EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.model.taxon;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import javax.persistence.Column;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.JoinTable;

import javax.persistence.ManyToOne;

import javax.persistence.OneToMany;

import javax.persistence.OrderColumn;

import javax.persistence.Table;

import javax.persistence.Transient;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlAttribute;

import javax.xml.bind.annotation.XmlElement;

import javax.xml.bind.annotation.XmlElementWrapper;

import javax.xml.bind.annotation.XmlIDREF;

import javax.xml.bind.annotation.XmlRootElement;

import javax.xml.bind.annotation.XmlSchemaType;

import javax.xml.bind.annotation.XmlType;

import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;

import org.apache.logging.log4j.LogManager;

import org.apache.logging.log4j.Logger;

import org.hibernate.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.annotations.Parameter;

import org.hibernate.annotations.Type;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.Analyze;

import org.hibernate.search.annotations.ContainedIn;

import org.hibernate.search.annotations.Field;

import org.hibernate.search.annotations.Index;

import org.hibernate.search.annotations.IndexedEmbedded;

import org.hibernate.search.annotations.Store;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;

import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.common.ITreeNode;

import eu.etaxonomy.cdm.model.common.Language;

import eu.etaxonomy.cdm.model.common.LanguageString;

import eu.etaxonomy.cdm.model.common.MultilanguageText;

import eu.etaxonomy.cdm.model.common.SingleSourcedEntityBase;

import eu.etaxonomy.cdm.model.name.Rank;

import eu.etaxonomy.cdm.model.name.TaxonName;

import eu.etaxonomy.cdm.model.reference.NamedSource;

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.model.term.DefinedTerm;

import eu.etaxonomy.cdm.validation.Level3;

import eu.etaxonomy.cdm.validation.annotation.ChildTaxaMustBeLowerRankThanParent;

import eu.etaxonomy.cdm.validation.annotation.ChildTaxaMustDeriveNameFromParent;

import eu.etaxonomy.cdm.validation.annotation.ChildTaxaMustNotSkipRanks;

/**

 * @author a.mueller

 * @since 31.03.2009

 */

@XmlAccessorType(XmlAccessType.FIELD)

@XmlType(name = "TaxonNode", propOrder = {

    "classification",

    "taxon",

    "parent",

    "treeIndex",

    "childNodes",

    "sortIndex",

    "countChildren",

    "agentRelations",

    "synonymToBeUsed",

    "status",

    "statusNote"

})

@XmlRootElement(name = "TaxonNode")

@Entity

//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search

//@Indexed(index = "eu.etaxonomy.cdm.model.taxon.TaxonNode")

@Audited

@Table(name="TaxonNode", indexes = { @javax.persistence.Index(name = "taxonNodeTreeIndex", columnList = "treeIndex") })

@ChildTaxaMustBeLowerRankThanParent(groups = Level3.class)

@ChildTaxaMustNotSkipRanks(groups = Level3.class)

@ChildTaxaMustDeriveNameFromParent(groups = Level3.class)

public class TaxonNode

            extends SingleSourcedEntityBase

            implements ITaxonTreeNode, ITreeNode<TaxonNode>{

    private static final long serialVersionUID = -4743289894926587693L;

    private static final Logger logger = LogManager.getLogger(TaxonNode.class);

    @XmlElement(name = "taxon")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

    @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})

    @ContainedIn

    private Taxon taxon;

    @XmlElement(name = "parent")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

//    @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})

    private TaxonNode parent;

    @XmlElement(name = "treeIndex")

    @Column(length=255)

    @Field(store = Store.YES, index = Index.YES, analyze = Analyze.NO)

    private String treeIndex;

    @XmlElement(name = "classification")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

    @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})

//	TODO @NotNull // avoids creating a UNIQUE key for this field

    @IndexedEmbedded(includeEmbeddedObjectId=true)

    private Classification classification;

    @XmlElementWrapper(name = "childNodes")

    @XmlElement(name = "childNode")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    //see https://dev.e-taxonomy.eu/redmine/issues/3722

