recent rebuild of the JPred client from WSDL2Java

diff --git a/src/ext/vamsas/JPredWS.java b/src/ext/vamsas/JPredWS.java
index 6d7eae1..801bf86 100755 (executable)
--- a/src/ext/vamsas/JPredWS.java
+++ b/src/ext/vamsas/JPredWS.java
@@ -2,7 +2,7 @@
  * JPredWS.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;

diff --git a/src/ext/vamsas/JPredWSService.java b/src/ext/vamsas/JPredWSService.java
index f6049ee..e1f8cbe 100755 (executable)
--- a/src/ext/vamsas/JPredWSService.java
+++ b/src/ext/vamsas/JPredWSService.java
@@ -2,7 +2,7 @@
  * JPredWSService.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;

diff --git a/src/ext/vamsas/JPredWSServiceLocator.java b/src/ext/vamsas/JPredWSServiceLocator.java
index 05fcd5a..0faea4c 100755 (executable)
--- a/src/ext/vamsas/JPredWSServiceLocator.java
+++ b/src/ext/vamsas/JPredWSServiceLocator.java
@@ -2,7 +2,7 @@
  * JPredWSServiceLocator.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
@@ -17,10 +17,6 @@ public class JPredWSServiceLocator extends org.apache.axis.client.Service implem
         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
     private java.lang.String jpred_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/jpred";
 

diff --git a/src/ext/vamsas/JpredResult.java b/src/ext/vamsas/JpredResult.java
index c968231..d798def 100755 (executable)
--- a/src/ext/vamsas/JpredResult.java
+++ b/src/ext/vamsas/JpredResult.java
@@ -2,7 +2,7 @@
  * JpredResult.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
@@ -110,13 +110,11 @@ public class JpredResult  extends ext.vamsas.Result  implements java.io.Serializ
         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);
     }
 

diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java
index e97ed2a..f11fbe3 100755 (executable)
--- a/src/ext/vamsas/JpredSoapBindingStub.java
+++ b/src/ext/vamsas/JpredSoapBindingStub.java
@@ -2,7 +2,7 @@
  * JpredSoapBindingStub.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
@@ -79,7 +79,6 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
         } 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;
@@ -92,9 +91,9 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
             java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
             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");
+            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence");
             cachedSerQNames.add(qName);
-            cls = ext.vamsas.Msfalignment.class;
+            cls = ext.vamsas.Sequence.class;
             cachedSerClasses.add(cls);
             cachedSerFactories.add(beansf);
             cachedDeserFactories.add(beandf);
@@ -106,23 +105,23 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
             cachedSerFactories.add(beansf);
             cachedDeserFactories.add(beandf);
 
-            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult");
+            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Msfalignment");
             cachedSerQNames.add(qName);
-            cls = ext.vamsas.JpredResult.class;
+            cls = ext.vamsas.Msfalignment.class;
             cachedSerClasses.add(cls);
             cachedSerFactories.add(beansf);
             cachedDeserFactories.add(beandf);
 
-            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Result");
+            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult");
             cachedSerQNames.add(qName);
-            cls = ext.vamsas.Result.class;
+            cls = ext.vamsas.JpredResult.class;
             cachedSerClasses.add(cls);
             cachedSerFactories.add(beansf);
             cachedDeserFactories.add(beandf);
 
-            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence");
+            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Result");
             cachedSerQNames.add(qName);
-            cls = ext.vamsas.Sequence.class;
+            cls = ext.vamsas.Result.class;
             cachedSerClasses.add(cls);
             cachedSerFactories.add(beansf);
             cachedDeserFactories.add(beandf);
@@ -169,21 +168,11 @@ 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.Object x = cachedSerFactories.get(i);
-                        if (x instanceof Class) {
-                            java.lang.Class sf = (java.lang.Class)
+                        java.lang.Class sf = (java.lang.Class)
                                  cachedSerFactories.get(i);
-                            java.lang.Class df = (java.lang.Class)
+                        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);
-                            org.apache.axis.encoding.DeserializerFactory df = (org.apache.axis.encoding.DeserializerFactory)
-                                 cachedDeserFactories.get(i);
-                            _call.registerTypeMapping(cls, qName, sf, df, false);
-                        }
+                        _call.registerTypeMapping(cls, qName, sf, df, false);
                     }
                 }
             }
@@ -210,7 +199,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
 
