.stub" target="2.1"
  				quiet="false">
  			</wsimport>
- 		
 +			<wsimport wsdl="${rnaalifold.wsdl}" 
 +				sourcedestdir="${basedir}/webservices/" 
 +				keep="true" extension="false" 
 +				verbose="true" xnocompile="true" xendorsed="true"
 +				package="compbio.ws.client.stub" target="2.1"
 +				quiet="false">
 +			</wsimport>
 +			
  		</target>
  
  	<!--