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 (file)
--- a/datamodel/compbio/data/sequence/JpredAlignment.java
+++ b/datamodel/compbio/data/sequence/JpredAlignment.java
@@ -43,7 +43,7 @@ import compbio.data.sequence.Alignment;
  * \r
  */\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-public final class JpredAlignment extends Alignment{\r
+public class JpredAlignment extends Alignment{\r
 \r
        private JpredAlignment() {\r
                // This has to has a default constructor for JaxB\r

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index eac049e..2a2f3d1 100644 (file)
--- 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);\r
                                if (serviceName.equalsIgnoreCase("JpredWS")) {\r
                                        writer.close();\r
-                                       JpredAlignment jpred = new JpredAlignment(alignment.getSequences(), alignment.getMetadata());\r
+                                       JpredAlignment jpred = (JpredAlignment)alignment;\r
                                        if (outfile != null) {\r
                                                FileOutputStream fout = new FileOutputStream(outfile);\r
                                                SequenceUtil.writeFastaKeepTheStream(fout, jpred.getJpredSequences(), 60);\r