New client code for JPred service includes return of msa and
authorjprocter <Jim Procter>
Wed, 6 Apr 2005 16:03:52 +0000 (16:03 +0000)
committerjprocter <Jim Procter>
Wed, 6 Apr 2005 16:03:52 +0000 (16:03 +0000)
Jprediction, and better job status information
(vamsas.dataTypes.Result).

src/ext/vamsas/JPredWS.java
src/ext/vamsas/JPredWSService.java
src/ext/vamsas/JPredWSServiceLocator.java
src/ext/vamsas/JpredResult.java [new file with mode: 0755]
src/ext/vamsas/JpredSoapBindingStub.java
src/ext/vamsas/Msfalignment.java [new file with mode: 0755]
src/ext/vamsas/Result.java [new file with mode: 0755]
src/ext/vamsas/Secstructpred.java
src/ext/vamsas/Sequence.java

index 86226c0..6d7eae1 100755 (executable)
@@ -2,12 +2,14 @@
  * JPredWS.java
  *
  * This file was auto-generated from WSDL
  * JPredWS.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis WSDL2Java emitter.
+ * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
 
 public interface JPredWS extends java.rmi.Remote {
     public java.lang.String predict(ext.vamsas.Sequence in0) throws java.rmi.RemoteException;
  */
 
 package ext.vamsas;
 
 public interface JPredWS extends java.rmi.Remote {
     public java.lang.String predict(ext.vamsas.Sequence in0) throws java.rmi.RemoteException;
+    public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0) throws java.rmi.RemoteException;
     public ext.vamsas.Secstructpred getpredict(java.lang.String in0) throws java.rmi.RemoteException;
     public ext.vamsas.Secstructpred getpredict(java.lang.String in0) throws java.rmi.RemoteException;
+    public ext.vamsas.JpredResult getresult(java.lang.String in0) throws java.rmi.RemoteException;
 }
 }
index c97627f..f6049ee 100755 (executable)
@@ -2,7 +2,7 @@
  * JPredWSService.java
  *
  * This file was auto-generated from WSDL
  * JPredWSService.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis WSDL2Java emitter.
+ * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
  */
 
 package ext.vamsas;
index 976d2fd..05fcd5a 100755 (executable)
@@ -2,15 +2,27 @@
  * JPredWSServiceLocator.java
  *
  * This file was auto-generated from WSDL
  * JPredWSServiceLocator.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis WSDL2Java emitter.
+ * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
 
 public class JPredWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.JPredWSService {
 
  */
 
 package ext.vamsas;
 
 public class JPredWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.JPredWSService {
 
+    public JPredWSServiceLocator() {
+    }
+
+
+    public JPredWSServiceLocator(org.apache.axis.EngineConfiguration config) {
+        super(config);
+    }
+
+    public JPredWSServiceLocator(java.lang.String wsdlLoc, javax.xml.namespace.QName sName) throws javax.xml.rpc.ServiceException {
+        super(wsdlLoc, sName);
+    }
+
     // Use to get a proxy class for jpred
     // Use to get a proxy class for jpred
-    private final java.lang.String jpred_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/jpred";
+    private java.lang.String jpred_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/jpred";
 
     public java.lang.String getjpredAddress() {
         return jpred_address;
 
     public java.lang.String getjpredAddress() {
         return jpred_address;
@@ -49,6 +61,10 @@ public class JPredWSServiceLocator extends org.apache.axis.client.Service implem
         }
     }
 
         }
     }
 
+    public void setjpredEndpointAddress(java.lang.String address) {
+        jpred_address = address;
+    }
+
     /**
      * For the given interface, get the stub implementation.
      * If this service has no port for the given interface,
     /**
      * For the given interface, get the stub implementation.
      * If this service has no port for the given interface,
@@ -77,7 +93,7 @@ public class JPredWSServiceLocator extends org.apache.axis.client.Service implem
         if (portName == null) {
             return getPort(serviceEndpointInterface);
         }
         if (portName == null) {
             return getPort(serviceEndpointInterface);
         }
-        String inputPortName = portName.getLocalPart();
+        java.lang.String inputPortName = portName.getLocalPart();
         if ("jpred".equals(inputPortName)) {
             return getjpred();
         }
         if ("jpred".equals(inputPortName)) {
             return getjpred();
         }
@@ -97,9 +113,28 @@ public class JPredWSServiceLocator extends org.apache.axis.client.Service implem
     public java.util.Iterator getPorts() {
         if (ports == null) {
             ports = new java.util.HashSet();
     public java.util.Iterator getPorts() {
         if (ports == null) {
             ports = new java.util.HashSet();
-            ports.add(new javax.xml.namespace.QName("jpred"));
+            ports.add(new javax.xml.namespace.QName("vamsas", "jpred"));
         }
         return ports.iterator();
     }
 
