/*
 * 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;

/**
 * contains unassociated trees and a number of analysis sets
 *  
 * 
 * @version $Revision$ $Date$
 */
public class VAMSAS 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 _treeList.
     */
    private java.util.Vector _treeList;

    /**
     * Field _dataSetList.
     */
    private java.util.Vector _dataSetList;


      //----------------/
     //- Constructors -/
    //----------------/

    public VAMSAS() {
        super();
        this._treeList = new java.util.Vector();
        this._dataSetList = new java.util.Vector();
    }


      //-----------/
     //- Methods -/
    //-----------/

    /**
     * 
     * 
     * @param vDataSet
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addDataSet(
            final uk.ac.vamsas.objects.core.DataSet vDataSet)
    throws java.lang.IndexOutOfBoundsException {
        this._dataSetList.addElement(vDataSet);
    }

    /**
     * 
     * 
     * @param index
     * @param vDataSet
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addDataSet(
            final int index,
            final uk.ac.vamsas.objects.core.DataSet vDataSet)
    throws java.lang.IndexOutOfBoundsException {
        this._dataSetList.add(index, vDataSet);
    }

    /**
     * 
     * 
     * @param vTree
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addTree(
            final uk.ac.vamsas.objects.core.Tree vTree)
    throws java.lang.IndexOutOfBoundsException {
        this._treeList.addElement(vTree);
    }

    /**
     * 
     * 
     * @param index
     * @param vTree
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addTree(
            final int index,
            final uk.ac.vamsas.objects.core.Tree vTree)
    throws java.lang.IndexOutOfBoundsException {
        this._treeList.add(index, vTree);
    }

    /**
     * Method enumerateDataSet.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.DataSet elements
     */
    public java.util.Enumeration enumerateDataSet(
    ) {
        return this._dataSetList.elements();
    }

    /**
     * Method enumerateTree.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.Tree elements
     */
    public java.util.Enumeration enumerateTree(
    ) {
        return this._treeList.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 VAMSAS) {
        
            VAMSAS temp = (VAMSAS)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._treeList != null) {
                if (temp._treeList == null) return false;
                if (this._treeList != temp._treeList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._treeList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._treeList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._treeList.equals(temp._treeList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
                    }
                }
            } else if (temp._treeList != null)
                return false;
            if (this._dataSetList != null) {
                if (temp._dataSetList == null) return false;
                if (this._dataSetList != temp._dataSetList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._dataSetList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._dataSetList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._dataSetList.equals(temp._dataSetList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
                    }
                }
            } else if (temp._dataSetList != null)
                return false;
            return true;
        }
        return false;
    }

    /**
     * Method getDataSet.
     * 
     * @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.DataSet
     * at the given index
     */
    public uk.ac.vamsas.objects.core.DataSet getDataSet(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._dataSetList.size()) {
            throw new IndexOutOfBoundsException("getDataSet: Index value '" + index + "' not in range [0.." + (this._dataSetList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.DataSet) _dataSetList.get(index);
    }

    /**
     * Method getDataSet.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.DataSet[] getDataSet(
    ) {
        uk.ac.vamsas.objects.core.DataSet[] array = new uk.ac.vamsas.objects.core.DataSet[0];
        return (uk.ac.vamsas.objects.core.DataSet[]) this._dataSetList.toArray(array);
    }

    /**
     * Method getDataSetAsReference.Returns a reference to
     * '_dataSetList'. No type checking is performed on any
     * modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getDataSetAsReference(
    ) {
        return this._dataSetList;
    }

    /**
     * Method getDataSetCount.
     * 
     * @return the size of this collection
     */
    public int getDataSetCount(
    ) {
        return this._dataSetList.size();
    }

    /**
     * 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 getTree.
     * 
     * @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.Tree at
     * the given index
     */
    public uk.ac.vamsas.objects.core.Tree getTree(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._treeList.size()) {
            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.Tree) _treeList.get(index);
    }

    /**
     * Method getTree.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.Tree[] getTree(
    ) {
        uk.ac.vamsas.objects.core.Tree[] array = new uk.ac.vamsas.objects.core.Tree[0];
        return (uk.ac.vamsas.objects.core.Tree[]) this._treeList.toArray(array);
    }

    /**
     * Method getTreeAsReference.Returns a reference to
     * '_treeList'. No type checking is performed on any
     * modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getTreeAsReference(
    ) {
        return this._treeList;
    }