    //see https://dev.e-taxonomy.eu/redmine/issues/4200

    //see https://dev.e-taxonomy.eu/redmine/issues/8127

    //see https://dev.e-taxonomy.eu/redmine/issues/10067

    @OrderColumn(name="sortIndex", nullable=true)

    @OneToMany(mappedBy="parent", fetch=FetchType.LAZY)

    //do not cascade

    private List<TaxonNode> childNodes = new ArrayList<>();

    //TODO remove

    //see https://dev.e-taxonomy.eu/redmine/issues/3722

    //see https://dev.e-taxonomy.eu/redmine/issues/4200

    @Transient

    private Integer sortIndex = -1;

    @XmlElement(name = "countChildren")

    private int countChildren;

    @XmlElementWrapper(name = "agentRelations")

    @XmlElement(name = "agentRelation")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @OneToMany(mappedBy="taxonNode", fetch=FetchType.LAZY)

    @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})

    private Set<TaxonNodeAgentRelation> agentRelations = new HashSet<>();

    /**

     * The {@link TaxonNodeStatus status} of this taxon node.

     */

    @XmlAttribute(name ="TaxonNodeStatus")

    @Column(name="status", length=10)

    @Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",

        parameters = {@Parameter(name  = "enumClass", value = "eu.etaxonomy.cdm.model.taxon.TaxonNodeStatus")}

    )

    @Audited

    private TaxonNodeStatus status;

    @XmlElement(name = "statusNote")

    @XmlJavaTypeAdapter(MultilanguageTextAdapter.class)

    @OneToMany(fetch = FetchType.LAZY, orphanRemoval=true)

//    @MapKeyJoinColumn(name="statusNote_mapkey_id")

    @JoinTable(name = "TaxonNode_StatusNote")  //to make possible to add also unplacedNote

    @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE, CascadeType.DELETE})

    private Map<Language,LanguageString> statusNote = new HashMap<>();

//	private Taxon originalConcept;

//	//or

    @XmlElement(name = "synonymToBeUsed")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

    @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})

    private Synonym synonymToBeUsed;

// ******************** CONSTRUCTOR **********************************************/

    //for hibernate use only, *packet* private required by bytebuddy

    @Deprecated

    TaxonNode(){}

    /**

     * to create nodes either use {@link Classification#addChildTaxon(Taxon, Reference, String, Synonym)}

     * or {@link TaxonNode#addChildTaxon(Taxon, Reference, String, Synonym)}

     * @param taxon

     * @param classification

     * @deprecated setting of classification is handled in the addTaxonNode() method,

     * use TaxonNode(taxon) instead

     */

    @Deprecated

    protected TaxonNode (Taxon taxon, Classification classification){

        this(taxon);

        setClassification(classification);

    }

    /**

     * To create nodes either use {@link Classification#addChildTaxon(Taxon, Reference, String, Synonym)}

     * or {@link TaxonNode#addChildTaxon(Taxon, Reference, String, Synonym)}

     *

     * @param taxon

     */

    protected TaxonNode(Taxon taxon){

        setTaxon(taxon);

    }

// ************************* GETTER / SETTER *******************************/

    public Taxon getTaxon() {

        return taxon;

    }

    public void setTaxon(Taxon taxon) {

        this.taxon = taxon;

        if (taxon != null){

            taxon.addTaxonNode(this);

        }

    }

    @Override

    public List<TaxonNode> getChildNodes() {

        return childNodes;

    }

	protected void setChildNodes(List<TaxonNode> childNodes) {

		this.childNodes = childNodes;

	}

    public Classification getClassification() {

        return classification;

    }

    /**

     * THIS METHOD SHOULD NOT BE CALLED!

     * invisible part of the bidirectional relationship, for public use Classification.addRoot() or TaxonNode.addChild()

     * @param classification

     * @deprecated for internal use only

     */

    @Deprecated

    protected void setClassification(Classification classification) {

        this.classification = classification;

    }

    public boolean isUnplaced() {return hasStatus(TaxonNodeStatus.UNPLACED);}

    //#8281 indicates a preliminary placement

    public boolean isDoubtful() {return hasStatus(TaxonNodeStatus.DOUBTFUL);}

    public boolean isExcluded() {return hasStatus(TaxonNodeStatus.EXCLUDED);}

//************************************************************/

    /**

     * The computed order index of this node being a child in the parents

     * childnode list.