         }
         return ports.iterator();
     }
 
+    /**
+    * Set the endpoint address for the specified port name.
+    */
+    public void setEndpointAddress(java.lang.String portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
+        if ("jpred".equals(portName)) {
+            setjpredEndpointAddress(address);
+        }
+        else { // Unknown Port Name
+            throw new javax.xml.rpc.ServiceException(" Cannot set Endpoint Address for Unknown Port" + portName);
+        }
+    }
+
+    /**
+    * Set the endpoint address for the specified port name.
+    */
+    public void setEndpointAddress(javax.xml.namespace.QName portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
+        setEndpointAddress(portName.getLocalPart(), address);
+    }
+
 }
 }
diff --git a/src/ext/vamsas/JpredResult.java b/src/ext/vamsas/JpredResult.java
new file mode 100755 (executable)
index 0000000..c968231
--- /dev/null
@@ -0,0 +1,154 @@
+/**
+ * JpredResult.java
+ *
+ * This file was auto-generated from WSDL
+ * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ */
+
+package ext.vamsas;
+
+public class JpredResult  extends ext.vamsas.Result  implements java.io.Serializable {
+    private java.lang.String aligfile;
+    private java.lang.String predfile;
+
+    public JpredResult() {
+    }
+
+    public JpredResult(
+           java.lang.String aligfile,
+           java.lang.String predfile) {
+           this.aligfile = aligfile;
+           this.predfile = predfile;
+    }
+
+
+    /**
+     * Gets the aligfile value for this JpredResult.
+     * 
+     * @return aligfile
+     */
+    public java.lang.String getAligfile() {
+        return aligfile;
+    }
+
+
+    /**
+     * Sets the aligfile value for this JpredResult.
+     * 
+     * @param aligfile
+     */
+    public void setAligfile(java.lang.String aligfile) {
+        this.aligfile = aligfile;
+    }
+
+
+    /**
+     * Gets the predfile value for this JpredResult.
+     * 
+     * @return predfile
+     */
+    public java.lang.String getPredfile() {
+        return predfile;
+    }
+
+
+    /**
+     * Sets the predfile value for this JpredResult.
+     * 
+     * @param predfile
+     */
+    public void setPredfile(java.lang.String predfile) {
+        this.predfile = predfile;
+    }
+
+    private java.lang.Object __equalsCalc = null;
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof JpredResult)) return false;
+        JpredResult other = (JpredResult) obj;
+        if (obj == null) return false;
+        if (this == obj) return true;
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+        __equalsCalc = obj;
+        boolean _equals;
+        _equals = super.equals(obj) && 
+            ((this.aligfile==null && other.getAligfile()==null) || 
+             (this.aligfile!=null &&
+              this.aligfile.equals(other.getAligfile()))) &&
+            ((this.predfile==null && other.getPredfile()==null) || 
+             (this.predfile!=null &&
+              this.predfile.equals(other.getPredfile())));
+        __equalsCalc = null;
+        return _equals;
+    }
+
+    private boolean __hashCodeCalc = false;
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+        __hashCodeCalc = true;
+        int _hashCode = super.hashCode();
+        if (getAligfile() != null) {
+            _hashCode += getAligfile().hashCode();
+        }
+        if (getPredfile() != null) {
+            _hashCode += getPredfile().hashCode();
+        }
+        __hashCodeCalc = false;
+        return _hashCode;
+    }
+
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc =
+        new org.apache.axis.description.TypeDesc(JpredResult.class, true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult"));
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("aligfile");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "aligfile"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
+        elemField.setNillable(true);
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("predfile");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "predfile"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
+        elemField.setNillable(true);
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    /**
+     * Return type metadata object
+     */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
+    /**
+     * Get Custom Serializer
+     */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanSerializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+    /**
+     * Get Custom Deserializer
+     */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanDeserializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+}
index 20ca810..e97ed2a 100755 (executable)
@@ -2,7 +2,7 @@
  * JpredSoapBindingStub.java
  *
  * This file was auto-generated from WSDL
  * JpredSoapBindingStub.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis WSDL2Java emitter.
+ * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
  */
 
