X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FJws2Client.java;h=eac049e3fd90259ffa8470275cf284dbb9516339;hb=4c022b67a736b6f79dbe212d73016607cf298422;hp=0aa02c59b644115f54a3138b9fe0dfea77942e19;hpb=811c3d0faf8c9c9ed2d493e1627db6bb94260e47;p=jabaws.git

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index 0aa02c5..eac049e 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -25,7 +25,9 @@ import static compbio.ws.client.Constraints.paramFile;
 import java.io.Closeable;
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.io.PrintWriter;
 import java.io.Writer;
 import java.net.ConnectException;
@@ -48,6 +50,8 @@ import compbio.data.msa.MsaWS;
 import compbio.data.msa.RegistryWS;
 import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
+import compbio.data.sequence.AlignmentMetadata;
+import compbio.data.sequence.JpredAlignment;
 import compbio.data.sequence.FastaSequence;
 import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
@@ -100,6 +104,7 @@ public class Jws2Client {
 	 *            command line options
 	 * @throws IOException
 	 */
+	@SuppressWarnings("unchecked")
 	<T> Jws2Client(String[] cmd) throws IOException {
 		
 
@@ -161,17 +166,29 @@ public class Jws2Client {
 			if (outfile != null) {
 				writer = IOHelper.getWriter(outfile);
 			} else {
-				// this stream is going to be closed later which is fine as std.out will not be
 				writer = new PrintWriter(System.out, true);
 			}
 			if (service.getServiceType() == SequenceAnnotation.class) {
 				ScoreManager result = analize(infile, ((SequenceAnnotation<T>) thews), preset, customOptions);
 				IOHelper.writeOut(writer, result);
+				writer.close();
 			} else if (service.getServiceType() == MsaWS.class) {
 				Alignment alignment = align(infile, (MsaWS<T>) thews, preset, customOptions);
-				IOHelper.writeOut(writer, alignment);
+				if (serviceName.equalsIgnoreCase("JpredWS")) {
+					writer.close();
+					JpredAlignment jpred = new JpredAlignment(alignment.getSequences(), alignment.getMetadata());
+					if (outfile != null) {
+						FileOutputStream fout = new FileOutputStream(outfile);
+						SequenceUtil.writeFastaKeepTheStream(fout, jpred.getJpredSequences(), 60);
+						fout.close();
+					} else {
+						SequenceUtil.writeFasta(System.out, jpred.getJpredSequences());
+					}
+				} else {
+					IOHelper.writeOut(writer, alignment);
+					writer.close();
+				}
 			}
-			writer.close();
 		}
 
 		if (CmdHelper.listParameters(cmd)) {
@@ -412,11 +429,10 @@ public class Jws2Client {
 	static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,
 			List<Option<T>> customOptions) {
 		FileInputStream instream = null;
-		List<FastaSequence> fastalist = null;
 		Alignment alignment = null;
 		try {
 			instream = new FileInputStream(file);
-			fastalist = SequenceUtil.readFasta(instream);
+			List<FastaSequence> fastalist = SequenceUtil.readFasta(instream);
 			instream.close();
 			String jobId = null;
 			if (customOptions != null && preset != null) {
@@ -429,22 +445,18 @@ public class Jws2Client {
 			} else {
 				jobId = msaws.align(fastalist);
 			}
-			System.out.println("\ncalling aligner.........");
-			Thread.sleep(1000);
+			System.out.println("\ncalling program.........");
+			Thread.sleep(100);
 			alignment = msaws.getResult(jobId);
-
 		} catch (IOException e) {
-			System.err.println("Exception while reading the input file. "
-						+ "Check that the input file contains a list of fasta formatted sequences! "
+			System.err.println("Exception while reading the input file. Check that the input file is a FASTA file! "
 						+ "Exception details are below:");
 			e.printStackTrace();
 		} catch (JobSubmissionException e) {
-			System.err.println("Exception while submitting job to a web server. "
-						+ "Exception details are below:");
+			System.err.println("Exception while submitting job to a web server. Exception details are below:");
 			e.printStackTrace();
 		} catch (ResultNotAvailableException e) {
-			System.err.println("Exception while waiting for results. "
-					+ "Exception details are below:");
+			System.err.println("Exception while waiting for results. Exception details are below:");
 			e.printStackTrace();
 		} catch (InterruptedException ignored) {
 			// ignore and propagate an interruption