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// $Id$
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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.taxon;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.ManyToOne;
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import javax.persistence.OneToMany;
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import javax.persistence.OneToOne;
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import javax.persistence.Transient;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlElement;
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import javax.xml.bind.annotation.XmlElementWrapper;
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import javax.xml.bind.annotation.XmlIDREF;
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import javax.xml.bind.annotation.XmlRootElement;
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import javax.xml.bind.annotation.XmlSchemaType;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.log4j.Logger;
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import org.hibernate.annotations.Cascade;
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import org.hibernate.annotations.CascadeType;
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import org.hibernate.envers.Audited;
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import eu.etaxonomy.cdm.model.common.IReferencedEntity;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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/**
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* @author a.mueller
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* @created 31.03.2009
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* @version 1.0
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "TaxonomicTree", propOrder = {
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"name",
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"rootNodes",
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"reference",
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"microReference"
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})
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@XmlRootElement(name = "TaxonomicTree")
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@Entity
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@Audited
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public class TaxonomicTree extends IdentifiableEntity implements IReferencedEntity{
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private static final long serialVersionUID = -753804821474209635L;
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private static final Logger logger = Logger.getLogger(TaxonomicTree.class);
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@XmlElement(name = "name")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToOne(fetch = FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE})
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private LanguageString name;
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// @XmlElementWrapper(name = "allNodes")
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// @XmlElement(name = "taxonNode")
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// @XmlIDREF
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// @XmlSchemaType(name = "IDREF")
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// @OneToMany(mappedBy="taxonomicTree", fetch=FetchType.LAZY)
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// @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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// @Deprecated // FIXME remove this. A set containing all nodes of the tree is a major performance killer, especially when it is not really in use
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// private Set<TaxonNode> allNodes = new HashSet<TaxonNode>();
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@XmlElementWrapper(name = "rootNodes")
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@XmlElement(name = "rootNode")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(fetch=FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private Set<TaxonNode> rootNodes = new HashSet<TaxonNode>();
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@XmlElement(name = "reference")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE})
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private ReferenceBase reference;
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@XmlElement(name = "microReference")
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private String microReference;
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// /**
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// * If this taxonomic view is an alternative view for a subtree in an other view(parent view),
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// * the alternativeViewRoot is the connection node from this view to the parent view.
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// * It replaces another node in the parent view.
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// */
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// private AlternativeViewRoot alternativeViewRoot;
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public static TaxonomicTree NewInstance(String name){
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return NewInstance(name, Language.DEFAULT());
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}
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public static TaxonomicTree NewInstance(String name, Language language){
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TaxonomicTree result = new TaxonomicTree();
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LanguageString langName = LanguageString.NewInstance(name, language);
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result.setName(langName);
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return result;
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}
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protected TaxonomicTree(){
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super();
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}
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/**
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* Adds a taxon to the taxonomic tree and makes it one of the root nodes.
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* @param taxon
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* @param synonymUsed
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* @return
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*/
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public TaxonNode addRoot(Taxon taxon, Synonym synonymUsed){
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TaxonNode newRoot = new TaxonNode(taxon, this);
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rootNodes.add(newRoot);
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newRoot.setParent(null);
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newRoot.setTaxonomicView(this);
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newRoot.setTaxon(taxon);
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// newRoot.setReferenceForParentChildRelation(ref); //ref not needed for root !!
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newRoot.setSynonymToBeUsed(synonymUsed);
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return newRoot;
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}
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public boolean removeRoot(TaxonNode node){
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boolean result = false;
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if(node.isRootNode()){
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for (TaxonNode childNode : node.getChildNodes()){
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node.removeChild(childNode);
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}
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result = rootNodes.remove(node);
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node.getTaxon().removeTaxonNode(node);
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node.setParent(null);
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node.setTaxonomicView(null);
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node.setTaxon(null);
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}
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return result;
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}
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/**
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* Appends an existing root node to another node of this tree. The existing root node becomes
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* an ordinary node.