 package ext.vamsas;
@@ -16,7 +16,11 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
     static org.apache.axis.description.OperationDesc [] _operations;
 
     static {
     static org.apache.axis.description.OperationDesc [] _operations;
 
     static {
-        _operations = new org.apache.axis.description.OperationDesc[2];
+        _operations = new org.apache.axis.description.OperationDesc[4];
+        _initOperationDesc1();
+    }
+
+    private static void _initOperationDesc1(){
         org.apache.axis.description.OperationDesc oper;
         oper = new org.apache.axis.description.OperationDesc();
         oper.setName("predict");
         org.apache.axis.description.OperationDesc oper;
         oper = new org.apache.axis.description.OperationDesc();
         oper.setName("predict");
@@ -24,19 +28,39 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
         oper.setReturnType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
         oper.setReturnClass(java.lang.String.class);
         oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "predictReturn"));
         oper.setReturnType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
         oper.setReturnClass(java.lang.String.class);
         oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "predictReturn"));
-        oper.setStyle(org.apache.axis.enum.Style.WRAPPED);
-        oper.setUse(org.apache.axis.enum.Use.LITERAL);
+        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+        oper.setUse(org.apache.axis.constants.Use.LITERAL);
         _operations[0] = oper;
 
         oper = new org.apache.axis.description.OperationDesc();
         _operations[0] = oper;
 
         oper = new org.apache.axis.description.OperationDesc();
+        oper.setName("predictOnMsa");
+        oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://dataTypes.vamsas", "Msfalignment"), ext.vamsas.Msfalignment.class, org.apache.axis.description.ParameterDesc.IN, false, false);
+        oper.setReturnType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
+        oper.setReturnClass(java.lang.String.class);
+        oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "predictOnMsaReturn"));
+        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+        oper.setUse(org.apache.axis.constants.Use.LITERAL);
+        _operations[1] = oper;
+
+        oper = new org.apache.axis.description.OperationDesc();
         oper.setName("getpredict");
         oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
         oper.setReturnType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Secstructpred"));
         oper.setReturnClass(ext.vamsas.Secstructpred.class);
         oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "getpredictReturn"));
         oper.setName("getpredict");
         oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
         oper.setReturnType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Secstructpred"));
         oper.setReturnClass(ext.vamsas.Secstructpred.class);
         oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "getpredictReturn"));
-        oper.setStyle(org.apache.axis.enum.Style.WRAPPED);
-        oper.setUse(org.apache.axis.enum.Use.LITERAL);
-        _operations[1] = oper;
+        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+        oper.setUse(org.apache.axis.constants.Use.LITERAL);
+        _operations[2] = oper;
+
+        oper = new org.apache.axis.description.OperationDesc();
+        oper.setName("getresult");
+        oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
+        oper.setReturnType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult"));
+        oper.setReturnClass(ext.vamsas.JpredResult.class);
+        oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "getresultReturn"));
+        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+        oper.setUse(org.apache.axis.constants.Use.LITERAL);
+        _operations[3] = oper;
 
     }
 
 
     }
 
@@ -55,6 +79,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
         } else {
             super.service = service;
         }
         } else {
             super.service = service;
         }
+        ((org.apache.axis.client.Service)super.service).setTypeMappingVersion("1.2");
             java.lang.Class cls;
             javax.xml.namespace.QName qName;
             java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
             java.lang.Class cls;
             javax.xml.namespace.QName qName;
             java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
@@ -65,9 +90,11 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
             java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
             java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
             java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
             java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
             java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
             java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
-            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence");
+            java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
+            java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
+            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Msfalignment");
             cachedSerQNames.add(qName);
             cachedSerQNames.add(qName);
-            cls = ext.vamsas.Sequence.class;
+            cls = ext.vamsas.Msfalignment.class;
             cachedSerClasses.add(cls);
             cachedSerFactories.add(beansf);
             cachedDeserFactories.add(beandf);
             cachedSerClasses.add(cls);
             cachedSerFactories.add(beansf);
             cachedDeserFactories.add(beandf);
@@ -79,9 +106,30 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
             cachedSerFactories.add(beansf);
             cachedDeserFactories.add(beandf);
 
             cachedSerFactories.add(beansf);
             cachedDeserFactories.add(beandf);
 