     */

    @Transient

    public Integer getSortIndex() {

        return getParent() == null ? null : getParent().getChildNodes().indexOf(CdmBase.deproxy(this));

    }

    //countChildren

    public int getCountChildren() {

        return countChildren;

    }

    /**

     * @deprecated for internal use only

     * @param countChildren

     */

    @Deprecated

    protected void setCountChildren(int countChildren) {

        this.countChildren = countChildren;

    }

    //parent

    @Override

    public TaxonNode getParent(){

        return parent;

    }

    /**

     * Sets the parent of this taxon node.<BR>

     *

     * In most cases you would want to call setParentTreeNode(ITreeNode) which

     * handles updating of the bidirectional relationship

     *

     * @see setParentTreeNode(ITreeNode)

     * @param parent

     *

     */

    protected void setParent(TaxonNode parent) {

        this.parent = parent;

//        this.treeIndex = parent.treeIndex() +

    }

    public TaxonNodeStatus getStatus() {

        return status;

    }

    public void setStatus(TaxonNodeStatus status) {

        this.status = status;

    }

// *************** Status Note ***************

    /**

     * Returns the {@link MultilanguageText multi-language text} to add a note to the

     * status. The different {@link LanguageString language strings}

     * contained in the multi-language text should all have the same meaning.

     * @see #getStatusNote(Language)

     * @see #putStatusNote(Language, String)

     */

    public Map<Language,LanguageString> getStatusNote(){

        return this.statusNote;

    }

    /**

     * Returns the status note string in the given {@link Language language}

     *

     * @param language  the language in which the description string looked for is formulated

     * @see             #getStatusNote()

     * @see             #putStatusNote(Language, String)

     */

    public String getStatusNote(Language language){

        LanguageString languageString = statusNote.get(language);

        if (languageString == null){

            return null;

        }else{

            return languageString.getText();

        }

    }

    /**

     * Adds a translated {@link LanguageString text in a particular language}

     * to the {@link MultilanguageText multilanguage text} used to add a note to

     * the {@link #getStatus() status}.

     *

     * @param statusNote   the language string adding a note to the status

     *                      in a particular language

     * @see                 #getStatusNote()

     * @see                 #putStatusNote(String, Language)

     */

    public void putStatusNote(LanguageString statusNote){

        this.statusNote.put(statusNote.getLanguage(), statusNote);

    }

    /**

     * Creates a {@link LanguageString language string} based on the given text string

     * and the given {@link Language language} and adds it to the {@link MultilanguageText

     * multi-language text} used to annotate the status.

     *

     * @param text      the string annotating the status

     *                  in a particular language

     * @param language  the language in which the text string is formulated

     * @see             #getStatusNote()

     * @see             #putStatusNote(LanguageString)

     * @see             #removeStatusNote(Language)

     */

    public void putStatusNote(Language language, String text){

        this.statusNote.put(language, LanguageString.NewInstance(text, language));

    }

    /**

     * Removes from the {@link MultilanguageText multilanguage text} used to annotate

     * the status the one {@link LanguageString language string}

     * with the given {@link Language language}.

     *

     * @param  lang the language in which the language string to be removed

     *       has been formulated

     * @see         #getStatusNote()

     */

    public void removeStatusNote(Language lang){

        this.statusNote.remove(lang);

    }

// ****************** Agent Relations ****************************/

    public Set<TaxonNodeAgentRelation> getAgentRelations() {

        return this.agentRelations;

    }

    public TaxonNodeAgentRelation addAgentRelation(DefinedTerm type, TeamOrPersonBase<?> agent){

        TaxonNodeAgentRelation result = TaxonNodeAgentRelation.NewInstance(this, agent, type);

        return result;

    }

    public void addAgentRelation(TaxonNodeAgentRelation agentRelation) {

        agentRelation.setTaxonNode(this);

        this.agentRelations.add(agentRelation);

