/* * 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 . */ package uk.ac.vamsas.objects.core; //---------------------------------/ //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; /** * Class ApplicationData. * * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007) * $ */ public class ApplicationData extends uk.ac.vamsas.objects.core.AppData implements java.io.Serializable { // --------------------------/ // - Class/Member Variables -/ // --------------------------/ /** * Version string describing the application specific data storage version * used */ private java.lang.String _version; /** * Canonical name of application */ private java.lang.String _name; /** * Field _userList. */ private java.util.Vector _userList; /** * Field _common. */ private uk.ac.vamsas.objects.core.Common _common; /** * Field _instanceList. */ private java.util.Vector _instanceList; // ----------------/ // - Constructors -/ // ----------------/ public ApplicationData() { super(); this._userList = new java.util.Vector(); this._instanceList = new java.util.Vector(); } // -----------/ // - Methods -/ // -----------/ /** * * * @param vInstance * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void addInstance(final uk.ac.vamsas.objects.core.Instance vInstance) throws java.lang.IndexOutOfBoundsException { this._instanceList.addElement(vInstance); } /** * * * @param index * @param vInstance * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void addInstance(final int index, final uk.ac.vamsas.objects.core.Instance vInstance) throws java.lang.IndexOutOfBoundsException { this._instanceList.add(index, vInstance); } /** * * * @param vUser * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void addUser(final uk.ac.vamsas.objects.core.User vUser) throws java.lang.IndexOutOfBoundsException { this._userList.addElement(vUser); } /** * * * @param index * @param vUser * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void addUser(final int index, final uk.ac.vamsas.objects.core.User vUser) throws java.lang.IndexOutOfBoundsException { this._userList.add(index, vUser); } /** * Method enumerateInstance. * * @return an Enumeration over all uk.ac.vamsas.objects.core.Instance elements */ public java.util.Enumeration enumerateInstance() { return this._instanceList.elements(); } /** * Method enumerateUser. * * @return an Enumeration over all uk.ac.vamsas.objects.core.User elements */ public java.util.Enumeration enumerateUser() { return this._userList.elements(); } /** * Overrides the java.lang.Object.equals method. * * @param obj * @return true if the objects are equal. */ public boolean equals(final java.lang.Object obj) { if (this == obj) return true; if (super.equals(obj) == false) return false; if (obj instanceof ApplicationData) { ApplicationData temp = (ApplicationData) obj; boolean thcycle; boolean tmcycle; if (this._version != null) { if (temp._version == null) return false; if (this._version != temp._version) { thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version); tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version); if (thcycle != tmcycle) { if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._version); } ; if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); } ; return false; } if (!thcycle) { if (!this._version.equals(temp._version)) { org.castor.util.CycleBreaker.releaseCycleHandle(this._version); org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); return false; } org.castor.util.CycleBreaker.releaseCycleHandle(this._version); org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); } } } else if (temp._version != null) return false; if (this._name != null) { if (temp._name == null) return false; if (this._name != temp._name) { thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name); tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name); if (thcycle != tmcycle) { if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._name); } ; if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); } ; return false; } if (!thcycle) { if (!this._name.equals(temp._name)) { org.castor.util.CycleBreaker.releaseCycleHandle(this._name); org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); return false; } org.castor.util.CycleBreaker.releaseCycleHandle(this._name); org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); } } } else if (temp._name != null) return false; if (this._userList != null) { if (temp._userList == null) return false; if (this._userList != temp._userList) { thcycle = org.castor.util.CycleBreaker .startingToCycle(this._userList); tmcycle = org.castor.util.CycleBreaker .startingToCycle(temp._userList); if (thcycle != tmcycle) { if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._userList); } ; if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList); } ; return false; } if (!thcycle) { if (!this._userList.equals(temp._userList)) { org.castor.util.CycleBreaker.releaseCycleHandle(this._userList); org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList); return false; } org.castor.util.CycleBreaker.releaseCycleHandle(this._userList); org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList); } } } else