+            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult");
+            cachedSerQNames.add(qName);
+            cls = ext.vamsas.JpredResult.class;
+            cachedSerClasses.add(cls);
+            cachedSerFactories.add(beansf);
+            cachedDeserFactories.add(beandf);
+
+            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Result");
+            cachedSerQNames.add(qName);
+            cls = ext.vamsas.Result.class;
+            cachedSerClasses.add(cls);
+            cachedSerFactories.add(beansf);
+            cachedDeserFactories.add(beandf);
+
+            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence");
+            cachedSerQNames.add(qName);
+            cls = ext.vamsas.Sequence.class;
+            cachedSerClasses.add(cls);
+            cachedSerFactories.add(beansf);
+            cachedDeserFactories.add(beandf);
+
     }
 
     }
 
-    private org.apache.axis.client.Call createCall() throws java.rmi.RemoteException {
+    protected org.apache.axis.client.Call createCall() throws java.rmi.RemoteException {
         try {
             org.apache.axis.client.Call _call =
                     (org.apache.axis.client.Call) super.service.createCall();
         try {
             org.apache.axis.client.Call _call =
                     (org.apache.axis.client.Call) super.service.createCall();
@@ -121,18 +169,28 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
                         java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
                         javax.xml.namespace.QName qName =
                                 (javax.xml.namespace.QName) cachedSerQNames.get(i);
                         java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
                         javax.xml.namespace.QName qName =
                                 (javax.xml.namespace.QName) cachedSerQNames.get(i);
-                        java.lang.Class sf = (java.lang.Class)
+                        java.lang.Object x = cachedSerFactories.get(i);
+                        if (x instanceof Class) {
+                            java.lang.Class sf = (java.lang.Class)
+                                 cachedSerFactories.get(i);
+                            java.lang.Class df = (java.lang.Class)
+                                 cachedDeserFactories.get(i);
+                            _call.registerTypeMapping(cls, qName, sf, df, false);
+                        }
+                        else if (x instanceof javax.xml.rpc.encoding.SerializerFactory) {
+                            org.apache.axis.encoding.SerializerFactory sf = (org.apache.axis.encoding.SerializerFactory)
                                  cachedSerFactories.get(i);
                                  cachedSerFactories.get(i);
-                        java.lang.Class df = (java.lang.Class)
+                            org.apache.axis.encoding.DeserializerFactory df = (org.apache.axis.encoding.DeserializerFactory)
                                  cachedDeserFactories.get(i);
                                  cachedDeserFactories.get(i);
-                        _call.registerTypeMapping(cls, qName, sf, df, false);
+                            _call.registerTypeMapping(cls, qName, sf, df, false);
+                        }
                     }
                 }
             }
             return _call;
         }
                     }
                 }
             }
             return _call;
         }
-        catch (java.lang.Throwable t) {
-            throw new org.apache.axis.AxisFault("Failure trying to get the Call object", t);
+        catch (java.lang.Throwable _t) {
+            throw new org.apache.axis.AxisFault("Failure trying to get the Call object", _t);
         }
     }
 
         }
     }
 
@@ -152,7 +210,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
 
         setRequestHeaders(_call);
         setAttachments(_call);
 
         setRequestHeaders(_call);
         setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
+ try {        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
 
         if (_resp instanceof java.rmi.RemoteException) {
             throw (java.rmi.RemoteException)_resp;
 
         if (_resp instanceof java.rmi.RemoteException) {
             throw (java.rmi.RemoteException)_resp;
@@ -165,9 +223,12 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
                 return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp, java.lang.String.class);
             }
         }
                 return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp, java.lang.String.class);
             }
         }
+  } catch (org.apache.axis.AxisFault axisFaultException) {
+  throw axisFaultException;
+}
     }
 
