From ab7718d904b6d95764e70f0d5034ac9d357235df Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 22 Aug 2005 16:18:40 +0000 Subject: [PATCH] regenerated stubs from wsdl and removed old vamsas object stubs in jalview.ext --- src/ext/vamsas/Jpred.java | 15 ++ src/ext/vamsas/JpredResult.java | 185 ------------- src/ext/vamsas/JpredService.java | 16 ++ src/ext/vamsas/JpredServiceLocator.java | 136 ++++++++++ src/ext/vamsas/Msfalignment.java | 182 ------------- src/ext/vamsas/Result.java | 441 ------------------------------- src/ext/vamsas/Secstructpred.java | 149 ----------- src/ext/vamsas/Sequence.java | 182 ------------- 8 files changed, 167 insertions(+), 1139 deletions(-) create mode 100755 src/ext/vamsas/Jpred.java delete mode 100755 src/ext/vamsas/JpredResult.java create mode 100755 src/ext/vamsas/JpredService.java create mode 100755 src/ext/vamsas/JpredServiceLocator.java delete mode 100755 src/ext/vamsas/Msfalignment.java delete mode 100755 src/ext/vamsas/Result.java delete mode 100755 src/ext/vamsas/Secstructpred.java delete mode 100755 src/ext/vamsas/Sequence.java diff --git a/src/ext/vamsas/Jpred.java b/src/ext/vamsas/Jpred.java new file mode 100755 index 0000000..4860339 --- /dev/null +++ b/src/ext/vamsas/Jpred.java @@ -0,0 +1,15 @@ +/** + * Jpred.java + * + * This file was auto-generated from WSDL + * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. + */ + +package ext.vamsas; + +public interface Jpred extends java.rmi.Remote { + public java.lang.String predict(vamsas.objects.simple.Sequence seq) throws java.rmi.RemoteException; + public java.lang.String predictOnMsa(vamsas.objects.simple.Msfalignment msf) throws java.rmi.RemoteException; + public vamsas.objects.simple.Secstructpred getpredict(java.lang.String job_id) throws java.rmi.RemoteException; + public vamsas.objects.simple.JpredResult getresult(java.lang.String job_id) throws java.rmi.RemoteException; +} diff --git a/src/ext/vamsas/JpredResult.java b/src/ext/vamsas/JpredResult.java deleted file mode 100755 index e7d089b..0000000 --- a/src/ext/vamsas/JpredResult.java +++ /dev/null @@ -1,185 +0,0 @@ -/** - * JpredResult.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. - */ - -/* -* 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 -*/ -package ext.vamsas; - -public class JpredResult extends ext.vamsas.Result - implements java.io.Serializable { - // 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")); - 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")); - typeDesc.addFieldDesc(elemField); - } - - private java.lang.String aligfile; - private java.lang.String predfile; - private java.lang.Object __equalsCalc = null; - private boolean __hashCodeCalc = false; - - 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; - } - - 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; - } - - 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; - } - - /** - * 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/JpredService.java b/src/ext/vamsas/JpredService.java new file mode 100755 index 0000000..0b95e68 --- /dev/null +++ b/src/ext/vamsas/JpredService.java @@ -0,0 +1,16 @@ +/** + * JpredService.java + * + * This file was auto-generated from WSDL + * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. + */ + +package ext.vamsas; + +public interface JpredService extends javax.xml.rpc.Service { + public java.lang.String getjpredAddress(); + + public ext.vamsas.Jpred getjpred() throws javax.xml.rpc.ServiceException; + + public ext.vamsas.Jpred getjpred(java.net.URL portAddress) throws javax.xml.rpc.ServiceException; +} diff --git a/src/ext/vamsas/JpredServiceLocator.java b/src/ext/vamsas/JpredServiceLocator.java new file mode 100755 index 0000000..813c340 --- /dev/null +++ b/src/ext/vamsas/JpredServiceLocator.java @@ -0,0 +1,136 @@ +/** + * JpredServiceLocator.java + * + * This file was auto-generated from WSDL + * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. + */ + +package ext.vamsas; + +public class JpredServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.JpredService { + + public JpredServiceLocator() { + } + + + public JpredServiceLocator(org.apache.axis.EngineConfiguration config) { + super(config); + } + + // Use to get a proxy class for jpred + private java.lang.String jpred_address = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred"; + + public java.lang.String getjpredAddress() { + return jpred_address; + } + + // The WSDD service name defaults to the port name. + private java.lang.String jpredWSDDServiceName = "jpred"; + + public java.lang.String getjpredWSDDServiceName() { + return jpredWSDDServiceName; + } + + public void setjpredWSDDServiceName(java.lang.String name) { + jpredWSDDServiceName = name; + } + + public ext.vamsas.Jpred getjpred() throws javax.xml.rpc.ServiceException { + java.net.URL endpoint; + try { + endpoint = new java.net.URL(jpred_address); + } + catch (java.net.MalformedURLException e) { + throw new javax.xml.rpc.ServiceException(e); + } + return getjpred(endpoint); + } + + public ext.vamsas.Jpred getjpred(java.net.URL portAddress) throws javax.xml.rpc.ServiceException { + try { + ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(portAddress, this); + _stub.setPortName(getjpredWSDDServiceName()); + return _stub; + } + catch (org.apache.axis.AxisFault e) { + return null; + } + } + + 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, + * then ServiceException is thrown. + */ + public java.rmi.Remote getPort(Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException { + try { + if (ext.vamsas.Jpred.class.isAssignableFrom(serviceEndpointInterface)) { + ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(new java.net.URL(jpred_address), this); + _stub.setPortName(getjpredWSDDServiceName()); + return _stub; + } + } + catch (java.lang.Throwable t) { + throw new javax.xml.rpc.ServiceException(t); + } + throw new javax.xml.rpc.ServiceException("There is no stub implementation for the interface: " + (serviceEndpointInterface == null ? "null" : serviceEndpointInterface.getName())); + } + + /** + * For the given interface, get the stub implementation. + * If this service has no port for the given interface, + * then ServiceException is thrown. + */ + public java.rmi.Remote getPort(javax.xml.namespace.QName