X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FTree.java;h=12b8031e550ccccd0cde556ca96b2a73682d69a1;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=39eb763c874053e2f0346b604c8c9290df3dc333;hpb=6f33f705957d674dc2ab6c994a6ea87f7a91f40f;p=vamsas.git diff --git a/src/uk/ac/vamsas/objects/core/Tree.java b/src/uk/ac/vamsas/objects/core/Tree.java index 39eb763..12b8031 100644 --- a/src/uk/ac/vamsas/objects/core/Tree.java +++ b/src/uk/ac/vamsas/objects/core/Tree.java @@ -1,14 +1,28 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * 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 -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -17,1022 +31,1052 @@ import org.exolab.castor.xml.Unmarshaller; /** * Class Tree. * - * @version $Revision$ $Date$ + * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007) + * $ */ -public class Tree 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; - - /** - * Field _title. - */ - private java.lang.String _title; - - /** - * Field _newickList. - */ - private java.util.Vector _newickList; - - /** - * node identity and mapping data between tree - * representations and vamsas document objects - */ - private java.util.Vector _treenodeList; - - /** - * Field _propertyList. - */ - private java.util.Vector _propertyList; - - /** - * Field _provenance. - */ - private uk.ac.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Tree() { - super(); - this._newickList = new java.util.Vector(); - this._treenodeList = new java.util.Vector(); - this._propertyList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vNewick - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addNewick( - final uk.ac.vamsas.objects.core.Newick vNewick) - throws java.lang.IndexOutOfBoundsException { - this._newickList.addElement(vNewick); - } - - /** - * - * - * @param index - * @param vNewick - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addNewick( - final int index, - final uk.ac.vamsas.objects.core.Newick vNewick) - throws java.lang.IndexOutOfBoundsException { - this._newickList.add(index, vNewick); - } - - /** - * - * - * @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 vTreenode - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addTreenode( - final uk.ac.vamsas.objects.core.Treenode vTreenode) - throws java.lang.IndexOutOfBoundsException { - this._treenodeList.addElement(vTreenode); - } - - /** - * - * - * @param index - * @param vTreenode - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addTreenode( - final int index, - final uk.ac.vamsas.objects.core.Treenode vTreenode) - throws java.lang.IndexOutOfBoundsException { - this._treenodeList.add(index, vTreenode); - } - - /** - * Method enumerateNewick. - * - * @return an Enumeration over all - * uk.ac.vamsas.objects.core.Newick elements - */ - public java.util.Enumeration enumerateNewick( - ) { - return this._newickList.elements(); - } - - /** - * Method enumerateProperty. - * - * @return an Enumeration over all - * uk.ac.vamsas.objects.core.Property elements - */ - public java.util.Enumeration enumerateProperty( - ) { - return this._propertyList.elements(); - } - - /** - * Method enumerateTreenode. - * - * @return an Enumeration over all - * uk.ac.vamsas.objects.core.Treenode elements - */ - public java.util.Enumeration enumerateTreenode( - ) { - return this._treenodeList.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) +public class Tree 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; + + /** + * Field _title. + */ + private java.lang.String _title; + + /** + * Field _newickList. + */ + private java.util.Vector _newickList; + + /** + * node identity and mapping data between tree representations and vamsas + * document objects + */ + private java.util.Vector _treenodeList; + + /** + * Field _propertyList. + */ + private java.util.Vector _propertyList; + + /** + * Field _provenance. + */ + private uk.ac.vamsas.objects.core.Provenance _provenance; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public Tree() { + super(); + this._newickList = new java.util.Vector(); + this._treenodeList = new java.util.Vector(); + this._propertyList = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vNewick + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addNewick(final uk.ac.vamsas.objects.core.Newick vNewick) + throws java.lang.IndexOutOfBoundsException { + this._newickList.addElement(vNewick); + } + + /** + * + * + * @param index + * @param vNewick + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addNewick(final int index, + final uk.ac.vamsas.objects.core.Newick vNewick) + throws java.lang.IndexOutOfBoundsException { + this._newickList.add(index, vNewick); + } + + /** + * + * + * @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 vTreenode + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addTreenode(final uk.ac.vamsas.objects.core.Treenode vTreenode) + throws java.lang.IndexOutOfBoundsException { + this._treenodeList.addElement(vTreenode); + } + + /** + * + * + * @param index + * @param vTreenode + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addTreenode(final int index, + final uk.ac.vamsas.objects.core.Treenode vTreenode) + throws java.lang.IndexOutOfBoundsException { + this._treenodeList.add(index, vTreenode); + } + + /** + * Method enumerateNewick. + * + * @return an Enumeration over all uk.ac.vamsas.objects.core.Newick elements + */ + public java.util.Enumeration enumerateNewick() { + return this._newickList.elements(); + } + + /** + * Method enumerateProperty. + * + * @return an Enumeration over all uk.ac.vamsas.objects.core.Property elements + */ + public java.util.Enumeration enumerateProperty() { + return this._propertyList.elements(); + } + + /** + * Method enumerateTreenode. + * + * @return an Enumeration over all uk.ac.vamsas.objects.core.Treenode elements + */ + public java.util.Enumeration enumerateTreenode() { + return this._treenodeList.