     }
 
-    public ext.vamsas.Secstructpred getpredict(java.lang.String in0) throws java.rmi.RemoteException {
+    public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0) throws java.rmi.RemoteException {
         if (super.cachedEndpoint == null) {
             throw new org.apache.axis.NoEndPointException();
         }
         if (super.cachedEndpoint == null) {
             throw new org.apache.axis.NoEndPointException();
         }
@@ -179,11 +240,45 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
         _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
         _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
         _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
         _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
         _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
         _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "predictOnMsa"));
+
+        setRequestHeaders(_call);
+        setAttachments(_call);
+ try {        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
+
+        if (_resp instanceof java.rmi.RemoteException) {
+            throw (java.rmi.RemoteException)_resp;
+        }
+        else {
+            extractAttachments(_call);
+            try {
+                return (java.lang.String) _resp;
+            } catch (java.lang.Exception _exception) {
+                return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp, java.lang.String.class);
+            }
+        }
+  } catch (org.apache.axis.AxisFault axisFaultException) {
+  throw axisFaultException;
+}
+    }
+
+    public ext.vamsas.Secstructpred getpredict(java.lang.String in0) throws java.rmi.RemoteException {
+        if (super.cachedEndpoint == null) {
+            throw new org.apache.axis.NoEndPointException();
+        }
+        org.apache.axis.client.Call _call = createCall();
+        _call.setOperation(_operations[2]);
+        _call.setUseSOAPAction(true);
+        _call.setSOAPActionURI("");
+        _call.setEncodingStyle(null);
+        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
+        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
+        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
         _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getpredict"));
 
         setRequestHeaders(_call);
         setAttachments(_call);
         _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getpredict"));
 
         setRequestHeaders(_call);
         setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
+ try {        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
 
         if (_resp instanceof java.rmi.RemoteException) {
             throw (java.rmi.RemoteException)_resp;
 
         if (_resp instanceof java.rmi.RemoteException) {
             throw (java.rmi.RemoteException)_resp;
@@ -196,6 +291,43 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
                 return (ext.vamsas.Secstructpred) org.apache.axis.utils.JavaUtils.convert(_resp, ext.vamsas.Secstructpred.class);
             }
         }
                 return (ext.vamsas.Secstructpred) org.apache.axis.utils.JavaUtils.convert(_resp, ext.vamsas.Secstructpred.class);
             }
         }
+  } catch (org.apache.axis.AxisFault axisFaultException) {
+  throw axisFaultException;
+}
+    }
+
+    public ext.vamsas.JpredResult getresult(java.lang.String in0) throws java.rmi.RemoteException {
+        if (super.cachedEndpoint == null) {
+            throw new org.apache.axis.NoEndPointException();
+        }
+        org.apache.axis.client.Call _call = createCall();
+        _call.setOperation(_operations[3]);
+        _call.setUseSOAPAction(true);
+        _call.setSOAPActionURI("");
+        _call.setEncodingStyle(null);
+        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
+        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
+        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getresult"));
+
+        setRequestHeaders(_call);
+        setAttachments(_call);
+ try {        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
+
+        if (_resp instanceof java.rmi.RemoteException) {
+            throw (java.rmi.RemoteException)_resp;
+        }
+        else {
+            extractAttachments(_call);
+            try {
+                return (ext.vamsas.JpredResult) _resp;
+            } catch (java.lang.Exception _exception) {
+                return (ext.vamsas.JpredResult) org.apache.axis.utils.JavaUtils.convert(_resp, ext.vamsas.JpredResult.class);
+            }
+        }
+  } catch (org.apache.axis.AxisFault axisFaultException) {
+  throw axisFaultException;
+}
     }
 