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* @param root
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* @param otherNode
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* @param ref
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* @param microReference
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* @throws IllegalArgumentException
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*/
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public void makeRootChildOfOtherNode(TaxonNode root, TaxonNode otherNode, ReferenceBase ref, String microReference)
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throws IllegalArgumentException{
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if (otherNode == null){
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throw new NullPointerException("other node must not be null");
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}
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if (! getRootNodes().contains(root)){
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throw new IllegalArgumentException("root node to be added as child must already be root node within this tree");
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}
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if (otherNode.getTaxonomicTree() == null || ! otherNode.getTaxonomicTree().equals(this)){
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throw new IllegalArgumentException("other node must already be node within this tree");
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}
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if (otherNode.equals(root)){
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throw new IllegalArgumentException("root node and other node must not be the same");
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}
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otherNode.addChildNote(root, ref, microReference, null);
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getRootNodes().remove(root);
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}
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// public void makeThisNodePartOfOtherView(TaxonNode oldRoot, TaxonNode replacedNodeInOtherView, ReferenceBase reference, String microReference){
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// AlternativeViewRoot newRoot = new AlternativeViewRoot(oldRoot, replacedNodeInOtherView, reference, microReference);
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// }
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/**
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* Checks if the given taxon is part of <b>this</b> tree.
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* @param taxon
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* @return
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*/
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public boolean isTaxonInTree(Taxon taxon){
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return (getNode(taxon) != null);
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}
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/**
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* Checks if the given taxon is part of <b>this</b> tree. If so the according TaxonNode is returned.
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* Otherwise null is returned.
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* @param taxon
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* @return
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*/
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public TaxonNode getNode(Taxon taxon){
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if (taxon == null){
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return null;
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}
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for (TaxonNode taxonNode: taxon.getTaxonNodes()){
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if (taxonNode.getTaxonomicTree().equals(this)){
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return taxonNode;
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}
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}
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return null;
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}
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/**
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* Checks if the given taxon is one of the root taxa in <b>this</b> tree.
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* @param taxon
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* @return
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*/
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public boolean isRootInTree(Taxon taxon){
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return (getRootNode(taxon) != null);
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}
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/**
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* Checks if the taxon is a root taxon in <b>this</b> tree and returns the according node if true.
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* Returns null otherwise.
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* @param taxon
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* @return
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*/
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public TaxonNode getRootNode(Taxon taxon){
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if (taxon == null){
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return null;
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}
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for (TaxonNode taxonNode: taxon.getTaxonNodes()){
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if (taxonNode.getTaxonomicTree().equals(this)){
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if (this.getRootNodes().contains(taxonNode)){
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if (taxonNode.getParent() != null){
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logger.warn("A root node should not have parent");
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}
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return taxonNode;
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}
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}
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}
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return null;
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}
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private boolean handleCitationOverwrite(TaxonNode childNode, ReferenceBase citation, String microCitation){
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if (citation != null){
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if (childNode.getReferenceForParentChildRelation() != null && ! childNode.getReferenceForParentChildRelation().equals(citation)){
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logger.warn("ReferenceForParentChildRelation will be overwritten");
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}
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childNode.setReferenceForParentChildRelation(citation);
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}
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if (microCitation != null){
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if (childNode.getMicroReferenceForParentChildRelation() != null && ! childNode.getMicroReferenceForParentChildRelation().equals(microCitation)){
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logger.warn("MicroReferenceForParentChildRelation will be overwritten");
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}
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childNode.setMicroReferenceForParentChildRelation(microCitation);
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}
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return true;
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}
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/**
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* Relates two taxa as parent-child nodes within a taxonomic tree. <BR>
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* If the taxa are not yet part of the tree they are added to it.<Br>
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* If the child taxon is a root still it is added as child and deleted from the rootNode set.<Br>
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* If the child is a child of another parent already an IllegalStateException is thrown because a child can have only
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* one parent. <Br>
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* If the parent-child relationship between these two taxa already exists nothing is changed. Only
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* citation and microcitation are overwritten by the new values if these values are not null.