    /**
     * Method getTreeCount.
     * 
     * @return the size of this collection
     */
    public int getTreeCount(
    ) {
        return this._treeList.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
            && !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 (_treeList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
           result = 37 * result + _treeList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
        }
        if (_dataSetList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_dataSetList)) {
           result = 37 * result + _dataSetList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetList);
        }
        
        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 removeAllDataSet(
    ) {
        this._dataSetList.clear();
    }

    /**
     */
    public void removeAllTree(
    ) {
        this._treeList.clear();
    }

    /**
     * Method removeDataSet.
     * 
     * @param vDataSet
     * @return true if the object was removed from the collection.
     */
    public boolean removeDataSet(
            final uk.ac.vamsas.objects.core.DataSet vDataSet) {
        boolean removed = _dataSetList.remove(vDataSet);
        return removed;
    }

    /**
     * Method removeDataSetAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.DataSet removeDataSetAt(
            final int index) {
        java.lang.Object obj = this._dataSetList.remove(index);
        return (uk.ac.vamsas.objects.core.DataSet) obj;
    }

    /**
     * Method removeTree.
     * 
     * @param vTree
     * @return true if the object was removed from the collection.
     */
    public boolean removeTree(
            final uk.ac.vamsas.objects.core.Tree vTree) {
        boolean removed = _treeList.remove(vTree);
        return removed;
    }

    /**
     * Method removeTreeAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.Tree removeTreeAt(
            final int index) {
        java.lang.Object obj = this._treeList.remove(index);
        return (uk.ac.vamsas.objects.core.Tree) obj;
    }

    /**
     * 
     * 
     * @param index
     * @param vDataSet
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setDataSet(
            final int index,
            final uk.ac.vamsas.objects.core.DataSet vDataSet)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._dataSetList.size()) {
            throw new IndexOutOfBoundsException("setDataSet: Index value '" + index + "' not in range [0.." + (this._dataSetList.size() - 1) + "]");
        }
        
        this._dataSetList.set(index, vDataSet);
    }

    /**
     * 
     * 
     * @param vDataSetArray
     */
    public void setDataSet(
            final uk.ac.vamsas.objects.core.DataSet[] vDataSetArray) {
        //-- copy array
        _dataSetList.clear();
        
        for (int i = 0; i < vDataSetArray.length; i++) {
                this._dataSetList.add(vDataSetArray[i]);
        }
    }

    /**
     * Sets the value of '_dataSetList' by copying the given
     * Vector. All elements will be checked for type safety.
     * 
     * @param vDataSetList the Vector to copy.
     */
    public void setDataSet(
            final java.util.Vector vDataSetList) {
        // copy vector
        this._dataSetList.clear();
        
        this._dataSetList.addAll(vDataSetList);
    }

    /**
     * Sets the value of '_dataSetList' by setting it to the given
     * Vector. No type checking is performed.
     * @deprecated
     * 
     * @param dataSetVector the Vector to set.
     */
    public void setDataSetAsReference(
            final java.util.Vector dataSetVector) {
        this._dataSetList = dataSetVector;
    }

    /**
     * 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 vTree
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setTree(
            final int index,
            final uk.ac.vamsas.objects.core.Tree vTree)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._treeList.size()) {
            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
        }
        
        this._treeList.set(index, vTree);
    }

    /**
     * 
     * 
     * @param vTreeArray
     */
    public void setTree(
            final uk.ac.vamsas.objects.core.Tree[] vTreeArray) {
        //-- copy array
        _treeList.clear();
        
        for (int i = 0; i < vTreeArray.length; i++) {
                this._treeList.add(vTreeArray[i]);
        }
    }

    /**
     * Sets the value of '_treeList' by copying the given Vector.
     * All elements will be checked for type safety.
     * 
     * @param vTreeList the Vector to copy.
     */
    public void setTree(
            final java.util.Vector vTreeList) {
        // copy vector
        this._treeList.clear();
        
        this._treeList.addAll(vTreeList);
    }

    /**
     * Sets the value of '_treeList' by setting it to the given
     * Vector. No type checking is performed.
     * @deprecated
     * 
     * @param treeVector the Vector to set.
     */
    public void setTreeAsReference(
            final java.util.Vector treeVector) {
        this._treeList = treeVector;
    }

    /**
     * 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.VAMSAS
     */
    public static uk.ac.vamsas.objects.core.VAMSAS unmarshal(
            final java.io.Reader reader)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        return (uk.ac.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.VAMSAS.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);
    }

}