From fcc1bd4d46b998cc86a85b31f763310e659707b7 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Fri, 13 Sep 2013 16:43:32 +0100 Subject: [PATCH] Fix problem with wrong casting Alignment -> JpredAlignment --- datamodel/compbio/data/sequence/JpredAlignment.java | 2 +- webservices/compbio/ws/client/Jws2Client.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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) 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); -- 1.7.10.2