From 5578f2d3e8226bd931755da3feeecb91fdb26c3f Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Tue, 17 Sep 2013 15:35:24 +0100
Subject: [PATCH] Final fixing of Jpred problem with casting

---
 datamodel/compbio/data/sequence/Alignment.java            |    4 +++-
 webservices/compbio/ws/client/Jws2Client.java             |    3 +++
 .../compbio/ws/server/resource/ClustalWS_schema1.xsd      |   13 +++++++++++--
 .../compbio/ws/server/resource/JpredWS_schema1.xsd        |   13 +++++++++++--
 .../compbio/ws/server/resource/MafftWS_schema1.xsd        |   13 +++++++++++--
 .../compbio/ws/server/resource/MuscleWS_schema1.xsd       |   13 +++++++++++--
 .../compbio/ws/server/resource/TcoffeeWS_schema1.xsd      |   13 +++++++++++--
 wsbuild.log                                               |    2 +-
 8 files changed, 62 insertions(+), 12 deletions(-)

diff --git a/datamodel/compbio/data/sequence/Alignment.java b/datamodel/compbio/data/sequence/Alignment.java
index 0893082..cf76839 100644
--- a/datamodel/compbio/data/sequence/Alignment.java
+++ b/datamodel/compbio/data/sequence/Alignment.java
@@ -22,6 +22,7 @@ import java.util.List;
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlSeeAlso;
 
 import compbio.util.annotation.Immutable;
 
@@ -40,6 +41,7 @@ import compbio.util.annotation.Immutable;
  * @version 1.0 September 2009
  * 
  */
+@XmlSeeAlso({JpredAlignment.class})
 @XmlAccessorType(XmlAccessType.FIELD)
 public class Alignment {
 
@@ -58,7 +60,7 @@ public class Alignment {
 	public Alignment(List<FastaSequence> sequences, Program program,
 			char gapchar) {
 		this.sequences = sequences;
-		this.metadata = new AlignmentMetadata(Program.CLUSTAL, gapchar);
+		this.metadata = new AlignmentMetadata(program, gapchar);
 	}
 
 	/**
diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index d46d978..666fa58 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -49,6 +49,7 @@ 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;
@@ -186,6 +187,8 @@ public class Jws2Client {
 					IOHelper.writeOut(writer, alignment);
 					writer.close();
 				}
+				AlignmentMetadata md = alignment.getMetadata();
+				System.out.println("Output has been prepared with " + md.getProgram());
 			}
 		}
 
diff --git a/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd b/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
index 7bd79b9..870ed7f 100644
--- a/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
@@ -155,6 +155,14 @@
     </xs:sequence>
   </xs:complexType>
 
+  <xs:complexType name="jpredAlignment">
+    <xs:complexContent>
+      <xs:extension base="tns:alignment">
+        <xs:sequence/>
+      </xs:extension>
+    </xs:complexContent>
+  </xs:complexType>
+
   <xs:complexType name="ResultNotAvailableException">
     <xs:sequence>
       <xs:element name="message" type="xs:string" minOccurs="0"/>
@@ -352,8 +360,9 @@
   <xs:simpleType name="program">
     <xs:restriction base="xs:string">
       <xs:enumeration value="CLUSTAL"/>
-      <xs:enumeration value="MAFFT"/>
-      <xs:enumeration value="MUSCLE"/>
+      <xs:enumeration value="ClustalO"/>
+      <xs:enumeration value="Mafft"/>
+      <xs:enumeration value="Muscle"/>
       <xs:enumeration value="Tcoffee"/>
       <xs:enumeration value="Probcons"/>
       <xs:enumeration value="Jpred"/>
diff --git a/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd b/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
index 3053136..4b7e61a 100644
--- a/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
@@ -310,6 +310,14 @@
     </xs:sequence>
   </xs:complexType>
 
