JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[jalview.git] / src / ext / vamsas / JpredSoapBindingStub.java

diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java
old mode 100755 (executable)
new mode 100644 (file)
index 5915dca..8345551
--- a/src/ext/vamsas/JpredSoapBindingStub.java
+++ b/src/ext/vamsas/JpredSoapBindingStub.java
@@ -1,20 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package ext.vamsas;
 
@@ -29,7 +31,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
 
   private java.util.Vector cachedDeserFactories = new java.util.Vector();
 
-  static org.apache.axis.description.OperationDesc[] _operations;
+  private static org.apache.axis.description.OperationDesc[] _operations;
 
   static
   {
@@ -96,9 +98,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
     oper.setReturnType(new javax.xml.namespace.QName(
             "http://simple.objects.vamsas", "JpredResult"));
     oper.setReturnClass(vamsas.objects.simple.JpredResult.class);
-    oper
-            .setReturnQName(new javax.xml.namespace.QName("",
-                    "getresultReturn"));
+    oper.setReturnQName(new javax.xml.namespace.QName("", "getresultReturn"));
     oper.setStyle(org.apache.axis.constants.Style.RPC);
     oper.setUse(org.apache.axis.constants.Use.ENCODED);
     _operations[3] = oper;
@@ -237,8 +237,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
         if (firstCall())
         {
           // must set encoding style before registering serializers
-          _call
-                  .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+          _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
           _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
           for (int i = 0; i < cachedSerFactories.size(); ++i)
           {
@@ -261,6 +260,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
     }
   }
 
+  @Override
   public java.lang.String predict(vamsas.objects.simple.Sequence seq)
           throws java.rmi.RemoteException
   {
@@ -272,15 +272,13 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
     _call.setOperation(_operations[0]);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("");
-    _call
-            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
     _call.setOperationName(new javax.xml.namespace.QName("vamsas",
             "predict"));
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { seq });
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[] { seq });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -300,6 +298,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
     }
   }
 
+  @Override
   public java.lang.String predictOnMsa(
           vamsas.objects.simple.Msfalignment msf)
           throws java.rmi.RemoteException
@@ -312,15 +311,13 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
     _call.setOperation(_operations[1]);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("");
-    _call
-            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
     _call.setOperationName(new javax.xml.namespace.QName("vamsas",
             "predictOnMsa"));
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { msf });
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[] { msf });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -340,6 +337,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
     }
   }
 
+  @Override
   public vamsas.objects.simple.Secstructpred getpredict(
           java.lang.String job_id) throws java.rmi.RemoteException
   {
@@ -351,15 +349,14 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
     _call.setOperation(_operations[2]);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("");
-    _call
-            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
     _call.setOperationName(new javax.xml.namespace.QName("vamsas",
             "getpredict"));
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { job_id });
+    java.lang.Object _resp = _call
+            .invoke(new java.lang.Object[] { job_id });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -379,6 +376,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
     }
   }
 
+  @Override
   public vamsas.objects.simple.JpredResult getresult(java.lang.String job_id)
           throws java.rmi.RemoteException
   {
@@ -390,15 +388,14 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
     _call.setOperation(_operations[3]);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("");
-    _call
-            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
     _call.setOperationName(new javax.xml.namespace.QName("vamsas",
             "getresult"));
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { job_id });
+    java.lang.Object _resp = _call
+            .invoke(new java.lang.Object[] { job_id });
 
     if (_resp instanceof java.rmi.RemoteException)
     {