         setRequestHeaders(_call);
         setAttachments(_call);
- try {        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
 
         if (_resp instanceof java.rmi.RemoteException) {
             throw (java.rmi.RemoteException)_resp;
@@ -223,9 +212,6 @@ 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);
             }
         }
-  } catch (org.apache.axis.AxisFault axisFaultException) {
-  throw axisFaultException;
-}
     }
 
     public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0) throws java.rmi.RemoteException {
@@ -244,7 +230,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
 
         setRequestHeaders(_call);
         setAttachments(_call);
- try {        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
 
         if (_resp instanceof java.rmi.RemoteException) {
             throw (java.rmi.RemoteException)_resp;
@@ -257,9 +243,6 @@ 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);
             }
         }
-  } catch (org.apache.axis.AxisFault axisFaultException) {
-  throw axisFaultException;
-}
     }
 
     public ext.vamsas.Secstructpred getpredict(java.lang.String in0) throws java.rmi.RemoteException {
@@ -278,7 +261,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
 
         setRequestHeaders(_call);
         setAttachments(_call);
- try {        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
 
         if (_resp instanceof java.rmi.RemoteException) {
             throw (java.rmi.RemoteException)_resp;
@@ -291,9 +274,6 @@ 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);
             }
         }
-  } catch (org.apache.axis.AxisFault axisFaultException) {
-  throw axisFaultException;
-}
     }
 
     public ext.vamsas.JpredResult getresult(java.lang.String in0) throws java.rmi.RemoteException {
@@ -312,7 +292,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
 
         setRequestHeaders(_call);
         setAttachments(_call);
- try {        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
 
         if (_resp instanceof java.rmi.RemoteException) {
             throw (java.rmi.RemoteException)_resp;
@@ -325,9 +305,6 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
                 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
index ff8aac1..70ed612 100755 (executable)
--- a/src/ext/vamsas/Msfalignment.java
+++ b/src/ext/vamsas/Msfalignment.java
@@ -2,7 +2,7 @@
  * Msfalignment.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
@@ -110,13 +110,11 @@ public class Msfalignment  implements java.io.Serializable {
         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);
     }
 

diff --git a/src/ext/vamsas/Result.java b/src/ext/vamsas/Result.java
index ef8b790..a2da004 100755 (executable)
--- a/src/ext/vamsas/Result.java
+++ b/src/ext/vamsas/Result.java
@@ -2,7 +2,7 @@
  * Result.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
@@ -376,7 +376,6 @@ public class Result  implements java.io.Serializable {
         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");

diff --git a/src/ext/vamsas/Secstructpred.java b/src/ext/vamsas/Secstructpred.java
index e30edeb..777b41f 100755 (executable)
--- a/src/ext/vamsas/Secstructpred.java
+++ b/src/ext/vamsas/Secstructpred.java
@@ -2,7 +2,7 @@
  * Secstructpred.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
@@ -81,7 +81,6 @@ 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.setNillable(true);
         typeDesc.addFieldDesc(elemField);
     }
 

diff --git a/src/ext/vamsas/Sequence.java b/src/ext/vamsas/Sequence.java
index 1fc4be7..7d2d730 100755 (executable)
--- a/src/ext/vamsas/Sequence.java
+++ b/src/ext/vamsas/Sequence.java
@@ -2,7 +2,7 @@
  * Sequence.java
  *
  * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter.
+ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
  */
 
 package ext.vamsas;
@@ -110,13 +110,11 @@ 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.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"));
-        elemField.setNillable(true);
         typeDesc.addFieldDesc(elemField);
     }