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 Tree) { + + Tree temp = (Tree) 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 (obj instanceof Tree) { - - Tree temp = (Tree)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._title != null) { - if (temp._title == null) return false; - if (this._title != temp._title) { - thcycle=org.castor.util.CycleBreaker.startingToCycle(this._title); - tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._title); - if (thcycle!=tmcycle) { - if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._title); }; - if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); }; - return false; - } - if (!thcycle) { - if (!this._title.equals(temp._title)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._title); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); - return false; - } - org.castor.util.CycleBreaker.releaseCycleHandle(this._title); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); - } - } - } else if (temp._title != null) - return false; - if (this._newickList != null) { - if (temp._newickList == null) return false; - if (this._newickList != temp._newickList) { - thcycle=org.castor.util.CycleBreaker.startingToCycle(this._newickList); - tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._newickList); - if (thcycle!=tmcycle) { - if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList); }; - if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList); }; - return false; - } - if (!thcycle) { - if (!this._newickList.equals(temp._newickList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList); - return false; - } - org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList); - } - } - } else if (temp._newickList != null) - return false; - if (this._treenodeList != null) { - if (temp._treenodeList == null) return false; - if (this._treenodeList != temp._treenodeList) { - thcycle=org.castor.util.CycleBreaker.startingToCycle(this._treenodeList); - tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._treenodeList); - if (thcycle!=tmcycle) { - if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList); }; - if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList); }; - return false; - } - if (!thcycle) { - if (!this._treenodeList.equals(temp._treenodeList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList); - return false; - } - org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList); - } - } - } else if (temp._treenodeList != 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; - if (this._provenance != null) { - if (temp._provenance == null) return false; - if (this._provenance != temp._provenance) { - thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance); - tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance); - if (thcycle!=tmcycle) { - if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); }; - if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); }; - return false; - } - if (!thcycle) { - if (!this._provenance.equals(temp._provenance)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); - return false; - } - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); - } - } - } else if (temp._provenance != null) - return false; - return true; + } + 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; - } - - /** - * 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; - } - - /** - * Method getNewick. - * - * @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.Newick at - * the given index - */ - public uk.ac.vamsas.objects.core.Newick getNewick( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._newickList.size()) { - throw new IndexOutOfBoundsException("getNewick: Index value '" + index + "' not in range [0.." + (this._newickList.size() - 1) + "]"); - } - - return (uk.ac.vamsas.objects.core.Newick) _newickList.get(index); - } - - /** - * Method getNewick.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.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 (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); + } } - if (_newickList != null - && !org.castor.util.CycleBreaker.startingToCycle(_newickList)) { - result = 37 * result + _newickList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_newickList); + } else if (temp._modifiable != null) + return false; + if (this._title != null) { + if (temp._title == null) + return false; + if (this._title != temp._title) { + thcycle = org.castor.util.CycleBreaker.startingToCycle(this._title); + tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._title); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._title); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); + } + ; + return false; + } + if (!thcycle) { + if (!this._title.equals(temp._title)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._title); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._title); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); + } } - if (_treenodeList != null - && !org.castor.util.CycleBreaker.startingToCycle(_treenodeList)) { - result = 37 * result + _treenodeList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_treenodeList); + } else if (temp._title != null) + return false; + if (this._newickList != null) { + if (temp._newickList == null) + return false; + if (this._newickList != temp._newickList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._newickList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._newickList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList); + } + ; + return false; + } + if (!thcycle) { + if (!this._newickList.equals(temp._newickList)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList); + } } - if (_propertyList != null - && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { - result = 37 * result + _propertyList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); + } else