 }
     }
 
 }
diff --git a/src/ext/vamsas/Msfalignment.java b/src/ext/vamsas/Msfalignment.java
new file mode 100755 (executable)
index 0000000..ff8aac1
--- /dev/null
@@ -0,0 +1,154 @@
+/**
+ * Msfalignment.java
+ *
+ * This file was auto-generated from WSDL
+ * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ */
+
+package ext.vamsas;
+
+public class Msfalignment  implements java.io.Serializable {
+    private java.lang.String msf;
+    private java.lang.String notes;
+
+    public Msfalignment() {
+    }
+
+    public Msfalignment(
+           java.lang.String msf,
+           java.lang.String notes) {
+           this.msf = msf;
+           this.notes = notes;
+    }
+
+
+    /**
+     * Gets the msf value for this Msfalignment.
+     * 
+     * @return msf
+     */
+    public java.lang.String getMsf() {
+        return msf;
+    }
+
+
+    /**
+     * Sets the msf value for this Msfalignment.
+     * 
+     * @param msf
+     */
+    public void setMsf(java.lang.String msf) {
+        this.msf = msf;
+    }
+
+
+    /**
+     * Gets the notes value for this Msfalignment.
+     * 
+     * @return notes
+     */
+    public java.lang.String getNotes() {
+        return notes;
+    }
+
+
+    /**
+     * Sets the notes value for this Msfalignment.
+     * 
+     * @param notes
+     */
+    public void setNotes(java.lang.String notes) {
+        this.notes = notes;
+    }
+
+    private java.lang.Object __equalsCalc = null;
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Msfalignment)) return false;
+        Msfalignment other = (Msfalignment) obj;
+        if (obj == null) return false;
+        if (this == obj) return true;
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+        __equalsCalc = obj;
+        boolean _equals;
+        _equals = true && 
+            ((this.msf==null && other.getMsf()==null) || 
+             (this.msf!=null &&
+              this.msf.equals(other.getMsf()))) &&
+            ((this.notes==null && other.getNotes()==null) || 
+             (this.notes!=null &&
+              this.notes.equals(other.getNotes())));
+        __equalsCalc = null;
+        return _equals;
+    }
+
+    private boolean __hashCodeCalc = false;
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+        __hashCodeCalc = true;
+        int _hashCode = 1;
+        if (getMsf() != null) {
+            _hashCode += getMsf().hashCode();
+        }
+        if (getNotes() != null) {
+            _hashCode += getNotes().hashCode();
+        }
+        __hashCodeCalc = false;
+        return _hashCode;
+    }
+
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc =
+        new org.apache.axis.description.TypeDesc(Msfalignment.class, true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Msfalignment"));
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("msf");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "msf"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
+        elemField.setNillable(true);
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("notes");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "notes"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
+        elemField.setNillable(true);
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    /**
+     * Return type metadata object
+     */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
+    /**
+     * Get Custom Serializer
+     */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanSerializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+    /**
+     * Get Custom Deserializer
+     */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanDeserializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+}
diff --git a/src/ext/vamsas/Result.java b/src/ext/vamsas/Result.java
new file mode 100755 (executable)
index 0000000..ef8b790
--- /dev/null
@@ -0,0 +1,419 @@
+/**
+ * Result.java
+ *
+ * This file was auto-generated from WSDL
+ * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ */
+
+package ext.vamsas;
+
+public class Result  implements java.io.Serializable {
+    private boolean broken;
+    private boolean failed;
+    private boolean finished;
+    private boolean invalid;
+    private boolean jobFailed;
+    private boolean queued;
+    private boolean running;
+    private boolean serverError;
+    private int state;
+    private java.lang.String status;
+    private boolean suspended;
+
+    public Result() {
+    }
+
+    public Result(
+           boolean broken,
+           boolean failed,
+           boolean finished,
+           boolean invalid,
+           boolean jobFailed,
+           boolean queued,
+           boolean running,
+           boolean serverError,
+           int state,
+           java.lang.String status,
+           boolean suspended) {
+           this.broken = broken;
+           this.failed = failed;
+           this.finished = finished;
+           this.invalid = invalid;
+           this.jobFailed = jobFailed;
+           this.queued = queued;
+           this.running = running;
+           this.serverError = serverError;
+           this.state = state;
+           this.status = status;
+           this.suspended = suspended;
+    }
+
+
+    /**
+     * Gets the broken value for this Result.
+     * 
+     * @return broken
+     */
+    public boolean isBroken() {
+        return broken;
+    }
+
+
+    /**
+     * Sets the broken value for this Result.
+     * 
+     * @param broken
+     */
+    public void setBroken(boolean broken) {
+        this.broken = broken;
+    }
+
+
+    /**
+     * Gets the failed value for this Result.
+     * 
+     * @return failed
+     */
+    public boolean isFailed() {
+        return failed;
+    }
+
+
+    /**
+     * Sets the failed value for this Result.
+     * 
+     * @param failed
+     */
+    public void setFailed(boolean failed) {
+        this.failed = failed;
+    }
+
+
+    /**
+     * Gets the finished value for this Result.
+     * 
+     * @return finished
+     */
+    public boolean isFinished() {
+        return finished;
+    }
+
+
+    /**
+     * Sets the finished value for this Result.
+     * 
+     * @param finished
+     */
+    public void setFinished(boolean finished) {
+        this.finished = finished;
+    }
+
+
+    /**
+     * Gets the invalid value for this Result.
+     * 
+     * @return invalid
+     */
+    public boolean isInvalid() {
+        return invalid;
+    }
+
+
+    /**
+     * Sets the invalid value for this Result.
+     * 
+     * @param invalid
+     */
+    public void setInvalid(boolean invalid) {
+        this.invalid = invalid;
+    }