    }

    public void removeAgentRelation(TaxonNodeAgentRelation agentRelation) {

        agentRelation.setTaxonNode(this);

        agentRelations.remove(agentRelation);

    }

//********************

    //synonymToBeused

    public Synonym getSynonymToBeUsed() {

        return synonymToBeUsed;

    }

    public void setSynonymToBeUsed(Synonym synonymToBeUsed) {

        this.synonymToBeUsed = synonymToBeUsed;

    }

    //treeindex

    @Override

    public String treeIndex() {

        return treeIndex;

    }

    @Override

    @Deprecated //for CDM lib internal use only, may be removed in future versions

    public void setTreeIndex(String treeIndex) {

        this.treeIndex = treeIndex;

    }

    @Override

    public String treeIndexLike() {

        return treeIndex + "%";

    }

    @Override

    public String treeIndexWc() {

        return treeIndex + "*";

    }

//************************ METHODS **************************/

   @Override

    public TaxonNode addChildTaxon(Taxon taxon, Reference citation, String microCitation) {

        return addChildTaxon(taxon, this.childNodes.size(), citation, microCitation);

    }

   @Override

   public TaxonNode addChildTaxon(Taxon taxon, NamedSource source) {

       return addChildTaxon(taxon, this.childNodes.size(), source);

   }

    @Override

    public TaxonNode addChildTaxon(Taxon taxon, int index, Reference citation, String microCitation) {

        return addChildTaxon(taxon, index, NamedSource.NewPrimarySourceInstance(citation, microCitation));

    }

    @Override

    public TaxonNode addChildTaxon(Taxon taxon, int index, NamedSource source) {

        Classification classification = CdmBase.deproxy(this.getClassification());

        taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);

        if (classification.isTaxonInTree(taxon)){

            throw new IllegalArgumentException(String.format("Taxon may not be in a classification twice: %s", taxon.getTitleCache()));

       }

       return addChildNode(new TaxonNode(taxon), index, source);

    }

    /**

     * Moves a taxon node to a new parent. Descendents of the node are moved as well

     *

     * @param childNode the taxon node to be moved to the new parent

     * @return the child node in the state of having a new parent

     */

    @Override

    public TaxonNode addChildNode(TaxonNode childNode, Reference reference, String microReference){

        addChildNode(childNode, childNodes.size(), reference, microReference);

        return childNode;

    }

    /**

     * Inserts the given taxon node in the list of children of <i>this</i> taxon node

     * at the given (index + 1) position. If the given index is out of bounds

     * an exception will arise.<BR>

     * Due to bidirectionality this method must also assign <i>this</i> taxon node

     * as the parent of the given child.

     *

     * @param	child	the taxon node to be added

     * @param	index	the integer indicating the position at which the child

     * 					should be added

     * @see				#getChildNodes()

     * @see				#addChildNode(TaxonNode, Reference, String, Synonym)

     * @see				#deleteChildNode(TaxonNode)

     * @see				#deleteChildNode(int)

     */

    @Override

    public TaxonNode addChildNode(TaxonNode child, int index, Reference reference, String microReference){

        return addChildNode(child, index, NamedSource.NewPrimarySourceInstance(reference, microReference));

    }

    /**

     * Inserts the given taxon node in the list of children of <i>this</i> taxon node

     * at the given (index + 1) position. If the given index is out of bounds

     * an exception will arise.<BR>

     * Due to bidirectionality this method must also assign <i>this</i> taxon node

     * as the parent of the given child.

     *

     * @param   child   the taxon node to be added

     * @param   index   the integer indicating the position at which the child

     *                  should be added

     * @see             #getChildNodes()

     * @see             #addChildNode(TaxonNode, Reference, String, Synonym)

     * @see             #deleteChildNode(TaxonNode)

     * @see             #deleteChildNode(int)

     */

    @Override

    public TaxonNode addChildNode(TaxonNode child, int index, NamedSource source){

        if (index < 0 || index > childNodes.size() + 1){

            throw new IndexOutOfBoundsException("Wrong index: " + index);

        }

           // check if this node is a descendant of the childNode

        if(child.getParent() != this && child.isAncestor(this)){

            throw new IllegalStateException("New parent node is a descendant of the node to be moved.");

        }

        child.setParentTreeNode(this, index);

        child.setSource(source);

        return child;

    }

    /**

     * Sets this nodes classification. Updates classification of child nodes recursively.

