/*
 * This class was automatically generated with 
 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
 * Schema.
 * $Id$
 */

package uk.ac.vamsas.objects.core;

  //---------------------------------/
 //- Imported classes and packages -/
//---------------------------------/

import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;

/**
 * Class Tree.
 * 
 * @version $Revision$ $Date$
 */
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;
            if (this._id != null) {
                if (temp._id == null) return false;
                else if (!(this._id.equals(temp._id))) 
                    return false;
            }
            else if (temp._id != null)
                return false;
            if (this._modifiable != null) {
                if (temp._modifiable == null) return false;
                else if (!(this._modifiable.equals(temp._modifiable))) 
                    return false;
            }
            else if (temp._modifiable != null)
                return false;
            if (this._title != null) {
                if (temp._title == null) return false;
                else if (!(this._title.equals(temp._title))) 
                    return false;
            }
            else if (temp._title != null)
                return false;
            if (this._newickList != null) {
                if (temp._newickList == null) return false;
                else if (!(this._newickList.equals(temp._newickList))) 
                    return false;
            }
            else if (temp._newickList != null)
                return false;
            if (this._treenodeList != null) {
                if (temp._treenodeList == null) return false;
                else if (!(this._treenodeList.equals(temp._treenodeList))) 
                    return false;
            }
            else if (temp._treenodeList != null)
                return false;
            if (this._propertyList != null) {
                if (temp._propertyList == null) return false;
                else if (!(this._propertyList.equals(temp._propertyList))) 
                    return false;
            }
            else if (temp._propertyList != null)
                return false;
            if (this._provenance != null) {
                if (temp._provenance == null) return false;
                else if (!(this._provenance.equals(temp._provenance))) 
                    return false;
            }
            else if (temp._provenance != null)
                return false;
            return true;
        }
        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.  <p>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 <i>know</i>
     * 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.  <p>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 <i>know</i>
     * 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.  <p>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 <i>know</i>
     * 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.
     * <p>
     * The following steps came from <b>Effective Java Programming
     * Language Guide</b> 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) {
           result = 37 * result + _id.hashCode();
        }
        if (_modifiable != null) {
           result = 37 * result + _modifiable.hashCode();
        }
        if (_title != null) {
           result = 37 * result + _title.hashCode();
        }
        if (_newickList != null) {
           result = 37 * result + _newickList.hashCode();
        }
        if (_treenodeList != null) {
           result = 37 * result + _treenodeList.hashCode();
        }
        if (_propertyList != null) {
           result = 37 * result + _propertyList.hashCode();
        }
        if (_provenance != null) {
           result = 37 * result + _provenance.hashCode();
        }
        
        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);
    }

}