Replaced by jpred.java and associated stubs.

diff --git a/src/ext/vamsas/JPredWS.java b/src/ext/vamsas/JPredWS.java
deleted file mode 100755 (executable)
index 194272e..0000000
--- a/src/ext/vamsas/JPredWS.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/**
- * JPredWS.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */\r
-\r
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* 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 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.
-*
-* 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
-*/\r
-package ext.vamsas;\r
-\r
-public interface JPredWS extends java.rmi.Remote {\r
-    public java.lang.String predict(ext.vamsas.Sequence in0)\r
-        throws java.rmi.RemoteException;\r
-\r
-    public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0)\r
-        throws java.rmi.RemoteException;\r
-\r
-    public ext.vamsas.Secstructpred getpredict(java.lang.String in0)\r
-        throws java.rmi.RemoteException;\r
-\r
-    public ext.vamsas.JpredResult getresult(java.lang.String in0)\r
-        throws java.rmi.RemoteException;\r
-}\r

diff --git a/src/ext/vamsas/JPredWSService.java b/src/ext/vamsas/JPredWSService.java
deleted file mode 100755 (executable)
index 3cb5e5d..0000000
--- a/src/ext/vamsas/JPredWSService.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/**
- * JPredWSService.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */\r
-\r
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* 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 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.
-*
-* 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
-*/\r
-package ext.vamsas;\r
-\r
-public interface JPredWSService extends javax.xml.rpc.Service {\r
-    public java.lang.String getjpredAddress();\r
-\r
-    public ext.vamsas.JPredWS getjpred() throws javax.xml.rpc.ServiceException;\r
-\r
-    public ext.vamsas.JPredWS getjpred(java.net.URL portAddress)\r
-        throws javax.xml.rpc.ServiceException;\r
-}\r

diff --git a/src/ext/vamsas/JPredWSServiceLocator.java b/src/ext/vamsas/JPredWSServiceLocator.java
deleted file mode 100755 (executable)
index cb4006d..0000000
--- a/src/ext/vamsas/JPredWSServiceLocator.java
+++ /dev/null
@@ -1,167 +0,0 @@
-/**
- * JPredWSServiceLocator.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */\r
-\r
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* 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 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.
-*
-* 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
-*/\r
-package ext.vamsas;\r
-\r
-public class JPredWSServiceLocator extends org.apache.axis.client.Service\r
-    implements ext.vamsas.JPredWSService {\r
-    // Use to get a proxy class for jpred\r
-    private java.lang.String jpred_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/jpred";\r
-\r
-    // The WSDD service name defaults to the port name.\r
-    private java.lang.String jpredWSDDServiceName = "jpred";\r
-    private java.util.HashSet ports = null;\r
-\r
-    public JPredWSServiceLocator() {\r
-    }\r
-\r
-    public JPredWSServiceLocator(org.apache.axis.EngineConfiguration config) {\r
-        super(config);\r
-    }\r
-\r
-    public java.lang.String getjpredAddress() {\r
-        return jpred_address;\r
-    }\r
-\r
-    public java.lang.String getjpredWSDDServiceName() {\r
-        return jpredWSDDServiceName;\r
-    }\r
-\r
-    public void setjpredWSDDServiceName(java.lang.String name) {\r
-        jpredWSDDServiceName = name;\r
-    }\r
-\r
-    public ext.vamsas.JPredWS getjpred() throws javax.xml.rpc.ServiceException {\r
-        java.net.URL endpoint;\r
-\r
-        try {\r
-            endpoint = new java.net.URL(jpred_address);\r
-        } catch (java.net.MalformedURLException e) {\r
-            throw new javax.xml.rpc.ServiceException(e);\r
-        }\r
-\r
-        return getjpred(endpoint);\r
-    }\r
-\r
-    public ext.vamsas.JPredWS getjpred(java.net.URL portAddress)\r
-        throws javax.xml.rpc.ServiceException {\r
-        try {\r
-            ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(portAddress,\r
-                    this);\r
-            _stub.setPortName(getjpredWSDDServiceName());\r
-\r
-            return _stub;\r
-        } catch (org.apache.axis.AxisFault e) {\r
-            return null;\r
-        }\r
-    }\r
-\r
-    public void setjpredEndpointAddress(java.lang.String address) {\r
-        jpred_address = address;\r
-    }\r
-\r
-    /**
- * For the given interface, get the stub implementation.
- * If this service has no port for the given interface,
- * then ServiceException is thrown.
- */\r
-    public java.rmi.Remote getPort(Class serviceEndpointInterface)\r
-        throws javax.xml.rpc.ServiceException {\r
-        try {\r
-            if (ext.vamsas.JPredWS.class.isAssignableFrom(\r
-                        serviceEndpointInterface)) {\r
-                ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(new java.net.URL(\r
-                            jpred_address), this);\r
-                _stub.setPortName(getjpredWSDDServiceName());\r
-\r
-                return _stub;\r
-            }\r
-        } catch (java.lang.Throwable t) {\r
-            throw new javax.xml.rpc.ServiceException(t);\r
-        }\r
-\r
-        throw new javax.xml.rpc.ServiceException(\r
-            "There is no stub implementation for the interface:  " +\r
-            ((serviceEndpointInterface == null) ? "null"\r
-                                                : serviceEndpointInterface.getName()));\r
-    }\r
-\r
-    /**
- * For the given interface, get the stub implementation.
- * If this service has no port for the given interface,
- * then ServiceException is thrown.
- */\r
-    public java.rmi.Remote getPort(javax.xml.namespace.QName portName,\r
-        Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {\r
-        if (portName == null) {\r
-            return getPort(serviceEndpointInterface);\r
-        }\r
-\r
-        java.lang.String inputPortName = portName.getLocalPart();\r
-\r
-        if ("jpred".equals(inputPortName)) {\r
-            return getjpred();\r
-        } else {\r
-            java.rmi.Remote _stub = getPort(serviceEndpointInterface);\r
-            ((org.apache.axis.client.Stub) _stub).setPortName(portName);\r
-\r
-            return _stub;\r
-        }\r
-    }\r
-\r
-    public javax.xml.namespace.QName getServiceName() {\r
-        return new javax.xml.namespace.QName("vamsas", "JPredWSService");\r
-    }\r
-\r
-    public java.util.Iterator getPorts() {\r
-        if (ports == null) {\r
-            ports = new java.util.HashSet();\r
-            ports.add(new javax.xml.namespace.QName("vamsas", "jpred"));\r
-        }\r
-\r
-        return ports.iterator();\r
-    }\r
-\r
-    /**
-* Set the endpoint address for the specified port name.
-*/\r
-    public void setEndpointAddress(java.lang.String portName,\r
-        java.lang.String address) throws javax.xml.rpc.ServiceException {\r
-        if ("jpred".equals(portName)) {\r
-            setjpredEndpointAddress(address);\r
-        } else { // Unknown Port Name\r
-            throw new javax.xml.rpc.ServiceException(\r
-                " Cannot set Endpoint Address for Unknown Port" + portName);\r
-        }\r
-    }\r
-\r
-    /**
-* Set the endpoint address for the specified port name.
-*/\r
-    public void setEndpointAddress(javax.xml.namespace.QName portName,\r
-        java.lang.String address) throws javax.xml.rpc.ServiceException {\r
-        setEndpointAddress(portName.getLocalPart(), address);\r
-    }\r
-}\r