X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FWSTester.java;h=483c1628f29b3021d623494d2742ae7ebd172983;hb=7b5d0822e864d35c099a9b3b9e463c59dfdd091e;hp=883890377832fb70363ca9a33782a53cc1a7d108;hpb=1e1c3681ba25ee1797a46f871b8c80f259afe2ca;p=jabaws.git

diff --git a/webservices/compbio/ws/client/WSTester.java b/webservices/compbio/ws/client/WSTester.java
index 8838903..483c162 100644
--- a/webservices/compbio/ws/client/WSTester.java
+++ b/webservices/compbio/ws/client/WSTester.java
@@ -32,8 +32,6 @@ import java.util.List;
 
 import javax.xml.ws.WebServiceException;
 
-import org.apache.log4j.Logger;
-
 import compbio.data.msa.JABAService;
 import compbio.data.msa.Metadata;
 import compbio.data.msa.MsaWS;
@@ -62,22 +60,24 @@ import compbio.util.Util;
  */
 public class WSTester {
 
-	private static Logger log = Logger.getLogger(WSTester.class);
 	/**
 	 * Sequences to be used as input for all WS
 	 */
-	static final String fastaInput = ">Foo\n"
+	public static final String fastaInput = ">Foo\n"
 			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"
 			+ "\n>Bar\n"
-			+ "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA";
+			+ "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";
 
-	static final String fastaAlignment = ">Foo\r\n"
-			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\r\n"
-			+ ">Bar\r\n"
-			+ "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\r\n"
+	public static final String fastaAlignment = ">Foo\n"
+			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"
+			+ ">Bar\n"
+			+ "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"
 			+ "";
 
-	static final List<FastaSequence> seqs = loadSeqs();
+	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";
 
 	private static final String FAILED = "FAILED";
 	private static final String OK = "OK";
@@ -103,7 +103,7 @@ public class WSTester {
 	/**
 	 * Converting input to a form accepted by WS
 	 * 
-	 * @return List of FastaSequence records
+	 * @return List of FastaSequence records with aligned protein sequences
 	 */
 	private static List<FastaSequence> loadAlignment() {
 		try {
@@ -115,6 +115,20 @@ public class WSTester {
 		}
 		return null;
 	}
+	/**
+	 * Converting input to a form accepted by WS
+	 * 
+	 * @return List of FastaSequence records with aligned RNA sequences
+	 */
+	private static List<FastaSequence> loadRNAAlignment() {
+		try {
+			return SequenceUtil.readFasta(new ByteArrayInputStream(fastaRNAAlignment.getBytes()));
+		} catch (IOException ignored) {
+			// Should not happen as a source is not a external stream
+			ignored.printStackTrace();
+		}
+		return null;
+	}
 
 	private final PrintWriter writer;
 	private final String hostname;
@@ -173,7 +187,7 @@ public class WSTester {
 			writer.print("Aligning with preset '" + preset.getName() + "'... ");
 			Alignment al = null;
 			try {
-				String taskId = msaws.presetAlign(seqs, preset);
+				String taskId = msaws.presetAlign(loadSeqs(), preset);
 				al = msaws.getResult(taskId);
 				if (al != null) {
 					writer.println(OK);
@@ -209,6 +223,7 @@ public class WSTester {
 		testMetadata(msaws);
 		return succeed;
 	}
+	
 	/**
 	 * Call most of web services functions and check the output
 	 * 
@@ -248,8 +263,10 @@ public class WSTester {
 		writer.print("Calling analyse.........");
 
 		List<FastaSequence> input = loadSeqs();
-		if (service == Services.AAConWS) {
+		if (service == Services.AAConWS ) {
 			input = loadAlignment();
+		} else if (service == Services.RNAalifoldWS) {
+			input = loadRNAAlignment();
 		}
 		boolean success = testDefaultAnalyse(input, wservice, null, null);
 
@@ -347,7 +364,7 @@ public class WSTester {
 		Alignment al = null;
 		boolean succeed = false;
 
-		String taskId = msaws.align(seqs);
+		String taskId = msaws.align(loadSeqs());
 		writer.print("\nQuerying job status...");
 		JobStatus status = msaws.getJobStatus(taskId);
 		while (status != JobStatus.FINISHED) {
@@ -363,6 +380,7 @@ public class WSTester {
 		}
 		return succeed;
 	}
+	
 	/**
 	 * Test JWS2 web services
 	 * 
@@ -412,7 +430,6 @@ public class WSTester {
 			tester.writer.println();
 			tester.checkService(serv);
 		}
-
 	}
 
 	/**
@@ -445,11 +462,9 @@ public class WSTester {
 
 	private void reportResults(Services serv, boolean succeed) {
 		if (succeed) {
-			writer.println("Check is completed. The Service " + serv
-					+ " IS WORKING\n");
+			writer.println("Check is completed. The Service " + serv + " IS WORKING\n");
 		} else {
-			writer.println("Check is aborted. The Service " + serv
-					+ " HAS SOME PROBLEMS\n");
+			writer.println("Check is aborted. The Service " + serv + " HAS SOME PROBLEMS\n");
 		}
 	}
 }