/*
* This file is part of the Vamsas Client version 0.2.
* Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
* Andrew Waterhouse and Dominik Lindner.
*
* Earlier versions have also been incorporated into Jalview version 2.4
* since 2008, and TOPALi version 2 since 2007.
*
* The Vamsas Client is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The Vamsas Client 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the Vamsas Client. If not, see
* Note: Just in case the collection contents are changing in another thread, * we pass a 0-length Array of the correct type into the API call. This way we * know that the Array returned is of exactly the correct length. * * @return this collection as an Array */ public uk.ac.vamsas.objects.core.Input[] getInput() { uk.ac.vamsas.objects.core.Input[] array = new uk.ac.vamsas.objects.core.Input[0]; return (uk.ac.vamsas.objects.core.Input[]) this._inputList.toArray(array); } /** * Method getInputAsReference.Returns a reference to '_inputList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getInputAsReference() { return this._inputList; } /** * Method getInputCount. * * @return the size of this collection */ public int getInputCount() { return this._inputList.size(); } /** * Method getParam. * * @param index * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection * @return the value of the uk.ac.vamsas.objects.core.Param at the given index */ public uk.ac.vamsas.objects.core.Param getParam(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._paramList.size()) { throw new IndexOutOfBoundsException("getParam: Index value '" + index + "' not in range [0.." + (this._paramList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Param) _paramList.get(index); } /** * Method getParam.Returns the contents of the collection in an Array. *
* Note: Just in case the collection contents are changing in another thread, * we pass a 0-length Array of the correct type into the API call. This way we * know that the Array returned is of exactly the correct length. * * @return this collection as an Array */ public uk.ac.vamsas.objects.core.Param[] getParam() { uk.ac.vamsas.objects.core.Param[] array = new uk.ac.vamsas.objects.core.Param[0]; return (uk.ac.vamsas.objects.core.Param[]) this._paramList.toArray(array); } /** * Method getParamAsReference.Returns a reference to '_paramList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getParamAsReference() { return this._paramList; } /** * Method getParamCount. * * @return the size of this collection */ public int getParamCount() { return this._paramList.size(); } /** * Method getProperty. * * @param index * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection * @return the value of the uk.ac.vamsas.objects.core.Property at the given * index */ public uk.ac.vamsas.objects.core.Property getProperty(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._propertyList.size()) { throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index); } /** * Method getProperty.Returns the contents of the collection in an Array. *
* Note: Just in case the collection contents are changing in another thread, * we pass a 0-length Array of the correct type into the API call. This way we * know that the Array returned is of exactly the correct length. * * @return this collection as an Array */ public uk.ac.vamsas.objects.core.Property[] getProperty() { uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0]; return (uk.ac.vamsas.objects.core.Property[]) this._propertyList .toArray(array); } /** * Method getPropertyAsReference.Returns a reference to '_propertyList'. No * type checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getPropertyAsReference() { return this._propertyList; } /** * Method getPropertyCount. * * @return the size of this collection */ public int getPropertyCount() { return this._propertyList.size(); } /** * Returns the value of field 'user'. The field 'user' has the following * description: Who * * @return the value of field 'User'. */ public java.lang.String getUser() { return this._user; } /** * Overrides the java.lang.Object.hashCode method. *
* The following steps came from Effective Java Programming Language * Guide by Joshua Bloch, Chapter 3 * * @return a hash code value for the object. */ public int hashCode() { int result = super.hashCode(); long tmp; if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_id); } if (_user != null && !org.castor.util.CycleBreaker.startingToCycle(_user)) { result = 37 * result + _user.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_user); } if (_app != null && !org.castor.util.CycleBreaker.startingToCycle(_app)) { result = 37 * result + _app.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_app); } if (_action != null && !org.castor.util.CycleBreaker.startingToCycle(_action)) { result = 37 * result + _action.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_action); } if (_date != null && !org.castor.util.CycleBreaker.startingToCycle(_date)) { result = 37 * result + _date.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_date); } if (_propertyList != null && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); } if (_paramList != null && !org.castor.util.CycleBreaker.startingToCycle(_paramList)) { result = 37 * result + _paramList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_paramList); } if (_inputList != null && !org.castor.util.CycleBreaker.startingToCycle(_inputList)) { result = 37 * result + _inputList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_inputList); } return result; } /** * Method isValid. * * @return true if this object is valid according to the schema */ public boolean isValid() { try { validate(); } catch (org.exolab.castor.xml.ValidationException vex) { return false; } return true; } /** * * * @param out * @throws org.exolab.castor.xml.MarshalException * if object is null or if any SAXException is thrown during * marshaling * @throws org.exolab.castor.xml.ValidationException * if this object is an invalid instance according to the schema */ public void marshal(final java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { Marshaller.marshal(this, out); } /** * * * @param handler * @throws java.io.IOException * if an IOException occurs during marshaling * @throws org.exolab.castor.xml.ValidationException * if this object is an invalid instance according to the schema * @throws org.exolab.castor.xml.MarshalException * if object is null or if any SAXException is thrown during * marshaling */ public void marshal(final org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { Marshaller.marshal(this, handler); } /** */ public void removeAllInput() { this._inputList.clear(); } /** */ public void removeAllParam() { this._paramList.clear(); } /** */ public void removeAllProperty() { this._propertyList.clear(); } /** * Method removeInput. * * @param