X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FJws2Client.java;h=ce4980d1c724c92f8239b199543434f2c88a9af6;hb=191ed00f52901ed7ee6d1137637e66c999913be8;hp=888ec5ffb9d6d07d9602208f7df46b3a8800c5df;hpb=fa61eaad52ffe5ee0db449c3dd9ec5fa67aec43f;p=jabaws.git

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index 888ec5f..ce4980d 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -50,7 +50,7 @@ import compbio.data.msa.RegistryWS;
 import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.RNAstruct;
+import compbio.data.sequence.RNAStruct;
 import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.SequenceUtil;
@@ -150,7 +150,6 @@ public class Jws2Client {
 		String presetName = CmdHelper.getPresetName(cmd);
 
 		Metadata<T> msaws = (Metadata<T>) connect(hostname, service);
-		Metadata<T> foldws = (Metadata<T>) connect(hostname, service);
 		Preset<T> preset = null;
 		if (presetName != null) {
 			preset = MetadataHelper.getPreset(msaws, presetName);
@@ -161,8 +160,9 @@ public class Jws2Client {
 			customOptions = MetadataHelper.processParameters(prms,
 					msaws.getRunnerOptions());
 		}
+//		System.out.println("The Options read from the command line: " + customOptions);
+		
 		Alignment alignment = null;
-		RNAstruct rnastruct = null;
 		if (inputFile != null) {
 			Writer writer = null;
 			if (outFile != null) {
@@ -176,17 +176,12 @@ public class Jws2Client {
 				ScoreManager result = analize(inputFile,
 						((SequenceAnnotation<T>) msaws), preset, customOptions);
 
+				System.out.println(result\.asRNAStruct().toString());
 				IOHelper.writeOut(writer, result);
 			} else if (service.getServiceType() == MsaWS.class) {
 				alignment = align(inputFile, (MsaWS<T>) msaws, preset,
 						customOptions);
 				IOHelper.writeOut(writer, alignment);
-			} else if (service.getServiceType() == FoldWS.class) {
-				rnastruct = fold(inputFile, (FoldWS<T>) foldws, preset, customOptions);
-				// No IOHelper method for rnastruct/String yet
-				if (writer != null) {
-					writer.write(rnastruct.toString());
-				}
 			}
 			writer.close();
 		}
@@ -532,14 +527,14 @@ public class Jws2Client {
 	 *            Preset to use optional
 	 * @param customOptions
 	 *            file which contains new line separated list of options
-	 * @return RNAstruct
+	 * @return String
 	 */
 	
-	static <T> RNAstruct fold(File file, FoldWS<T> foldws, Preset<T> preset,
+	static <T> String fold(File file, FoldWS<T> foldws, Preset<T> preset,
 			List<Option<T>> customOptions) {
 		FileInputStream instream = null;
 		Alignment alignment = null;
-		RNAstruct rnastruct = null;
+		String rnastruct = null;
 		try {
 			instream = new FileInputStream(file);
 			alignment = ClustalAlignmentUtil.readClustalFile(instream);
@@ -559,8 +554,6 @@ public class Jws2Client {
 			System.out.println("\n\ncalling fold.........");
 			Thread.sleep(1000);
 			rnastruct = foldws.getResult(jobId);
-			log.info("log test print results:\n" + rnastruct.toString());
-			System.out.println("print test results:\n " + rnastruct.toString());
 				
 		} catch (IOException e) {
 			System.err.println("Exception while reading the input file. Exception details: ");