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* @param parent
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* @param child
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* @param citation
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* @param microCitation
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* @return
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* @throws IllegalStateException If the child is a child of another parent already
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*/
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public boolean addParentChild (Taxon parent, Taxon child, ReferenceBase citation, String microCitation)
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throws IllegalStateException{
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try {
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TaxonNode parentNode = this.getNode(parent);
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TaxonNode childNode = this.getNode(child);
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//if child exists in tree and has a parent
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//no multiple parents are allowed in the tree
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if (childNode != null && childNode.getParent() != null){
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//...different to the parent taxon throw exception
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if (! childNode.getParent().getTaxon().equals(parent) ){
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throw new IllegalStateException("The child taxon is already part of the tree but has an other parent taxon than the one than the parent to be added. Child: " + child.toString() + ", new parent:" + parent.toString() + ", old parent: " + childNode.getParent().getTaxon().toString()) ;
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//... same as the parent taxon do nothing but overwriting citation and microCitation
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}else{
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handleCitationOverwrite(childNode, citation, microCitation);
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return true;
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}
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}
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//add parent node if not exist
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if (parentNode == null){
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parentNode = this.addRoot(parent, null);
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}
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//add child if not exists
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if (childNode == null){
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parentNode.addChild(child, citation, microCitation);
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}else{
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//child is still root
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//TODO test if child is rootNode otherwise thrwo IllegalStateException
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if (! this.isRootInTree(child)){
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throw new IllegalStateException("Child is not a root but must be");
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}
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this.makeRootChildOfOtherNode(childNode, parentNode, citation, microCitation);
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}
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} catch (IllegalStateException e) {
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throw e;
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} catch (RuntimeException e){
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throw e;
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}
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return true;
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}
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@Transient
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public ReferenceBase getCitation() {
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return reference;
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}
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public LanguageString getName() {
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return name;
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}
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public void setName(LanguageString name) {
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this.name = name;
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}
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/**
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* Returns a set containing all nodes in this taxonomic tree.
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*
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* Caution: Use this method with care. It can be very time and resource consuming and might
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* run into OutOfMemoryExceptions for big trees.
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*
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* @return
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*/
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@Transient
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@Deprecated
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public Set<TaxonNode> getAllNodes() {
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Set<TaxonNode> allNodes = new HashSet<TaxonNode>();
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for(TaxonNode rootNode : getRootNodes()){
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allNodes.addAll(rootNode.getAllNodes());
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}
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return allNodes;
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}
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public Set<TaxonNode> getRootNodes() {
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return rootNodes;
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}
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public void setRootNodes(Set<TaxonNode> rootNodes) {
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this.rootNodes = rootNodes;
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}
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public ReferenceBase getReference() {
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return reference;
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}
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public void setReference(ReferenceBase reference) {
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this.reference = reference;
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}
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/**
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* @return the microReference
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*/
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public String getMicroReference() {
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return microReference;
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}
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/**
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* @param microReference the microReference to set
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*/
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public void setMicroReference(String microReference) {
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this.microReference = microReference;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
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*/
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@Override
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public String generateTitle() {
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return name.getText();
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}
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public int compareTo(Object o) {
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return 0;
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}
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/**
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* Returns all TaxonNodes of the tree for a given Rank.
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* If a branch does not contain a TaxonNode with a TaxonName at the given
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* Rank the node associated with the next lower Rank is taken as root node.
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* If the <code>rank</code> is null the absolute root nodes will be returned.
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*
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* @param rank may be null
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* @return
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*/
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public List<TaxonNode> getRankSpecificRootNodes(Rank rank) {
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List<TaxonNode> baseNodes = new ArrayList<TaxonNode>();
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if(rank != null){
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findNodesForRank(rank, getRootNodes(), baseNodes);
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} else {
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baseNodes.addAll(getRootNodes());
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}
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return baseNodes;
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}
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/**
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* Walks the tree returning all nodes of exactly the given <code>rank</code>
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* or the next lower rank if an exact match by rank is not possible.
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*
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* @param baseRank
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* the rank to return nodes for
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* @param nodeSet
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* the set of nodes to search in
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* @param rootNodes
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* a List to put the found nodes in
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* @return the <code>rootNodes</code> List given as parameter
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*/
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private List<TaxonNode> findNodesForRank(Rank baseRank, Set<TaxonNode> nodeSet, List<TaxonNode> rootNodes) {
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for(TaxonNode node : nodeSet){
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Rank thisRank = node.getTaxon().getName().getRank();
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if(thisRank.isHigher(baseRank)){
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// if the current rank still is higher than the given baseRank iterate deeper into tree
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findNodesForRank(baseRank, node.getChildNodes(), rootNodes);
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} else {
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// gotsha! It is a base node of this level
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rootNodes.add(node);
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}
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}
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return rootNodes;
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}
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}
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