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.MapKeyJoinColumn;

import javax.persistence.OneToMany;

import javax.persistence.OrderBy;

import javax.persistence.OrderColumn;

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.log4j.Logger;

import org.hibernate.LazyInitializationException;

import org.hibernate.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.annotations.Index;

import org.hibernate.annotations.Table;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.ContainedIn;

import org.hibernate.search.annotations.IndexedEmbedded;

import eu.etaxonomy.cdm.hibernate.HHH_9751_Util;

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.AnnotatableEntity;

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

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

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.name.Rank;

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

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

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

 * @created 31.03.2009

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

    "classification",

    "taxon",

    "parent",

    "treeIndex",

    "sortIndex",

    "childNodes",

    "referenceForParentChildRelation",

    "microReferenceForParentChildRelation",

    "countChildren",

    "agentRelations",

    "synonymToBeUsed",

    "excludedNote"

})

@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(appliesTo="TaxonNode", indexes = { @Index(name = "taxonNodeTreeIndex", columnNames = { "treeIndex" }) })

@ChildTaxaMustBeLowerRankThanParent(groups = Level3.class)

@ChildTaxaMustNotSkipRanks(groups = Level3.class)

@ChildTaxaMustDeriveNameFromParent(groups = Level3.class)

public class TaxonNode extends AnnotatableEntity implements ITaxonTreeNode, ITreeNode<TaxonNode>, Cloneable{

    private static final long serialVersionUID = -4743289894926587693L;

    private static final Logger logger = Logger.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)

    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/trac/ticket/3722

    @OrderColumn(name="sortIndex")

    @OrderBy("sortIndex")

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

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

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

    //see https://dev.e-taxonomy.eu/trac/ticket/3722

    //see https://dev.e-taxonomy.eu/trac/ticket/4200

    private Integer sortIndex = -1;

	@XmlElement(name = "reference")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

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

    private Reference referenceForParentChildRelation;

    @XmlElement(name = "microReference")

    private String microReferenceForParentChildRelation;

    @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<>();

    @XmlAttribute(name= "unplaced")

    private boolean unplaced = false;

    public boolean isUnplaced() {return unplaced;}

    public void setUnplaced(boolean unplaced) {this.unplaced = unplaced;}

    @XmlAttribute(name= "excluded")

    private boolean excluded = false;

    public boolean isExcluded() {return excluded;}

    public void setExcluded(boolean excluded) {this.excluded = excluded;}

    @XmlElement(name = "excludedNote")

    @XmlJavaTypeAdapter(MultilanguageTextAdapter.class)

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

    @MapKeyJoinColumn(name="excludedNote_mapkey_id")

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

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

    private Map<Language,LanguageString> excludedNote = 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 **********************************************/

    protected TaxonNode(){super();}

    /**

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

    @Transient

    public Integer getSortIndex() {

        return sortIndex;

	}

    /**

     * SortIndex shall be handled only internally, therefore not public.

     * However, as javaassist only supports protected methods it needs to be protected, not private.

     * Alternatively we could use deproxy on every call of this method (see commented code)

     * @param i

     * @return

     * @deprecated for internal use only

     */

     @Deprecated

    protected void setSortIndex(Integer i) {

//    	 CdmBase.deproxy(this, TaxonNode.class).sortIndex = i;  //alternative solution for private, DON'T remove

    	 sortIndex = i;

	}

    public Taxon getTaxon() {

        return taxon;

    }

    protected 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 TaxonomicView.addRoot() or TaxonNode.addChild()

     * @param classification

     * @deprecated for internal use only

     */

    @Deprecated

    protected void setClassification(Classification classification) {

        this.classification = classification;

    }

    @Override

    public String getMicroReference() {

        return microReferenceForParentChildRelation;

    }

    public void setMicroReference(String microReference) {

        this.microReferenceForParentChildRelation = microReference;

    }

    @Override

    public Reference getReference() {

        return referenceForParentChildRelation;

    }

    public void setReference(Reference reference) {

        this.referenceForParentChildRelation = reference;

    }

    //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;

    }

    // *************** Excluded Note ***************

    /**

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

     * excluded flag. The different {@link LanguageString language strings}

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

     * @see #getExcludedNote()

     * @see #putExcludedNote(Language, String)

     */

    public Map<Language,LanguageString> getExcludedNote(){

        return this.excludedNote;

    }

    /**

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

     *

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

     * @see             #getExcludedNote()

     * @see             #putExcludedNote(Language, String)

     */

    public String getExcludedNote(Language language){

        LanguageString languageString = excludedNote.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 #isExcluded() excluded} flag.

     *

     * @param excludedNote   the language string adding a note to the excluded flag

     *                      in a particular language

     * @see                 #getExcludedNote()

     * @see                 #putExcludedNote(String, Language)

     */

    public void putExcludedNote(LanguageString excludedNote){

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

    }

    /**

     * 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 excluded flag.