     *

     * If the former and the actual tree are equal() this method does nothing.

     *

     * @throws IllegalArgumentException if newClassifciation is null

     *

     * @param newClassification

     */

    @Transient

    private void setClassificationRecursively(Classification newClassification) {

        if (newClassification == null){

        	throw new IllegalArgumentException("New Classification must not be 'null' when setting new classification.");

        }

    	if(! newClassification.equals(this.getClassification())){

            this.setClassification(newClassification);

            for(TaxonNode childNode : this.getChildNodes()){

                childNode.setClassificationRecursively(newClassification);

            }

        }

    }

    @Override

    public boolean deleteChildNode(TaxonNode node) {

        boolean result = removeChildNode(node);

        Taxon taxon = deproxy(node.getTaxon());

        node = deproxy(node);

        node.setTaxon(null);

        ArrayList<TaxonNode> childNodes = new ArrayList<>(node.getChildNodes());

        for(TaxonNode childNode : childNodes){

            HibernateProxyHelper.deproxy(childNode, TaxonNode.class);

            node.deleteChildNode(childNode);

        }

        taxon.removeTaxonNode(node);

        return result;

    }

    /**

     * Deletes the child node and also removes children of childnode

     * recursively if delete children is <code>true</code>

     * @param node

     * @param deleteChildren

     * @return

     */

    public boolean deleteChildNode(TaxonNode node, boolean deleteChildren) {

        boolean result = removeChildNode(node);

        Taxon taxon = node.getTaxon();

        node.setTaxon(null);

        taxon.removeTaxonNode(node);

        if (deleteChildren){

            ArrayList<TaxonNode> childNodes = new ArrayList<>(node.getChildNodes());

            for(TaxonNode childNode : childNodes){

                node.deleteChildNode(childNode, deleteChildren);

            }

        } else{

        	ArrayList<TaxonNode> childNodes = new ArrayList<>(node.getChildNodes());

            for(TaxonNode childNode : childNodes){

             this.addChildNode(childNode, null, null);

            }

        }

        return result;

    }

    /**

     * Removes the child node from this node. Sets the parent and the classification of the child

     * node to null

     *

     * @param childNode

     * @return

     */

    protected boolean removeChildNode(TaxonNode childNode){

        boolean result = true;

        //removeNullValueFromChildren();

        if(childNode == null){

            throw new IllegalArgumentException("TaxonNode may not be null");

        }

        int index = childNodes.indexOf(childNode);

        if (index >= 0){

            removeChild(index);

        } else {

            result = false;

        }

        return result;

    }

    /**

     * Removes the child node placed at the given (index + 1) position

     * from the list of {@link #getChildNodes() children} of <i>this</i> taxon node.

     * Sets the parent and the classification of the child

     * node to null.

     * If the given index is out of bounds no child will be removed.<BR>

     * NOTE: this is more for inner use. It does not remove the node from the taxon!!

     * Use deleteChildNode(TaxonNode) instead

     *

     * @param  index	the integer indicating the position of the taxon node to

     * 					be removed

     * @see     		#getChildNodes()

     * @see				#addChildNode(TaxonNode, Reference, String)

     * @see				#addChildNode(TaxonNode, int, Reference, String)

     * @see				#deleteChildNode(TaxonNode)

     */

    public void removeChild(int index){

        //TODO: Only as a workaround. We have to find out why merge creates null entries.