if (temp._newickList != null) + return false; + if (this._treenodeList != null) { + if (temp._treenodeList == null) + return false; + if (this._treenodeList != temp._treenodeList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._treenodeList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._treenodeList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._treenodeList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._treenodeList); + } + ; + return false; + } + if (!thcycle) { + if (!this._treenodeList.equals(temp._treenodeList)) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._treenodeList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._treenodeList); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList); + } } - if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { - result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + } else if (temp._treenodeList != 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); + } } - - 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) { + } else if (temp._propertyList != null) + return false; + if (this._provenance != null) { + if (temp._provenance == null) + return false; + if (this._provenance != temp._provenance) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._provenance); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._provenance); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + } + ; return false; + } + if (!thcycle) { + if (!this._provenance.equals(temp._provenance)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + } } - 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; + } else if (temp._provenance != null) + return false; + return true; } - - /** - * 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; + return false; + } + + /** + * 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; + } + + /** + * Method getNewick. + * + * @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.Newick at the given + * index + */ + public uk.ac.vamsas.objects.core.Newick getNewick(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._newickList.size()) { + throw new IndexOutOfBoundsException("getNewick: Index value '" + index + + "' not in range [0.." + (this._newickList.size() - 1) + "]"); } - /** - * 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; + return (uk.ac.vamsas.objects.core.Newick) _newickList.get(index); + } + + /** + * Method getNewick.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.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) + "]"); } - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable( - final java.lang.String modifiable) { - this._modifiable = modifiable; + 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) + "]"); } - /** - * - * - * @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); + 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); } - - /** - * - * - * @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]); - } + if (_modifiable != null + && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) { + result = 37 * result + _modifiable.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable); } - - /** - * 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); + if (_title != null && !org.castor.util.CycleBreaker.startingToCycle(_title)) { + result = 37 * result + _title.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_title); } - - /** - * 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; + if (_newickList != null + && !org.castor.util.CycleBreaker.startingToCycle(_newickList)) { + result = 37 * result + _newickList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_newickList); } - - /** - * - * - * @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); + if (_treenodeList != null + && !org.castor.util.CycleBreaker.startingToCycle(_treenodeList)) { + result = 37 * result + _treenodeList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_treenodeList); } - - /** - * - * - * @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]); - } + if (_propertyList != null + && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + result = 37 * result + _propertyList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); } - - /** - * 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); + if (_provenance != null + && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + result = 37 * result + _provenance.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); } - /** - * 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; + 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; } - - /** - * 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; + 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) + "]"); } - /** - * Sets the value of field 'title'. - * - * @param title the value of field 'title'. - */ - public void setTitle( - final java.lang.String title) { - this._title = title; - } + this._newickList.set(index, vNewick); + } - /** - * - * - * @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 vNewickArray + */ + public void setNewick(final uk.ac.vamsas.objects.core.Newick[] vNewickArray) { + // -- copy array + _newickList.clear(); - /** - * - * - * @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]); - } + for (int i = 0; i < vNewickArray.length; i++) { + this._newickList.add(vNewickArray[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 '_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) + "]"); } - /** - * 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; + 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]); } - - /** - * 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); + } + + /** + * 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) + "]"); } - /** - * - * - * @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); + 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); + } }