From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 13 Sep 2013 15:43:32 +0000 (+0100)
Subject: Fix problem with wrong casting Alignment -> JpredAlignment
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fcc1bd4d46b998cc86a85b31f763310e659707b7;p=jabaws.git

Fix problem with wrong casting Alignment -> JpredAlignment
---

diff --git a/datamodel/compbio/data/sequence/JpredAlignment.java b/datamodel/compbio/data/sequence/JpredAlignment.java
index 768ac9e..d7d8c5d 100644
--- a/datamodel/compbio/data/sequence/JpredAlignment.java
+++ b/datamodel/compbio/data/sequence/JpredAlignment.java
@@ -43,7 +43,7 @@ import compbio.data.sequence.Alignment;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-public final class JpredAlignment extends Alignment{
+public class JpredAlignment extends Alignment{
 
 	private JpredAlignment() {
 		// This has to has a default constructor for JaxB
diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index eac049e..2a2f3d1 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -176,7 +176,7 @@ public class Jws2Client {
 				Alignment alignment = align(infile, (MsaWS<T>) thews, preset, customOptions);
 				if (serviceName.equalsIgnoreCase("JpredWS")) {
 					writer.close();
-					JpredAlignment jpred = new JpredAlignment(alignment.getSequences(), alignment.getMetadata());
+					JpredAlignment jpred = (JpredAlignment)alignment;
 					if (outfile != null) {
 						FileOutputStream fout = new FileOutputStream(outfile);
 						SequenceUtil.writeFastaKeepTheStream(fout, jpred.getJpredSequences(), 60);