+
+
+    /**
+     * Gets the jobFailed value for this Result.
+     * 
+     * @return jobFailed
+     */
+    public boolean isJobFailed() {
+        return jobFailed;
+    }
+
+
+    /**
+     * Sets the jobFailed value for this Result.
+     * 
+     * @param jobFailed
+     */
+    public void setJobFailed(boolean jobFailed) {
+        this.jobFailed = jobFailed;
+    }
+
+
+    /**
+     * Gets the queued value for this Result.
+     * 
+     * @return queued
+     */
+    public boolean isQueued() {
+        return queued;
+    }
+
+
+    /**
+     * Sets the queued value for this Result.
+     * 
+     * @param queued
+     */
+    public void setQueued(boolean queued) {
+        this.queued = queued;
+    }
+
+
+    /**
+     * Gets the running value for this Result.
+     * 
+     * @return running
+     */
+    public boolean isRunning() {
+        return running;
+    }
+
+
+    /**
+     * Sets the running value for this Result.
+     * 
+     * @param running
+     */
+    public void setRunning(boolean running) {
+        this.running = running;
+    }
+
+
+    /**
+     * Gets the serverError value for this Result.
+     * 
+     * @return serverError
+     */
+    public boolean isServerError() {
+        return serverError;
+    }
+
+
+    /**
+     * Sets the serverError value for this Result.
+     * 
+     * @param serverError
+     */
+    public void setServerError(boolean serverError) {
+        this.serverError = serverError;
+    }
+
+
+    /**
+     * Gets the state value for this Result.
+     * 
+     * @return state
+     */
+    public int getState() {
+        return state;
+    }
+
+
+    /**
+     * Sets the state value for this Result.
+     * 
+     * @param state
+     */
+    public void setState(int state) {
+        this.state = state;
+    }
+
+
+    /**
+     * Gets the status value for this Result.
+     * 
+     * @return status
+     */
+    public java.lang.String getStatus() {
+        return status;
+    }
+
+
+    /**
+     * Sets the status value for this Result.
+     * 
+     * @param status
+     */
+    public void setStatus(java.lang.String status) {
+        this.status = status;
+    }
+
+
+    /**
+     * Gets the suspended value for this Result.
+     * 
+     * @return suspended
+     */
+    public boolean isSuspended() {
+        return suspended;
+    }
+
+
+    /**
+     * Sets the suspended value for this Result.
+     * 
+     * @param suspended
+     */
+    public void setSuspended(boolean suspended) {
+        this.suspended = suspended;
+    }
+
+    private java.lang.Object __equalsCalc = null;
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Result)) return false;
+        Result other = (Result) obj;
+        if (obj == null) return false;
+        if (this == obj) return true;
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+        __equalsCalc = obj;
+        boolean _equals;
+        _equals = true && 
+            this.broken == other.isBroken() &&
+            this.failed == other.isFailed() &&
+            this.finished == other.isFinished() &&
+            this.invalid == other.isInvalid() &&
+            this.jobFailed == other.isJobFailed() &&
+            this.queued == other.isQueued() &&
+            this.running == other.isRunning() &&
+            this.serverError == other.isServerError() &&
+            this.state == other.getState() &&
+            ((this.status==null && other.getStatus()==null) || 
+             (this.status!=null &&
+              this.status.equals(other.getStatus()))) &&
+            this.suspended == other.isSuspended();
+        __equalsCalc = null;
+        return _equals;
+    }
+
+    private boolean __hashCodeCalc = false;
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+        __hashCodeCalc = true;
+        int _hashCode = 1;
+        _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += getState();
+        if (getStatus() != null) {
+            _hashCode += getStatus().hashCode();
+        }
+        _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        __hashCodeCalc = false;
+        return _hashCode;
+    }
+
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc =
+        new org.apache.axis.description.TypeDesc(Result.class, true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Result"));
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("broken");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "broken"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("failed");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "failed"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("finished");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "finished"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("invalid");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "invalid"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("jobFailed");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "jobFailed"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("queued");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "queued"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("running");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "running"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("serverError");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "serverError"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("state");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "state"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("status");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "status"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
+        elemField.setNillable(true);
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("suspended");
+        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "suspended"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    /**
+     * Return type metadata object
+     */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
+    /**
+     * Get Custom Serializer
+     */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanSerializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+    /**
+     * Get Custom Deserializer
+     */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanDeserializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+}
index cac8ff3..e30edeb 100755 (executable)
@@ -2,7 +2,7 @@
  * Secstructpred.java
  *
  * This file was auto-generated from WSDL
  * Secstructpred.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis WSDL2Java emitter.
+ * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
  */
 
