X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FJws2Client.java;h=eda6533fc8d2d02ed04fd7a52724f729c66b1b89;hb=3644426ec0e9e9ceb798bd426085d8d9dd8dbb56;hp=1673e18338d2bccd640c695b1b74416daed06260;hpb=8033a51860de2200a54e64add0809d6780f5b092;p=jabaws.git

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index 1673e18..eda6533 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -38,20 +38,19 @@ import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Arrays;
 import java.util.List;
-import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
 import javax.xml.ws.Service;
 import javax.xml.ws.WebServiceException;
 
-import compbio.data.msa.Annotation;
 import compbio.data.msa.JABAService;
 import compbio.data.msa.Metadata;
 import compbio.data.msa.MsaWS;
+import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
 import compbio.metadata.JobSubmissionException;
@@ -159,17 +158,17 @@ public class Jws2Client {
 				// std.out will not be
 				outStream = System.out;
 			}
-			if (service == Services.AAConWS) {
-				Set<Score> result = analize(inputFile, ((Annotation<T>) msaws),
-						preset, customOptions);
+			if (service.getServiceType() == SequenceAnnotation.class) {
+				ScoreManager result = analize(inputFile,
+						((SequenceAnnotation<T>) msaws), preset, customOptions);
+
 				IOHelper.writeOut(outStream, result);
 			} else {
 				alignment = align(inputFile, (MsaWS<T>) msaws, preset,
 						customOptions);
 				IOHelper.writeOut(outStream, alignment);
 			}
-
-			// stream is closed in the method no need to close it here
+			outStream.close();
 		}
 
 		boolean listParameters = CmdHelper.listParameters(cmd);
@@ -202,13 +201,14 @@ public class Jws2Client {
 	 * @return Set<Score> the conservation scores
 	 * @throws UnknownFileFormatException
 	 */
-	<T> Set<Score> analize(File file, Annotation<T> wsproxy, Preset<T> preset,
-			List<Option<T>> customOptions) {
+	<T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,
+			Preset<T> preset, List<Option<T>> customOptions) {
 
 		List<FastaSequence> fastalist = null;
-		Set<Score> scores = null;
+		ScoreManager scores = null;
 		try {
 			fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());
+			assert !fastalist.isEmpty() : "Input is empty!";
 
 			String jobId = null;
 			if (customOptions != null && preset != null) {
@@ -220,9 +220,11 @@ public class Jws2Client {
 			} else if (preset != null) {
 				jobId = wsproxy.presetAnalize(fastalist, preset);
 			} else {
+				System.out.println("\n\ncalling analise.........");
 				jobId = wsproxy.analize(fastalist);
 			}
-			Thread.sleep(1000);
+			Thread.sleep(2000);
+
 			scores = wsproxy.getAnnotation(jobId);
 
 		} catch (IOException e) {
@@ -287,8 +289,13 @@ public class Jws2Client {
 				serv = service.getService(url, V2_QUALIFIED_SERVICE_NAME);
 			}
 		}
+		if (serv == null) {
+			System.err.println("Could not connect to " + url
+					+ " the server is down?");
+			// FIXME
+		}
 		JABAService serviceIF = service.getInterface(serv);
-		log.log(Level.FINE, "Connected successfully!");
+		log.log(Level.INFO, "Connected successfully!");
 
 		return serviceIF;
 	}
@@ -426,7 +433,7 @@ public class Jws2Client {
 
 	/**
 	 * Starts command line client, if no parameter are supported print help. Two
-	 * parameters are required for successfull call the JWS2 host name and a
+	 * parameters are required for successful call the JWS2 host name and a
 	 * service name.
 	 * 
 	 * @param args