     *

     * @param text      the string annotating the excluded flag

     *                  in a particular language

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

     * @see             #getExcludedNote()

     * @see             #putExcludedNote(LanguageString)

     * @see             #removeExcludedNote(Language)

     */

    public void putExcludedNote(Language language, String text){

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

    }

    /**

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

     * the excluded flag 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         #getExcludedNote()

     */

    public void removeExcludedNote(Language lang){

        this.excludedNote.remove(lang);

    }

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

    /**

     * @return

     */

    public Set<TaxonNodeAgentRelation> getAgentRelations() {

        return this.agentRelations;

    }

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

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

        return result;

    }

    /**

     * @param nodeAgentRelation

     */

    protected void addAgentRelation(TaxonNodeAgentRelation agentRelation) {

        agentRelation.setTaxonNode(this);

        this.agentRelations.add(agentRelation);

    }

    /**

     * @param nodeAgentRelation

     */

    public void removeNodeAgent(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;

    }

//************************ 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, int index, Reference citation, String microCitation) {

        Classification classification = HibernateProxyHelper.deproxy(this.getClassification(), Classification.class);

        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, citation, microCitation);

    }

    /**

     * 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){

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

        }

        child.setParentTreeNode(this, index);

        child.setReference(reference);

        child.setMicroReference(microReference);

        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 = HibernateProxyHelper.deproxy(node.getTaxon(), Taxon.class);

        node = HibernateProxyHelper.deproxy(node, TaxonNode.class);

        node.setTaxon(null);

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

            for(TaxonNode childNode : childNodes){

                node.deleteChildNode(childNode, deleteChildren);

            }

        } else{

        	ArrayList<TaxonNode> childNodes = new ArrayList<TaxonNode>(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.

     *

     * @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, TaxonNode.class); //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.class);

            TaxonNode thisNode = HibernateProxyHelper.deproxy(this, TaxonNode.class);

            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);

            //update sortindex

            //TODO workaround (see sortIndex doc)

            this.countChildren = childNodes.size();

            child.setParent(null);

            child.setTreeIndex(null);

            updateSortIndex(index);

            child.setSortIndex(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

     *

     * @param parent

     */

    @Transient

    protected void setParentTreeNode(TaxonNode parent, int index){

        // remove ourselves from the old parent

        TaxonNode formerParent = this.getParent();

        formerParent = HibernateProxyHelper.deproxy(formerParent, TaxonNode.class);

        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 = HibernateProxyHelper.deproxy(classification, Classification.class);

        setClassificationRecursively(classification);

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

        parent = HibernateProxyHelper.deproxy(parent, TaxonNode.class);

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

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

//        HHH_9751_Util.removeAllNull(parentChildren);

//        parent.updateSortIndex(0);

        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);

        }

        //sortIndex

        //TODO workaround (see sortIndex doc)

       // this.getParent().removeNullValueFromChildren();

        this.getParent().updateSortIndex(index);

        //only for debugging

        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());

    }

	/**

	 * As long as the sort index is not correctly handled through hibernate this is a workaround method

	 * to update the sort index manually

	 * @param parentChildren

	 * @param index

	 */

	private void updateSortIndex(int index) {

	    if (this.hasChildNodes()){

    	    List<TaxonNode> children = this.getChildNodes();

    	    HHH_9751_Util.removeAllNull(children);

    	    for(int i = index; i < children.size(); i++){

                	TaxonNode child = children.get(i);

                	if (child != null){

        //        		child = CdmBase.deproxy(child, TaxonNode.class);  //deproxy not needed as long as setSortIndex is protected or public #4200

                		child.setSortIndex(i);

                	}else{

                		String message = "A node in a taxon tree must never be null but is (ParentId: %d; sort index: %d; index: %d; i: %d)";

                		throw new IllegalStateException(String.format(message, getId(), sortIndex, index, i));

                	}

            }

	    }

	}

    /**

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

     *

     * @return

     */

    protected Set<TaxonNode> getDescendants(){

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

        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 = (TaxonNode)this.clone();

        TaxonNode childClone;

        for(TaxonNode childNode : getChildNodes()){

            childClone = (TaxonNode) 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

     */

    protected Set<TaxonNode> getAncestors(){

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

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

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

        	nodeSet.add(parent);

            nodeSet.addAll(parent.getAncestors());

        }

        return nodeSet;

    }

    /**

     * Retrieves the first ancestor of the given rank

     * @param rank the rank the ancestor should have

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

     */

    public TaxonNode getAncestorOfRank(Rank rank){

        TaxonBase taxon = HibernateProxyHelper.deproxy(this.getTaxon(), Taxon.class);

        if (taxon == null){

            return null;

        }

        TaxonNameBase name = HibernateProxyHelper.deproxy(taxon.getName(), TaxonNameBase.class);

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

        	return null;

        }

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

        	return this;

        }

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

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

            return parent.getAncestorOfRank(rank);

        }

		return null;

    }

    /**

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

     * @return

     */

    @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());

    		}

    	}

    	return parentCheck;

    }

    /**

     * Whether this TaxonNode is a descendant of the given TaxonNode

     *