From af7d55faa6df986fda34b245de48e7423f1b79e0 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 6 Apr 2005 16:03:52 +0000 Subject: [PATCH 1/1] New client code for JPred service includes return of msa and Jprediction, and better job status information (vamsas.dataTypes.Result). --- src/ext/vamsas/JPredWS.java | 4 +- src/ext/vamsas/JPredWSService.java | 2 +- src/ext/vamsas/JPredWSServiceLocator.java | 43 ++- src/ext/vamsas/JpredResult.java | 154 +++++++++++ src/ext/vamsas/JpredSoapBindingStub.java | 168 ++++++++++-- src/ext/vamsas/Msfalignment.java | 154 +++++++++++ src/ext/vamsas/Result.java | 419 +++++++++++++++++++++++++++++ src/ext/vamsas/Secstructpred.java | 22 +- src/ext/vamsas/Sequence.java | 37 ++- 9 files changed, 975 insertions(+), 28 deletions(-) create mode 100755 src/ext/vamsas/JpredResult.java create mode 100755 src/ext/vamsas/Msfalignment.java create mode 100755 src/ext/vamsas/Result.java diff --git a/src/ext/vamsas/JPredWS.java b/src/ext/vamsas/JPredWS.java index 86226c0..6d7eae1 100755 --- a/src/ext/vamsas/JPredWS.java +++ b/src/ext/vamsas/JPredWS.java @@ -2,12 +2,14 @@ * 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; + 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.JpredResult getresult(java.lang.String in0) throws java.rmi.RemoteException; } diff --git a/src/ext/vamsas/JPredWSService.java b/src/ext/vamsas/JPredWSService.java index c97627f..f6049ee 100755 --- 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 WSDL2Java emitter. + * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter. */ package ext.vamsas; diff --git a/src/ext/vamsas/JPredWSServiceLocator.java b/src/ext/vamsas/JPredWSServiceLocator.java index 976d2fd..05fcd5a 100755 --- a/src/ext/vamsas/JPredWSServiceLocator.java +++ b/src/ext/vamsas/JPredWSServiceLocator.java @@ -2,15 +2,27 @@ * 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 { + 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 - 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; @@ -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, @@ -77,7 +93,7 @@ public class JPredWSServiceLocator extends org.apache.axis.client.Service implem if (portName == null) { return getPort(serviceEndpointInterface); } - String inputPortName = portName.getLocalPart(); + java.lang.String inputPortName = portName.getLocalPart(); 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(); - ports.add(new javax.xml.namespace.QName("jpred")); + ports.add(new javax.xml.namespace.QName("vamsas", "jpred")); } 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 index 0000000..c968231 --- /dev/null +++ b/src/ext/vamsas/JpredResult.java @@ -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); + } + +} diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java index 20ca810..e97ed2a 100755 --- 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 WSDL2Java emitter. + * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter. */ 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 { - _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"); @@ -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.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(); + 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.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; } + ((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; @@ -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; - 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); - cls = ext.vamsas.Sequence.class; + cls = ext.vamsas.Msfalignment.class; 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); + 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(); @@ -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 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); - java.lang.Class df = (java.lang.Class) + 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); + } } } } 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); - 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; @@ -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); } } + } 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(); } @@ -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.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); - 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; @@ -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); } } + } 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 index 0000000..ff8aac1 --- /dev/null +++ b/src/ext/vamsas/Msfalignment.java @@ -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 index 0000000..ef8b790 --- /dev/null +++ b/src/ext/vamsas/Result.java @@ -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); + } + +} diff --git a/src/ext/vamsas/Secstructpred.java b/src/ext/vamsas/Secstructpred.java index cac8ff3..e30edeb 100755 --- 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 WSDL2Java emitter. + * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter. */ package ext.vamsas; @@ -13,10 +13,27 @@ public class Secstructpred implements java.io.Serializable { 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; } + + /** + * Sets the output value for this Secstructpred. + * + * @param 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 = - 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")); @@ -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.setNillable(true); typeDesc.addFieldDesc(elemField); } diff --git a/src/ext/vamsas/Sequence.java b/src/ext/vamsas/Sequence.java index 2ee347a..1fc4be7 100755 --- 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 WSDL2Java emitter. + * by the Apache Axis 1.2RC3 Feb 28, 2005 (10:15:14 EST) WSDL2Java emitter. */ package ext.vamsas; @@ -14,18 +14,49 @@ public class Sequence implements java.io.Serializable { 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; } + + /** + * Sets the id value for this Sequence. + * + * @param 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; } + + /** + * Sets the seq value for this Sequence. + * + * @param 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 = - 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")); @@ -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.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); } -- 1.7.10.2