/*
* 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
* 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); } }