        TaxonNode child = childNodes.get(index);

        child = HibernateProxyHelper.deproxy(child); //strange that this is required, but otherwise child.getParent() returns null for some lazy-loaded items.

        if (child != null){

            TaxonNode parent = HibernateProxyHelper.deproxy(child.getParent());

            TaxonNode thisNode = HibernateProxyHelper.deproxy(this);

            if(parent != null && parent != thisNode){

                throw new IllegalArgumentException("Child TaxonNode (id:" + child.getId() +") must be a child of this (id:" + thisNode.getId() + " node. Sortindex is: " + index + ", parent-id:" + parent.getId());

            }else if (parent == null){

                throw new IllegalStateException("Parent of child is null in TaxonNode.removeChild(int). This should not happen.");

            }

            childNodes.remove(index);

            child.setClassification(null);

            this.countChildren = childNodes.size();

            child.setParent(null);

            child.setTreeIndex(null);

        }

    }

    /**

     * Remove this taxonNode From its taxonomic parent

     *

     * @return true on success

     */

    public boolean delete(){

        if(isTopmostNode()){

            return classification.deleteChildNode(this);

        }else{

            return getParent().deleteChildNode(this);

        }

    }

    /**

     * Remove this taxonNode From its taxonomic parent

     *

     * @return true on success

     */

    public boolean delete(boolean deleteChildren){

        if(isTopmostNode()){

            return classification.deleteChildNode(this, deleteChildren);

        }else{

            return getParent().deleteChildNode(this, deleteChildren);

        }

    }

    @Override

    @Deprecated //for CDM lib internal use only, may be removed in future versions

    public int treeId() {

        if (this.classification == null){

        	logger.warn("TaxonNode has no classification. This should not happen.");  //#3840

        	return -1;

        }else{

        	return this.classification.getId();

        }

    }

    /**

     * Sets the parent of this taxon node to the given parent. Cleans up references to

     * old parents and sets the classification to the new parents classification

     */

    @Transient

    protected void setParentTreeNode(TaxonNode parent, int index){

        // remove ourselves from the old parent

        TaxonNode formerParent = this.getParent();

        formerParent = CdmBase.deproxy(formerParent);

        if (formerParent != null){

        	//special case, child already exists for same parent

            //FIXME document / check for correctness

            if (formerParent.equals(parent)){

                int currentIndex = formerParent.getChildNodes().indexOf(this);

                if (currentIndex != -1 && currentIndex < index){

                    index--;

                }

        	}

        	//remove from old parent

            formerParent.removeChildNode(this);

        }

        // set the new parent

        setParent(parent);

        // set the classification to the parents classification

        Classification classification = parent.getClassification();

        //FIXME also set the tree index here for performance reasons

        classification = CdmBase.deproxy(classification);

        setClassificationRecursively(classification);

        // add this node to the parent's child nodes

        parent = CdmBase.deproxy(parent);

        List<TaxonNode> parentChildren = parent.getChildNodes();

        if (index > parent.getChildNodes().size()){

            index = parent.getChildNodes().size();

        }

        if (parentChildren.contains(this)){

            //avoid duplicates

            if (parentChildren.indexOf(this) < index){

                index = index-1;

            }

            parentChildren.remove(this);

            parentChildren.add(index, this);

        }else{

            parentChildren.add(index, this);

        }

//        //only for debugging

//        if (this.getSortIndex() == null){

//            logger.warn("sortindex is null. This should not happen.");

//        }else if (! this.getSortIndex().equals(index)){

//        	logger.warn("index and sortindex are not equal: " +  this.getSortIndex() + ";" + index);

//        }

        // update the children count

        parent.setCountChildren(parent.getChildNodes().size());

    }

    /**

     * Returns a set containing this node and all nodes that are descendants of this node.

     */

	@Transient

    protected Set<TaxonNode> getDescendants(){

        Set<TaxonNode> nodeSet = new HashSet<>();

        nodeSet.add(this);

        for(TaxonNode childNode : getChildNodes()){

            nodeSet.addAll(childNode.getDescendants());

        }

        return nodeSet;

    }

    /**

     * Returns a set containing a clone of this node and of all nodes that are descendants of this node

     *

     * @return

     */

    protected TaxonNode cloneDescendants(){

        TaxonNode clone = this.clone();