vInput * @return true if the object was removed from the collection. */ public boolean removeInput(final uk.ac.vamsas.objects.core.Input vInput) { boolean removed = _inputList.remove(vInput); return removed; } /** * Method removeInputAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Input removeInputAt(final int index) { java.lang.Object obj = this._inputList.remove(index); return (uk.ac.vamsas.objects.core.Input) obj; } /** * Method removeParam. * * @param vParam * @return true if the object was removed from the collection. */ public boolean removeParam(final uk.ac.vamsas.objects.core.Param vParam) { boolean removed = _paramList.remove(vParam); return removed; } /** * Method removeParamAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Param removeParamAt(final int index) { java.lang.Object obj = this._paramList.remove(index); return (uk.ac.vamsas.objects.core.Param) obj; } /** * Method removeProperty. * * @param vProperty * @return true if the object was removed from the collection. */ public boolean removeProperty( final uk.ac.vamsas.objects.core.Property vProperty) { boolean removed = _propertyList.remove(vProperty); return removed; } /** * Method removePropertyAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Property removePropertyAt(final int index) { java.lang.Object obj = this._propertyList.remove(index); return (uk.ac.vamsas.objects.core.Property) obj; } /** * Sets the value of field 'action'. The field 'action' has the following * description: Did what * * @param action * the value of field 'action'. */ public void setAction(final java.lang.String action) { this._action = action; } /** * Sets the value of field 'app'. The field 'app' has the following * description: With which application * * @param app * the value of field 'app'. */ public void setApp(final java.lang.String app) { this._app = app; } /** * Sets the value of field 'date'. The field 'date' has the following * description: When * * @param date * the value of field 'date'. */ public void setDate(final java.util.Date date) { this._date = date; } /** * Sets the value of field 'id'. The field 'id' has the following description: * Primary Key for vamsas object referencing * * * @param id * the value of field 'id'. */ public void setId(final java.lang.String id) { this._id = id; } /** * * * @param index * @param vInput * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setInput(final int index, final uk.ac.vamsas.objects.core.Input vInput) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._inputList.size()) { throw new IndexOutOfBoundsException("setInput: Index value '" + index + "' not in range [0.." + (this._inputList.size() - 1) + "]"); } this._inputList.set(index, vInput); } /** * * * @param vInputArray */ public void setInput(final uk.ac.vamsas.objects.core.Input[] vInputArray) { // -- copy array _inputList.clear(); for (int i = 0; i < vInputArray.length; i++) { this._inputList.add(vInputArray[i]); } } /** * Sets the value of '_inputList' by copying the given Vector. All elements * will be checked for type safety. * * @param vInputList * the Vector to copy. */ public void setInput(final java.util.Vector vInputList) { // copy vector this._inputList.clear(); this._inputList.addAll(vInputList); } /** * Sets the value of '_inputList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param inputVector * the Vector to set. */ public void setInputAsReference(final java.util.Vector inputVector) { this._inputList = inputVector; } /** * * * @param index * @param vParam * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setParam(final int index, final uk.ac.vamsas.objects.core.Param vParam) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._paramList.size()) { throw new IndexOutOfBoundsException("setParam: Index value '" + index + "' not in range [0.." + (this._paramList.size() - 1) + "]"); } this._paramList.set(index, vParam); } /** * * * @param vParamArray */ public void setParam(final uk.ac.vamsas.objects.core.Param[] vParamArray) { // -- copy array _paramList.clear(); for (int i = 0; i < vParamArray.length; i++) { this._paramList.add(vParamArray[i]); } } /** * Sets the value of '_paramList' by copying the given Vector. All elements * will be checked for type safety. * * @param vParamList * the Vector to copy. */ public void setParam(final java.util.Vector vParamList) { // copy vector this._paramList.clear(); this._paramList.addAll(vParamList); } /** * Sets the value of '_paramList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param paramVector * the Vector to set. */ public void setParamAsReference(final java.util.Vector paramVector) { this._paramList = paramVector; } /** * * * @param index * @param vProperty * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setProperty(final int index, final uk.ac.vamsas.objects.core.Property vProperty) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._propertyList.size()) { throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); } this._propertyList.set(index, vProperty); } /** * * * @param vPropertyArray */ public void setProperty( final uk.ac.vamsas.objects.core.Property[] vPropertyArray) { // -- copy array _propertyList.clear(); for (int i = 0; i < vPropertyArray.length; i++) { this._propertyList.add(vPropertyArray[i]); } } /** * Sets the value of '_propertyList' by copying the given Vector. All elements * will be checked for type safety. * * @param vPropertyList * the Vector to copy. */ public void setProperty(final java.util.Vector vPropertyList) { // copy vector this._propertyList.clear(); this._propertyList.addAll(vPropertyList); } /** * Sets the value of '_propertyList' by setting it to the given Vector. No * type checking is performed. * * @deprecated * * @param propertyVector * the Vector to set. */ public void setPropertyAsReference(final java.util.Vector propertyVector) { this._propertyList = propertyVector; } /** * Sets the value of field 'user'. The field 'user' has the following * description: Who * * @param user * the value of field 'user'. */ public void setUser(final java.lang.String user) { this._user = user; } /** * Method unmarshal. * * @param reader * @throws org.exolab.castor.xml.MarshalException * if object is null or if any SAXException is thrown during * marshaling * @throws org.exolab.castor.xml.ValidationException * if this object is an invalid instance according to the schema * @return the unmarshaled uk.ac.vamsas.objects.core.Entry */ public static uk.ac.vamsas.objects.core.Entry unmarshal( final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (uk.ac.vamsas.objects.core.Entry) Unmarshaller.unmarshal( uk.ac.vamsas.objects.core.Entry.class, reader); } /** * * * @throws org.exolab.castor.xml.ValidationException * if this object is an invalid instance according to the schema */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); } }