/*
 * 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 VamsasDocument.
 * 
 * @version $Revision$ $Date$
 */
public class VamsasDocument extends uk.ac.vamsas.client.Vobject 
implements java.io.Serializable
{


      //--------------------------/
     //- Class/Member Variables -/
    //--------------------------/

    /**
     * Vamsas Document Version Number
     */
    private java.lang.String _version;

    /**
     * Field _lockFile.
     */
    private uk.ac.vamsas.objects.core.LockFile _lockFile;

    /**
     * Field _provenance.
     */
    private uk.ac.vamsas.objects.core.Provenance _provenance;

    /**
     * contains unassociated trees and a number of analysis sets
     *  
     */
    private java.util.Vector _VAMSASList;

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

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


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

    public VamsasDocument() {
        super();
        this._VAMSASList = new java.util.Vector();
        this._applicationDataList = new java.util.Vector();
        this._attachmentList = new java.util.Vector();
    }


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

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

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

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

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

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

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

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

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

    /**
     * Method enumerateVAMSAS.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.VAMSAS elements
     */
    public java.util.Enumeration enumerateVAMSAS(
    ) {
        return this._VAMSASList.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 VamsasDocument) {
        
            VamsasDocument temp = (VamsasDocument)obj;
            boolean thcycle;
            boolean tmcycle;
            if (this._version != null) {
                if (temp._version == null) return false;
                if (this._version != temp._version) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._version);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._version);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._version); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._version.equals(temp._version)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
                    }
                }
            } else if (temp._version != null)
                return false;
            if (this._lockFile != null) {
                if (temp._lockFile == null) return false;
                if (this._lockFile != temp._lockFile) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._lockFile);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._lockFile);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._lockFile.equals(temp._lockFile)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
                    }
                }
            } else if (temp._lockFile != 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;
            if (this._VAMSASList != null) {
                if (temp._VAMSASList == null) return false;
                if (this._VAMSASList != temp._VAMSASList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._VAMSASList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._VAMSASList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._VAMSASList.equals(temp._VAMSASList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
                    }
                }
            } else if (temp._VAMSASList != null)
                return false;
            if (this._applicationDataList != null) {
                if (temp._applicationDataList == null) return false;
                if (this._applicationDataList != temp._applicationDataList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._applicationDataList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._applicationDataList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._applicationDataList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._applicationDataList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._applicationDataList.equals(temp._applicationDataList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._applicationDataList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._applicationDataList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._applicationDataList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._applicationDataList);
                    }
                }
            } else if (temp._applicationDataList != null)
                return false;
            if (this._attachmentList != null) {
                if (temp._attachmentList == null) return false;
                if (this._attachmentList != temp._attachmentList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._attachmentList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._attachmentList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._attachmentList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._attachmentList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._attachmentList.equals(temp._attachmentList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._attachmentList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._attachmentList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._attachmentList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._attachmentList);
                    }
                }
            } else if (temp._attachmentList != null)
                return false;
            return true;
        }
        return false;
    }

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

    /**
     * Method getApplicationData.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.ApplicationData[] getApplicationData(
    ) {
        uk.ac.vamsas.objects.core.ApplicationData[] array = new uk.ac.vamsas.objects.core.ApplicationData[0];
        return (uk.ac.vamsas.objects.core.ApplicationData[]) this._applicationDataList.toArray(array);
    }

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

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

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

    /**
     * Method getAttachment.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.Attachment[] getAttachment(
    ) {
        uk.ac.vamsas.objects.core.Attachment[] array = new uk.ac.vamsas.objects.core.Attachment[0];
        return (uk.ac.vamsas.objects.core.Attachment[]) this._attachmentList.toArray(array);
    }

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

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

    /**
     * Returns the value of field 'lockFile'.
     * 
     * @return the value of field 'LockFile'.
     */
    public uk.ac.vamsas.objects.core.LockFile getLockFile(
    ) {
        return this._lockFile;
    }

    /**
     * Returns the value of field 'provenance'.
     * 
     * @return the value of field 'Provenance'.
     */
    public uk.ac.vamsas.objects.core.Provenance getProvenance(
    ) {
        return this._provenance;
    }

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

    /**
     * Method getVAMSAS.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.VAMSAS[] getVAMSAS(
    ) {
        uk.ac.vamsas.objects.core.VAMSAS[] array = new uk.ac.vamsas.objects.core.VAMSAS[0];
        return (uk.ac.vamsas.objects.core.VAMSAS[]) this._VAMSASList.toArray(array);
    }

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

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

    /**
     * Returns the value of field 'version'. The field 'version'
     * has the following description: Vamsas Document Version
     * Number
     * 
     * @return the value of field 'Version'.
     */
    public java.lang.String getVersion(
    ) {
        return this._version;
    }

    /**
     * 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 (_version != null
            && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
           result = 37 * result + _version.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_version);
        }
        if (_lockFile != null
            && !org.castor.util.CycleBreaker.startingToCycle(_lockFile)) {
           result = 37 * result + _lockFile.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_lockFile);
        }
        if (_provenance != null
            && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
           result = 37 * result + _provenance.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
        }
        if (_VAMSASList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_VAMSASList)) {
           result = 37 * result + _VAMSASList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_VAMSASList);
        }
        if (_applicationDataList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_applicationDataList)) {
           result = 37 * result + _applicationDataList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_applicationDataList);
        }
        if (_attachmentList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_attachmentList)) {
           result = 37 * result + _attachmentList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_attachmentList);
        }
        
        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 removeAllApplicationData(
    ) {
        this._applicationDataList.clear();
    }

    /**
     */
    public void removeAllAttachment(
    ) {
        this._attachmentList.clear();
    }

    /**
     */
    public void removeAllVAMSAS(
    ) {
        this._VAMSASList.clear();
    }

    /**
     * Method removeApplicationData.
     * 
     * @param vApplicationData
     * @return true if the object was removed from the collection.
     */
    public boolean removeApplicationData(
            final uk.ac.vamsas.objects.core.ApplicationData vApplicationData) {
        boolean removed = _applicationDataList.remove(vApplicationData);
        return removed;
    }

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

    /**
     * Method removeAttachment.
     * 
     * @param vAttachment
     * @return true if the object was removed from the collection.
     */
    public boolean removeAttachment(
            final uk.ac.vamsas.objects.core.Attachment vAttachment) {
        boolean removed = _attachmentList.remove(vAttachment);
        return removed;
    }

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

    /**
     * Method removeVAMSAS.
     * 
     * @param vVAMSAS
     * @return true if the object was removed from the collection.
     */
    public boolean removeVAMSAS(
            final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS) {
        boolean removed = _VAMSASList.remove(vVAMSAS);
        return removed;
    }

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

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

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

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

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

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

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

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

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

    /**
     * Sets the value of field 'lockFile'.
     * 
     * @param lockFile the value of field 'lockFile'.
     */
    public void setLockFile(
            final uk.ac.vamsas.objects.core.LockFile lockFile) {
        this._lockFile = lockFile;
    }

    /**
     * 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;
    }

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

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

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

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

    /**
     * Sets the value of field 'version'. The field 'version' has
     * the following description: Vamsas Document Version Number
     * 
     * @param version the value of field 'version'.
     */
    public void setVersion(
            final java.lang.String version) {
        this._version = version;
    }

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

}