if (temp._userList != null) return false; if (this._common != null) { if (temp._common == null) return false; if (this._common != temp._common) { thcycle = org.castor.util.CycleBreaker.startingToCycle(this._common); tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._common); if (thcycle != tmcycle) { if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._common); } ; if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._common); } ; return false; } if (!thcycle) { if (!this._common.equals(temp._common)) { org.castor.util.CycleBreaker.releaseCycleHandle(this._common); org.castor.util.CycleBreaker.releaseCycleHandle(temp._common); return false; } org.castor.util.CycleBreaker.releaseCycleHandle(this._common); org.castor.util.CycleBreaker.releaseCycleHandle(temp._common); } } } else if (temp._common != null) return false; if (this._instanceList != null) { if (temp._instanceList == null) return false; if (this._instanceList != temp._instanceList) { thcycle = org.castor.util.CycleBreaker .startingToCycle(this._instanceList); tmcycle = org.castor.util.CycleBreaker .startingToCycle(temp._instanceList); if (thcycle != tmcycle) { if (!thcycle) { org.castor.util.CycleBreaker .releaseCycleHandle(this._instanceList); } ; if (!tmcycle) { org.castor.util.CycleBreaker .releaseCycleHandle(temp._instanceList); } ; return false; } if (!thcycle) { if (!this._instanceList.equals(temp._instanceList)) { org.castor.util.CycleBreaker .releaseCycleHandle(this._instanceList); org.castor.util.CycleBreaker .releaseCycleHandle(temp._instanceList); return false; } org.castor.util.CycleBreaker.releaseCycleHandle(this._instanceList); org.castor.util.CycleBreaker.releaseCycleHandle(temp._instanceList); } } } else if (temp._instanceList != null) return false; return true; } return false; } /** * Returns the value of field 'common'. * * @return the value of field 'Common'. */ public uk.ac.vamsas.objects.core.Common getCommon() { return this._common; } /** * Method getInstance. * * @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.Instance at the given * index */ public uk.ac.vamsas.objects.core.Instance getInstance(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._instanceList.size()) { throw new IndexOutOfBoundsException("getInstance: Index value '" + index + "' not in range [0.." + (this._instanceList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Instance) _instanceList.get(index); } /** * Method getInstance.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.Instance[] getInstance() { uk.ac.vamsas.objects.core.Instance[] array = new uk.ac.vamsas.objects.core.Instance[0]; return (uk.ac.vamsas.objects.core.Instance[]) this._instanceList .toArray(array); } /** * Method getInstanceAsReference.Returns a reference to '_instanceList'. No * type checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getInstanceAsReference() { return this._instanceList; } /** * Method getInstanceCount. * * @return the size of this collection */ public int getInstanceCount() { return this._instanceList.size(); } /** * Returns the value of field 'name'. The field 'name' has the following * description: Canonical name of application * * @return the value of field 'Name'. */ public java.lang.String getName() { return this._name; } /** * Method getUser. * * @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.User at the given index */ public uk.ac.vamsas.objects.core.User getUser(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._userList.size()) { throw new IndexOutOfBoundsException("getUser: Index value '" + index + "' not in range [0.." + (this._userList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.User) _userList.get(index); } /** * Method getUser.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.User[] getUser() { uk.ac.vamsas.objects.core.User[] array = new uk.ac.vamsas.objects.core.User[0]; return (uk.ac.vamsas.objects.core.User[]) this._userList.toArray(array); } /** * Method getUserAsReference.Returns a reference to '_userList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getUserAsReference() { return this._userList; } /** * Method getUserCount. * * @return the size of this collection */ public int getUserCount() { return this._userList.size(); } /** * Returns the value of field 'version'. The field 'version' has the following * description: Version string describing the application specific data * storage version used * * @return the value of field 'Version'. */ public java.lang.String getVersion() { return this._version; } /** * 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 (_version != null && !org.castor.util.CycleBreaker.startingToCycle(_version)) { result = 37 * result + _version.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_version); } if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) { result = 37 * result + _name.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_name); } if (_userList != null && !org.castor.util.CycleBreaker.startingToCycle(_userList)) { result = 37 * result + _userList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_userList); } if (_common != null && !org.castor.util.CycleBreaker.startingToCycle(_common)) { result = 37 * result + _common.