+  <xs:complexType name="jpredAlignment">
+    <xs:complexContent>
+      <xs:extension base="tns:alignment">
+        <xs:sequence/>
+      </xs:extension>
+    </xs:complexContent>
+  </xs:complexType>
+
   <xs:complexType name="ResultNotAvailableException">
     <xs:sequence>
       <xs:element name="message" type="xs:string" minOccurs="0"/>
@@ -338,8 +346,9 @@
   <xs:simpleType name="program">
     <xs:restriction base="xs:string">
       <xs:enumeration value="CLUSTAL"/>
-      <xs:enumeration value="MAFFT"/>
-      <xs:enumeration value="MUSCLE"/>
+      <xs:enumeration value="ClustalO"/>
+      <xs:enumeration value="Mafft"/>
+      <xs:enumeration value="Muscle"/>
       <xs:enumeration value="Tcoffee"/>
       <xs:enumeration value="Probcons"/>
       <xs:enumeration value="Jpred"/>
diff --git a/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd b/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
index 7bd79b9..870ed7f 100644
--- a/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
@@ -155,6 +155,14 @@
     </xs:sequence>
   </xs:complexType>
 
+  <xs:complexType name="jpredAlignment">
+    <xs:complexContent>
+      <xs:extension base="tns:alignment">
+        <xs:sequence/>
+      </xs:extension>
+    </xs:complexContent>
+  </xs:complexType>
+
   <xs:complexType name="ResultNotAvailableException">
     <xs:sequence>
       <xs:element name="message" type="xs:string" minOccurs="0"/>
@@ -352,8 +360,9 @@
   <xs:simpleType name="program">
     <xs:restriction base="xs:string">
       <xs:enumeration value="CLUSTAL"/>
-      <xs:enumeration value="MAFFT"/>
-      <xs:enumeration value="MUSCLE"/>
+      <xs:enumeration value="ClustalO"/>
+      <xs:enumeration value="Mafft"/>
+      <xs:enumeration value="Muscle"/>
       <xs:enumeration value="Tcoffee"/>
       <xs:enumeration value="Probcons"/>
       <xs:enumeration value="Jpred"/>
diff --git a/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd b/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
index 0cd8da8..4f205ab 100644
--- a/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
@@ -310,6 +310,14 @@
     </xs:sequence>
   </xs:complexType>
 
+  <xs:complexType name="jpredAlignment">
+    <xs:complexContent>
+      <xs:extension base="tns:alignment">
+        <xs:sequence/>
+      </xs:extension>
+    </xs:complexContent>
+  </xs:complexType>
+
   <xs:complexType name="ResultNotAvailableException">
     <xs:sequence>
       <xs:element name="message" type="xs:string" minOccurs="0"/>
@@ -338,8 +346,9 @@
   <xs:simpleType name="program">
     <xs:restriction base="xs:string">
       <xs:enumeration value="CLUSTAL"/>
-      <xs:enumeration value="MAFFT"/>
-      <xs:enumeration value="MUSCLE"/>
+      <xs:enumeration value="ClustalO"/>
+      <xs:enumeration value="Mafft"/>
+      <xs:enumeration value="Muscle"/>
       <xs:enumeration value="Tcoffee"/>
       <xs:enumeration value="Probcons"/>
       <xs:enumeration value="Jpred"/>
diff --git a/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd b/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
index de826f8..2095e1a 100644
--- a/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
@@ -310,6 +310,14 @@
     </xs:sequence>
   </xs:complexType>
 
+  <xs:complexType name="jpredAlignment">
+    <xs:complexContent>
+      <xs:extension base="tns:alignment">
+        <xs:sequence/>
+      </xs:extension>
+    </xs:complexContent>
+  </xs:complexType>
+
   <xs:complexType name="ResultNotAvailableException">
     <xs:sequence>
       <xs:element name="message" type="xs:string" minOccurs="0"/>
@@ -338,8 +346,9 @@
   <xs:simpleType name="program">
     <xs:restriction base="xs:string">
       <xs:enumeration value="CLUSTAL"/>
-      <xs:enumeration value="MAFFT"/>
-      <xs:enumeration value="MUSCLE"/>
+      <xs:enumeration value="ClustalO"/>
+      <xs:enumeration value="Mafft"/>
+      <xs:enumeration value="Muscle"/>
       <xs:enumeration value="Tcoffee"/>
       <xs:enumeration value="Probcons"/>
       <xs:enumeration value="Jpred"/>
diff --git a/wsbuild.log b/wsbuild.log
index 466275f..5b45197 100644
--- a/wsbuild.log
+++ b/wsbuild.log
@@ -1333,4 +1333,4 @@ build-server:
     [wsgen] Note: 	ap round: 2
 
 BUILD SUCCESSFUL
-Total time: 9 seconds
+Total time: 8 seconds
-- 
1.7.10.2