portName, Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException { + if (portName == null) { + return getPort(serviceEndpointInterface); + } + java.lang.String inputPortName = portName.getLocalPart(); + if ("jpred".equals(inputPortName)) { + return getjpred(); + } + else { + java.rmi.Remote _stub = getPort(serviceEndpointInterface); + ((org.apache.axis.client.Stub) _stub).setPortName(portName); + return _stub; + } + } + + public javax.xml.namespace.QName getServiceName() { + return new javax.xml.namespace.QName("vamsas", "jpredService"); + } + + private java.util.HashSet ports = null; + + public java.util.Iterator getPorts() { + if (ports == null) { + ports = new java.util.HashSet(); + 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/Msfalignment.java b/src/ext/vamsas/Msfalignment.java deleted file mode 100755 index c9fbf85..0000000 --- a/src/ext/vamsas/Msfalignment.java +++ /dev/null @@ -1,182 +0,0 @@ -/** - * Msfalignment.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. - */ - -/* -* 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 -*/ -package ext.vamsas; - -public class Msfalignment implements java.io.Serializable { - // 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")); - 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")); - typeDesc.addFieldDesc(elemField); - } - - private java.lang.String msf; - private java.lang.String notes; - private java.lang.Object __equalsCalc = null; - private boolean __hashCodeCalc = false; - - 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; - } - - 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; - } - - 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; - } - - /** - * 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 deleted file mode 100755 index 3115fd1..0000000 --- a/src/ext/vamsas/Result.java +++ /dev/null @@ -1,441 +0,0 @@ -/** - * Result.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. - */ - -/* -* 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 -*/ -package ext.vamsas; - -public class Result implements java.io.Serializable { - // 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")); - 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); - } - - 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; - private java.lang.Object __equalsCalc = null; - private boolean __hashCodeCalc = false; - - 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; - } - - 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; - } - - 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; - } - - /** - * 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 deleted file mode 100755 index d1da9be..0000000 --- a/src/ext/vamsas/Secstructpred.java +++ /dev/null @@ -1,149 +0,0 @@ -/** - * Secstructpred.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. - */ - -/* -* 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 -*/ -package ext.vamsas; - -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, - true); - - static { - typeDesc.setXmlType(new javax.xml.namespace.QName( - "http://dataTypes.vamsas", "Secstructpred")); - - org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc(); - 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")); - typeDesc.addFieldDesc(elemField); - } - - private java.lang.String output; - private java.lang.Object __equalsCalc = null; - private boolean __hashCodeCalc = false; - - 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; - } - - public synchronized boolean equals(java.lang.Object obj) { - if (!(obj instanceof Secstructpred)) { - return false; - } - - Secstructpred other = (Secstructpred) obj; - - if (obj == null) { - return false; - } - - if (this == obj) { - return true; - } - - if (__equalsCalc != null) { - return (__equalsCalc == obj); - } - - __equalsCalc = obj; - - boolean _equals; - _equals = true && - (((this.output == null) && (other.getOutput() == null)) || - ((this.output != null) && this.output.equals(other.getOutput()))); - __equalsCalc = null; - - return _equals; - } - - public synchronized int hashCode() { - if (__hashCodeCalc) { - return 0; - } - - __hashCodeCalc = true; - - int _hashCode = 1; - - if (getOutput() != null) { - _hashCode += getOutput().hashCode(); - } - - __hashCodeCalc = false; - - return _hashCode; - } - - /** - * 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/Sequence.java b/src/ext/vamsas/Sequence.java deleted file mode 100755 index 4d73bcf..0000000 --- a/src/ext/vamsas/Sequence.java +++ /dev/null @@ -1,182 +0,0 @@ -/** - * Sequence.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. - */ - -/* -* 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 -*/ -package ext.vamsas; - -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, - true); - - static { - typeDesc.setXmlType(new javax.xml.namespace.QName( - "http://dataTypes.vamsas", "Sequence")); - - org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc(); - 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")); - 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); - } - - private java.lang.String id; - private java.lang.String seq; - private java.lang.Object __equalsCalc = null; - private boolean __hashCodeCalc = false; - - 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; - } - - public synchronized boolean equals(java.lang.Object obj) { - if (!(obj instanceof Sequence)) { - return false; - } - - Sequence other = (Sequence) obj; - - if (obj == null) { - return false; - } - - if (this == obj) { - return true; - } - - if (__equalsCalc != null) { - return (__equalsCalc == obj); - } - - __equalsCalc = obj; - - boolean _equals; - _equals = true && - (((this.id == null) && (other.getId() == null)) || - ((this.id != null) && this.id.equals(other.getId()))) && - (((this.seq == null) && (other.getSeq() == null)) || - ((this.seq != null) && this.seq.equals(other.getSeq()))); - __equalsCalc = null; - - return _equals; - } - - public synchronized int hashCode() { - if (__hashCodeCalc) { - return 0; - } - - __hashCodeCalc = true; - - int _hashCode = 1; - - if (getId() != null) { - _hashCode += getId().hashCode(); - } - - if (getSeq() != null) { - _hashCode += getSeq().hashCode(); - } - - __hashCodeCalc = false; - - return _hashCode; - } - - /** - * 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); - } -} -- 1.7.10.2