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_common); } if (_instanceList != null && !org.castor.util.CycleBreaker.startingToCycle(_instanceList)) { result = 37 * result + _instanceList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_instanceList); } 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 removeAllInstance() { this._instanceList.clear(); } /** */ public void removeAllUser() { this._userList.clear(); } /** * Method removeInstance. * * @param vInstance * @return true if the object was removed from the collection. */ public boolean removeInstance( final uk.ac.vamsas.objects.core.Instance vInstance) { boolean removed = _instanceList.remove(vInstance); return removed; } /** * Method removeInstanceAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Instance removeInstanceAt(final int index) { java.lang.Object obj = this._instanceList.remove(index); return (uk.ac.vamsas.objects.core.Instance) obj; } /** * Method removeUser. * * @param vUser * @return true if the object was removed from the collection. */ public boolean removeUser(final uk.ac.vamsas.objects.core.User vUser) { boolean removed = _userList.remove(vUser); return removed; } /** * Method removeUserAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.User removeUserAt(final int index) { java.lang.Object obj = this._userList.remove(index); return (uk.ac.vamsas.objects.core.User) obj; } /** * Sets the value of field 'common'. * * @param common * the value of field 'common'. */ public void setCommon(final uk.ac.vamsas.objects.core.Common common) { this._common = common; } /** * * * @param index * @param vInstance * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setInstance(final int index, final uk.ac.vamsas.objects.core.Instance vInstance) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._instanceList.size()) { throw new IndexOutOfBoundsException("setInstance: Index value '" + index + "' not in range [0.." + (this._instanceList.size() - 1) + "]"); } this._instanceList.set(index, vInstance); } /** * * * @param vInstanceArray */ public void setInstance( final uk.ac.vamsas.objects.core.Instance[] vInstanceArray) { // -- copy array _instanceList.clear(); for (int i = 0; i < vInstanceArray.length; i++) { this._instanceList.add(vInstanceArray[i]); } } /** * Sets the value of '_instanceList' by copying the given Vector. All elements * will be checked for type safety. * * @param vInstanceList * the Vector to copy. */ public void setInstance(final java.util.Vector vInstanceList) { // copy vector this._instanceList.clear(); this._instanceList.addAll(vInstanceList); } /** * Sets the value of '_instanceList' by setting it to the given Vector. No * type checking is performed. * * @deprecated * * @param instanceVector * the Vector to set. */ public void setInstanceAsReference(final java.util.Vector instanceVector) { this._instanceList = instanceVector; } /** * Sets the value of field 'name'. The field 'name' has the following * description: Canonical name of application * * @param name * the value of field 'name'. */ public void setName(final java.lang.String name) { this._name = name; } /** * * * @param index * @param vUser * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setUser(final int index, final uk.ac.vamsas.objects.core.User vUser) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._userList.size()) { throw new IndexOutOfBoundsException("setUser: Index value '" + index + "' not in range [0.." + (this._userList.size() - 1) + "]"); } this._userList.set(index, vUser); } /** * * * @param vUserArray */ public void setUser(final uk.ac.vamsas.objects.core.User[] vUserArray) { // -- copy array _userList.clear(); for (int i = 0; i < vUserArray.length; i++) { this._userList.add(vUserArray[i]); } } /** * Sets the value of '_userList' by copying the given Vector. All elements * will be checked for type safety. * * @param vUserList * the Vector to copy. */ public void setUser(final java.util.Vector vUserList) { // copy vector this._userList.clear(); this._userList.addAll(vUserList); } /** * Sets the value of '_userList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param userVector * the Vector to set. */ public void setUserAsReference(final java.util.Vector userVector) { this._userList = userVector; } /** * Sets the value of field 'version'. The field 'version' has the following * description: Version string describing the application specific data * storage version used * * @param version * the value of field 'version'. */ public void setVersion(final java.lang.String version) { this._version = version; } /** * 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.AppData */ public static uk.ac.vamsas.objects.core.AppData unmarshal( final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (uk.ac.vamsas.objects.core.AppData) Unmarshaller.unmarshal( uk.ac.vamsas.objects.core.ApplicationData.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); } }