 package ext.vamsas;
@@ -13,10 +13,27 @@ public class Secstructpred  implements java.io.Serializable {
     public Secstructpred() {
     }
 
     public Secstructpred() {
     }
 
+    public Secstructpred(
+           java.lang.String output) {
+           this.output = output;
+    }
+
+
+    /**
+     * Gets the output value for this Secstructpred.
+     * 
+     * @return output
+     */
     public java.lang.String getOutput() {
         return output;
     }
 
     public java.lang.String getOutput() {
         return output;
     }
 
+
+    /**
+     * Sets the output value for this Secstructpred.
+     * 
+     * @param output
+     */
     public void setOutput(java.lang.String output) {
         this.output = output;
     }
     public void setOutput(java.lang.String output) {
         this.output = output;
     }
@@ -56,7 +73,7 @@ public class Secstructpred  implements java.io.Serializable {
 
     // Type metadata
     private static org.apache.axis.description.TypeDesc typeDesc =
 
     // Type metadata
     private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Secstructpred.class);
+        new org.apache.axis.description.TypeDesc(Secstructpred.class, true);
 
     static {
         typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Secstructpred"));
 
     static {
         typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Secstructpred"));
@@ -64,6 +81,7 @@ public class Secstructpred  implements java.io.Serializable {
         elemField.setFieldName("output");
         elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "output"));
         elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
         elemField.setFieldName("output");
         elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "output"));
         elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
+        elemField.setNillable(true);
         typeDesc.addFieldDesc(elemField);
     }
 
         typeDesc.addFieldDesc(elemField);
     }
 
index 2ee347a..1fc4be7 100755 (executable)
@@ -2,7 +2,7 @@
  * Sequence.java
  *
  * This file was auto-generated from WSDL
  * Sequence.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis WSDL2Java emitter.
+ * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
  */
 
 package ext.vamsas;
@@ -14,18 +14,49 @@ public class Sequence  implements java.io.Serializable {
     public Sequence() {
     }
 
     public Sequence() {
     }
 
+    public Sequence(
+           java.lang.String id,
+           java.lang.String seq) {
+           this.id = id;
+           this.seq = seq;
+    }
+
+
+    /**
+     * Gets the id value for this Sequence.
+     * 
+     * @return id
+     */
     public java.lang.String getId() {
         return id;
     }
 
     public java.lang.String getId() {
         return id;
     }
 
+
+    /**
+     * Sets the id value for this Sequence.
+     * 
+     * @param id
+     */
     public void setId(java.lang.String id) {
         this.id = id;
     }
 
     public void setId(java.lang.String id) {
         this.id = id;
     }
 
+
+    /**
+     * Gets the seq value for this Sequence.
+     * 
+     * @return seq
+     */
     public java.lang.String getSeq() {
         return seq;
     }
 
     public java.lang.String getSeq() {
         return seq;
     }
 
+
+    /**
+     * Sets the seq value for this Sequence.
+     * 
+     * @param seq
+     */
     public void setSeq(java.lang.String seq) {
         this.seq = seq;
     }
     public void setSeq(java.lang.String seq) {
         this.seq = seq;
     }
@@ -71,7 +102,7 @@ public class Sequence  implements java.io.Serializable {
 
     // Type metadata
     private static org.apache.axis.description.TypeDesc typeDesc =
 
     // Type metadata
     private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Sequence.class);
+        new org.apache.axis.description.TypeDesc(Sequence.class, true);
 
     static {
         typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence"));
 
     static {
         typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence"));
@@ -79,11 +110,13 @@ public class Sequence  implements java.io.Serializable {
         elemField.setFieldName("id");
         elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "id"));
         elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
         elemField.setFieldName("id");
         elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "id"));
         elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
+        elemField.setNillable(true);
         typeDesc.addFieldDesc(elemField);
         elemField = new org.apache.axis.description.ElementDesc();
         elemField.setFieldName("seq");
         elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "seq"));
         elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
         typeDesc.addFieldDesc(elemField);
         elemField = new org.apache.axis.description.ElementDesc();
         elemField.setFieldName("seq");
         elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "seq"));
         elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
+        elemField.setNillable(true);
         typeDesc.addFieldDesc(elemField);
     }
 
         typeDesc.addFieldDesc(elemField);
     }