/*
* 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 java.lang.Object[] getTreeId() { java.lang.Object[] array = new java.lang.Object[0]; return (java.lang.Object[]) this._treeId.toArray(array); } /** * Method getTreeIdAsReference.Returns a reference to '_treeId'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getTreeIdAsReference() { return this._treeId; } /** * Method getTreeIdCount. * * @return the size of this collection */ public int getTreeIdCount() { return this._treeId.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 (_treeId != null && !org.castor.util.CycleBreaker.startingToCycle(_treeId)) { result = 37 * result + _treeId.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_treeId); } if (_nodespec != null && !org.castor.util.CycleBreaker.startingToCycle(_nodespec)) { result = 37 * result + _nodespec.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_nodespec); } 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 removeAllTreeId() { this._treeId.clear(); } /** * Method removeTreeId. * * @param vTreeId * @return true if the object was removed from the collection. */ public boolean removeTreeId(final java.lang.Object vTreeId) { boolean removed = _treeId.remove(vTreeId); return removed; } /** * Method removeTreeIdAt. * * @param index * @return the element removed from the collection */ public java.lang.Object removeTreeIdAt(final int index) { java.lang.Object obj = this._treeId.remove(index); return obj; } /** * Sets the value of field 'nodespec'. The field 'nodespec' has the following * description: String uniquely identifying a particular node in the * referenced tree according to the format of the tree representation that is * referenced. * * * @param nodespec * the value of field 'nodespec'. */ public void setNodespec(final java.lang.String nodespec) { this._nodespec = nodespec; } /** * * * @param index * @param vTreeId * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setTreeId(final int index, final java.lang.Object vTreeId) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._treeId.size()) { throw new IndexOutOfBoundsException("setTreeId: Index value '" + index + "' not in range [0.." + (this._treeId.size() - 1) + "]"); } this._treeId.set(index, vTreeId); } /** * * * @param vTreeIdArray */ public void setTreeId(final java.lang.Object[] vTreeIdArray) { // -- copy array _treeId.clear(); for (int i = 0; i < vTreeIdArray.length; i++) { this._treeId.add(vTreeIdArray[i]); } } /** * Sets the value of '_treeId' by copying the given Vector. All elements will * be checked for type safety. * * @param vTreeIdList * the Vector to copy. */ public void setTreeId(final java.util.Vector vTreeIdList) { // copy vector this._treeId.clear(); this._treeId.addAll(vTreeIdList); } /** * Sets the value of '_treeId' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param treeIdVector * the Vector to set. */ public void setTreeIdAsReference(final java.util.Vector treeIdVector) { this._treeId = treeIdVector; } /** * 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.Treenode.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); } }