/*
* 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.Newick[] getNewick() { uk.ac.vamsas.objects.core.Newick[] array = new uk.ac.vamsas.objects.core.Newick[0]; return (uk.ac.vamsas.objects.core.Newick[]) this._newickList.toArray(array); } /** * Method getNewickAsReference.Returns a reference to '_newickList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getNewickAsReference() { return this._newickList; } /** * Method getNewickCount. * * @return the size of this collection */ public int getNewickCount() { return this._newickList.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 'provenance'. * * @return the value of field 'Provenance'. */ public uk.ac.vamsas.objects.core.Provenance getProvenance() { return this._provenance; } /** * Returns the value of field 'title'. * * @return the value of field 'Title'. */ public java.lang.String getTitle() { return this._title; } /** * Method getTreenode. * * @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.Treenode at the given * index */ public uk.ac.vamsas.objects.core.Treenode getTreenode(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._treenodeList.size()) { throw new IndexOutOfBoundsException("getTreenode: Index value '" + index + "' not in range [0.." + (this._treenodeList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Treenode) _treenodeList.get(index); } /** * Method getTreenode.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.Treenode[] getTreenode() { uk.ac.vamsas.objects.core.Treenode[] array = new uk.ac.vamsas.objects.core.Treenode[0]; return (uk.ac.vamsas.objects.core.Treenode[]) this._treenodeList .toArray(array); } /** * Method getTreenodeAsReference.Returns a reference to '_treenodeList'. No * type checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getTreenodeAsReference() { return this._treenodeList; } /** * Method getTreenodeCount. * * @return the size of this collection */ public int getTreenodeCount() { return this._treenodeList.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 (_title != null && !org.castor.util.CycleBreaker.startingToCycle(_title)) { result = 37 * result + _title.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_title); } if (_newickList != null && !org.castor.util.CycleBreaker.startingToCycle(_newickList)) { result = 37 * result + _newickList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_newickList); } if (_treenodeList != null && !org.castor.util.CycleBreaker.startingToCycle(_treenodeList)) { result = 37 * result + _treenodeList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_treenodeList); } if (_propertyList != null && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); } if (_provenance != null && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); } 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 removeAllNewick() { this._newickList.clear(); } /** */ public void removeAllProperty() { this._propertyList.clear(); } /** */ public void removeAllTreenode() { this._treenodeList.clear(); } /** * Method removeNewick. * * @param vNewick * @return true if the object was removed from the collection. */ public boolean removeNewick(final uk.ac.vamsas.objects.core.Newick vNewick) { boolean removed = _newickList.remove(vNewick); return removed; } /** * Method removeNewickAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Newick removeNewickAt(final int index) { java.lang.Object obj = this._newickList.remove(index); return (uk.ac.vamsas.objects.core.Newick) 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; } /** * Method removeTreenode. * * @param vTreenode * @return true if the object was removed from the collection. */ public boolean removeTreenode( final uk.ac.vamsas.objects.core.Treenode vTreenode) { boolean removed = _treenodeList.remove(vTreenode); return removed; } /** * Method removeTreenodeAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Treenode removeTreenodeAt(final int index) { java.lang.Object obj = this._treenodeList.remove(index); return (uk.ac.vamsas.objects.core.Treenode) obj; } /** * 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; } /** * * * @param index * @param vNewick * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setNewick(final int index, final uk.ac.vamsas.objects.core.Newick vNewick) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._newickList.size()) { throw new IndexOutOfBoundsException("setNewick: Index value '" + index + "' not in range [0.." + (this._newickList.size() - 1) + "]"); } this._newickList.set(index, vNewick); } /** * * * @param vNewickArray */ public void setNewick(final uk.ac.vamsas.objects.core.Newick[] vNewickArray) { // -- copy array _newickList.clear(); for (int i = 0; i < vNewickArray.length; i++) { this._newickList.add(vNewickArray[i]); } } /** * Sets the value of '_newickList' by copying the given Vector. All elements * will be checked for type safety. * * @param vNewickList * the Vector to copy. */ public void setNewick(final java.util.Vector vNewickList) { // copy vector this._newickList.clear(); this._newickList.addAll(vNewickList); } /** * Sets the value of '_newickList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param newickVector * the Vector to set. */ public void setNewickAsReference(final java.util.Vector newickVector) { this._newickList = newickVector; } /** * * * @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 'provenance'. * * @param provenance * the value of field 'provenance'. */ public void setProvenance( final uk.ac.vamsas.objects.core.Provenance provenance) { this._provenance = provenance; } /** * Sets the value of field 'title'. * * @param title * the value of field 'title'. */ public void setTitle(final java.lang.String title) { this._title = title; } /** * * * @param index * @param vTreenode * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setTreenode(final int index, final uk.ac.vamsas.objects.core.Treenode vTreenode) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._treenodeList.size()) { throw new IndexOutOfBoundsException("setTreenode: Index value '" + index + "' not in range [0.." + (this._treenodeList.size() - 1) + "]"); } this._treenodeList.set(index, vTreenode); } /** * * * @param vTreenodeArray */ public void setTreenode( final uk.ac.vamsas.objects.core.Treenode[] vTreenodeArray) { // -- copy array _treenodeList.clear(); for (int i = 0; i < vTreenodeArray.length; i++) { this._treenodeList.add(vTreenodeArray[i]); } } /** * Sets the value of '_treenodeList' by copying the given Vector. All elements * will be checked for type safety. * * @param vTreenodeList * the Vector to copy. */ public void setTreenode(final java.util.Vector vTreenodeList) { // copy vector this._treenodeList.clear(); this._treenodeList.addAll(vTreenodeList); } /** * Sets the value of '_treenodeList' by setting it to the given Vector. No * type checking is performed. * * @deprecated * * @param treenodeVector * the Vector to set. */ public void setTreenodeAsReference(final java.util.Vector treenodeVector) { this._treenodeList = treenodeVector; } /** * 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.Tree */ public static uk.ac.vamsas.objects.core.Tree unmarshal( final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (uk.ac.vamsas.objects.core.Tree) Unmarshaller.unmarshal( uk.ac.vamsas.objects.core.Tree.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); } }