/* * This file is part of the Vamsas Client version 0.1. * Copyright 2009 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 NodeType. * * @version $Revision$ $Date$ */ public class NodeType extends uk.ac.vamsas.client.Vobject implements java.io.Serializable { // --------------------------/ // - Class/Member Variables -/ // --------------------------/ /** * Primary Key for vamsas object referencing */ private java.lang.String _id; /** * Field _modifiable. */ private java.lang.String _modifiable; /** * Short name for this node */ private java.lang.String _name; /** * Descriptive text for this node */ private java.lang.String _description; /** * Direct associations between this node and any vamsas objects */ private java.util.Vector _vrefList; /** * Field _propertyList. */ private java.util.Vector _propertyList; // ----------------/ // - Constructors -/ // ----------------/ public NodeType() { super(); this._vrefList = new java.util.Vector(); this._propertyList = new java.util.Vector(); } // -----------/ // - Methods -/ // -----------/ /** * * * @param vProperty * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void addProperty(final uk.ac.vamsas.objects.core.Property vProperty) throws java.lang.IndexOutOfBoundsException { this._propertyList.addElement(vProperty); } /** * * * @param index * @param vProperty * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void addProperty(final int index, final uk.ac.vamsas.objects.core.Property vProperty) throws java.lang.IndexOutOfBoundsException { this._propertyList.add(index, vProperty); } /** * * * @param vVref * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void addVref(final uk.ac.vamsas.objects.core.Vref vVref) throws java.lang.IndexOutOfBoundsException { this._vrefList.addElement(vVref); } /** * * * @param index * @param vVref * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void addVref(final int index, final uk.ac.vamsas.objects.core.Vref vVref) throws java.lang.IndexOutOfBoundsException { this._vrefList.add(index, vVref); } /** * Method enumerateProperty. * * @return an Enumeration over all uk.ac.vamsas.objects.core.Property elements */ public java.util.Enumeration enumerateProperty() { return this._propertyList.elements(); } /** * Method enumerateVref. * * @return an Enumeration over all uk.ac.vamsas.objects.core.Vref elements */ public java.util.Enumeration enumerateVref() { return this._vrefList.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 NodeType) { NodeType temp = (NodeType) obj; boolean thcycle; boolean tmcycle; if (this._id != null) { if (temp._id == null) return false; if (this._id != temp._id) { thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } org.castor.util.CycleBreaker.releaseCycleHandle(this._id); org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) return false; if (this._modifiable != null) { if (temp._modifiable == null) return false; if (this._modifiable != temp._modifiable) { thcycle = org.castor.util.CycleBreaker .startingToCycle(this._modifiable); tmcycle = org.castor.util.CycleBreaker .startingToCycle(temp._modifiable); if (thcycle != tmcycle) { if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); } ; if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } ; return false; } if (!thcycle) { if (!this._modifiable.equals(temp._modifiable)) { org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); return false; } org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } } } else if (temp._modifiable != 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._description != null) { if (temp._description == null) return false; if (this._description != temp._description) { thcycle = org.castor.util.CycleBreaker .startingToCycle(this._description); tmcycle = org.castor.util.CycleBreaker .startingToCycle(temp._description); if (thcycle != tmcycle) { if (!thcycle) { org.castor.util.CycleBreaker .releaseCycleHandle(this._description); } ; if (!tmcycle) { org.castor.util.CycleBreaker .releaseCycleHandle(temp._description); } ; return false; } if (!thcycle) { if (!this._description.equals(temp._description)) { org.castor.util.CycleBreaker .releaseCycleHandle(this._description); org.castor.util.CycleBreaker .releaseCycleHandle(temp._description); return false; } org.castor.util.CycleBreaker.releaseCycleHandle(this._description); org.castor.util.CycleBreaker.releaseCycleHandle(temp._description); } } } else if (temp._description != null) return false; if (this._vrefList != null) { if (temp._vrefList == null) return false; if (this._vrefList != temp._vrefList) { thcycle = org.castor.util.CycleBreaker .startingToCycle(this._vrefList); tmcycle = org.castor.util.CycleBreaker .startingToCycle(temp._vrefList); if (thcycle != tmcycle) { if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._vrefList); } ; if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._vrefList); } ; return false; } if (!thcycle) { if (!this._vrefList.equals(temp._vrefList)) { org.castor.util.CycleBreaker.releaseCycleHandle(this._vrefList); org.castor.util.CycleBreaker.releaseCycleHandle(temp._vrefList); return false; } org.castor.util.CycleBreaker.releaseCycleHandle(this._vrefList); org.castor.util.CycleBreaker.releaseCycleHandle(temp._vrefList); } } } else if (temp._vrefList != null) return false; if (this._propertyList != null) { if (temp._propertyList == null) return false; if (this._propertyList != temp._propertyList) { thcycle = org.castor.util.CycleBreaker .startingToCycle(this._propertyList); tmcycle = org.castor.util.CycleBreaker .startingToCycle(temp._propertyList); if (thcycle != tmcycle) { if (!thcycle) { org.castor.util.CycleBreaker .releaseCycleHandle(this._propertyList); } ; if (!tmcycle) { org.castor.util.CycleBreaker .releaseCycleHandle(temp._propertyList); } ; return false; } if (!thcycle) { if (!this._propertyList.equals(temp._propertyList)) { org.castor.util.CycleBreaker .releaseCycleHandle(this._propertyList); org.castor.util.CycleBreaker .releaseCycleHandle(temp._propertyList); return false; } org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); } } } else if (temp._propertyList != null) return false; return true; } return false; } /** * Returns the value of field 'description'. The field 'description' has the * following description: Descriptive text for this node * * @return the value of field 'Description'. */ public java.lang.String getDescription() { return this._description; } /** * Returns the value of field 'id'. The field 'id' has the following * description: Primary Key for vamsas object referencing * * @return the value of field 'Id'. */ public java.lang.String getId() { return this._id; } /** * Returns the value of field 'modifiable'. * * @return the value of field 'Modifiable'. */ public java.lang.String getModifiable() { return this._modifiable; } /** * Returns the value of field 'name'. The field 'name' has the following * description: Short name for this node * * @return the value of field 'Name'. */ public java.lang.String getName() { return this._name; } /** * 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(); } /** * Method getVref. * * @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.Vref at the given index */ public uk.ac.vamsas.objects.core.Vref getVref(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._vrefList.size()) { throw new IndexOutOfBoundsException("getVref: Index value '" + index + "' not in range [0.." + (this._vrefList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Vref) _vrefList.get(index); } /** * Method getVref.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.Vref[] getVref() { uk.ac.vamsas.objects.core.Vref[] array = new uk.ac.vamsas.objects.core.Vref[0]; return (uk.ac.vamsas.objects.core.Vref[]) this._vrefList.toArray(array); } /** * Method getVrefAsReference.Returns a reference to '_vrefList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getVrefAsReference() { return this._vrefList; } /** * Method getVrefCount. * * @return the size of this collection */ public int getVrefCount() { return this._vrefList.size(); } /** * 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 (_modifiable != null && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) { result = 37 * result + _modifiable.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable); } if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) { result = 37 * result + _name.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_name); } if (_description != null && !org.castor.util.CycleBreaker.startingToCycle(_description)) { result = 37 * result + _description.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_description); } if (_vrefList != null && !org.castor.util.CycleBreaker.startingToCycle(_vrefList)) { result = 37 * result + _vrefList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_vrefList); } if (_propertyList != null && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); } 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 removeAllProperty() { this._propertyList.clear(); } /** */ public void removeAllVref() { this._vrefList.clear(); } /** * 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; } /** * Method removeVref. * * @param vVref * @return true if the object was removed from the collection. */ public boolean removeVref(final uk.ac.vamsas.objects.core.Vref vVref) { boolean removed = _vrefList.remove(vVref); return removed; } /** * Method removeVrefAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Vref removeVrefAt(final int index) { java.lang.Object obj = this._vrefList.remove(index); return (uk.ac.vamsas.objects.core.Vref) obj; } /** * Sets the value of field 'description'. The field 'description' has the * following description: Descriptive text for this node * * @param description * the value of field 'description'. */ public void setDescription(final java.lang.String description) { this._description = description; } /** * 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; } /** * Sets the value of field 'modifiable'. * * @param modifiable * the value of field 'modifiable'. */ public void setModifiable(final java.lang.String modifiable) { this._modifiable = modifiable; } /** * Sets the value of field 'name'. The field 'name' has the following * description: Short name for this node * * @param name * the value of field 'name'. */ public void setName(final java.lang.String name) { this._name = name; } /** * * * @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; } /** * * * @param index * @param vVref * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setVref(final int index, final uk.ac.vamsas.objects.core.Vref vVref) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._vrefList.size()) { throw new IndexOutOfBoundsException("setVref: Index value '" + index + "' not in range [0.." + (this._vrefList.size() - 1) + "]"); } this._vrefList.set(index, vVref); } /** * * * @param vVrefArray */ public void setVref(final uk.ac.vamsas.objects.core.Vref[] vVrefArray) { // -- copy array _vrefList.clear(); for (int i = 0; i < vVrefArray.length; i++) { this._vrefList.add(vVrefArray[i]); } } /** * Sets the value of '_vrefList' by copying the given Vector. All elements * will be checked for type safety. * * @param vVrefList * the Vector to copy. */ public void setVref(final java.util.Vector vVrefList) { // copy vector this._vrefList.clear(); this._vrefList.addAll(vVrefList); } /** * Sets the value of '_vrefList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param vrefVector * the Vector to set. */ public void setVrefAsReference(final java.util.Vector vrefVector) { this._vrefList = vrefVector; } /** * 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.NodeType */ public static uk.ac.vamsas.objects.core.NodeType unmarshal( final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (uk.ac.vamsas.objects.core.NodeType) Unmarshaller.unmarshal( uk.ac.vamsas.objects.core.NodeType.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); } }