Final fixing of Jpred problem with casting

diff --git a/datamodel/compbio/data/sequence/Alignment.java b/datamodel/compbio/data/sequence/Alignment.java
index 0893082..cf76839 100644 (file)
--- a/datamodel/compbio/data/sequence/Alignment.java
+++ b/datamodel/compbio/data/sequence/Alignment.java
@@ -22,6 +22,7 @@ import java.util.List;
 \r
 import javax.xml.bind.annotation.XmlAccessType;\r
 import javax.xml.bind.annotation.XmlAccessorType;\r
+import javax.xml.bind.annotation.XmlSeeAlso;\r
 \r
 import compbio.util.annotation.Immutable;\r
 \r
@@ -40,6 +41,7 @@ import compbio.util.annotation.Immutable;
  * @version 1.0 September 2009\r
  * \r
  */\r
+@XmlSeeAlso({JpredAlignment.class})\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
 public class Alignment {\r
 \r
@@ -58,7 +60,7 @@ public class Alignment {
        public Alignment(List<FastaSequence> sequences, Program program,\r
                        char gapchar) {\r
                this.sequences = sequences;\r
-               this.metadata = new AlignmentMetadata(Program.CLUSTAL, gapchar);\r
+               this.metadata = new AlignmentMetadata(program, gapchar);\r
        }\r
 \r
        /**\r

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index d46d978..666fa58 100644 (file)
--- 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;\r
 import compbio.data.msa.SequenceAnnotation;\r
 import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.AlignmentMetadata;\r
 import compbio.data.sequence.JpredAlignment;\r
 import compbio.data.sequence.FastaSequence;\r
 import compbio.data.sequence.ScoreManager;\r
@@ -186,6 +187,8 @@ public class Jws2Client {
                                        IOHelper.writeOut(writer, alignment);\r
                                        writer.close();\r
                                }\r
+                               AlignmentMetadata md = alignment.getMetadata();\r
+                               System.out.println("Output has been prepared with " + md.getProgram());\r
                        }\r
                }\r
 \r

diff --git a/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd b/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
index 7bd79b9..870ed7f 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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