        TaxonNode childClone;

        for(TaxonNode childNode : getChildNodes()){

            childClone = childNode.clone();

            for (TaxonNode childChild:childNode.getChildNodes()){

                childClone.addChildNode(childChild.cloneDescendants(), childChild.getReference(), childChild.getMicroReference());

            }

            clone.addChildNode(childClone, childNode.getReference(), childNode.getMicroReference());

            //childClone.addChildNode(childNode.cloneDescendants());

        }

        return clone;

    }

    /**

     * Returns all ancestor nodes of this node

     *

     * @return a set of all parent nodes

     */

    @Transient

    protected Set<TaxonNode> getAncestors(){

        Set<TaxonNode> nodeSet = new HashSet<>();

        if(this.getParent() != null){

        	TaxonNode parent =  CdmBase.deproxy(this.getParent());

        	nodeSet.add(parent);

            nodeSet.addAll(parent.getAncestors());

        }

        return nodeSet;

    }

    /**

     * Retrieves the first ancestor of the given rank. If any of the ancestors

     * has no taxon or has a rank > the given rank <code>null</code> is returned.

     * If <code>this</code> taxon is already of given rank this taxon is returned.

     * @param rank the rank the ancestor should have

     * @return the first found instance of a parent taxon node with the given rank

     */

    @Transient

    public TaxonNode getAncestorOfRank(Rank rank){

        Taxon taxon = CdmBase.deproxy(this.getTaxon());

        if (taxon == null){

            return null;

        }

        TaxonName name = CdmBase.deproxy(taxon.getName());

        if (name != null && name.getRank() != null){

            if (name.getRank().isHigher(rank)){

                return null;

            }

            if (name.getRank().equals(rank)){

                return this;

            }

        }

        if(this.getParent() != null){

        	TaxonNode parent =  CdmBase.deproxy(this.getParent());

            return parent.getAncestorOfRank(rank);

        }

		return null;

    }

    /**

     * Returns the ancestor taxa, starting with the highest (e.g. kingdom)

     * @return

     */

    @Transient

    public List<Taxon> getAncestorTaxaList(){

        List<Taxon> result = new ArrayList<>();

        TaxonNode current = this;

        while (current != null){

            if (current.getTaxon() != null){

                result.add(0, current.getTaxon());

            }

            current = current.getParent();

        }

        return result;

    }

    /**

     * Returns the ancestor taxon nodes, that do have a taxon attached

     * (excludes the root node) starting with the highest

     */

    @Transient

    public List<TaxonNode> getAncestorList(){

        List<TaxonNode> result = new ArrayList<>();

        TaxonNode current = this.getParent();

        while (current != null){

            if (current.getTaxon() != null){

                result.add(0, current);

            }

            current = current.getParent();

        }

        return result;

    }

    /**

     * Whether this TaxonNode is a direct child of the classification TreeNode

     */

    @Transient

    public boolean isTopmostNode(){

    	boolean parentCheck = false;

    	boolean classificationCheck = false;

    	if(getParent() != null) {

    		if(getParent().getTaxon() == null) {

    			parentCheck = true;

    		}

    	}

    	//TODO remove

    	// FIXME This should work but doesn't, due to missing sort indexes, can be removed after fixing #4200, #4098

    	if (classification != null){

    		classificationCheck = classification.getRootNode().getChildNodes().contains(this);

    	}else{

    		classificationCheck = false;

    	}

    	// The following is just for logging purposes for the missing sort indexes problem

    	// ticket #4098

    	if(parentCheck != classificationCheck) {

    		logger.warn("isTopmost node check " + parentCheck + " not same as classificationCheck : " + classificationCheck + " for taxon node ");

    		if(this.getParent() != null) {

    			logger.warn("-- with parent uuid " + this.getParent().getUuid().toString());

    			logger.warn("-- with parent id " + this.getParent().getId());

    			for(TaxonNode node : this.getParent().getChildNodes()) {

    				if(node == null) {

    					logger.warn("-- child node is null");

    				} else if (node.getTaxon() == null) {

    					logger.warn("-- child node taxon is null");

    				}

    			}

    			logger.warn("-- parent child count" + this.getParent().getChildNodes().size());

    		}

    	}