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Kaflib-naf is a java library to create and edit NAF documents.
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package ixa.kaflib;

import ixa.kaflib.KAFDocument.AnnotationType;
import ixa.kaflib.KAFDocument.Utils;

import java.util.List;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;


/** A named entity is a term (or a multiword) that clearly identifies one item. The optional Named Entity layer is used to reference terms that are named entities. */
public class Entity extends IdentifiableAnnotation implements Relational, SentenceLevelAnnotation {

    /** Type of the named entity (optional). Currently, 8 values are possible: 
     * - Person
     * - Organization
     * - Location
     * - Date
     * - Time
     * - Money
     * - Percent
     * - Misc
     * - GPE (stands for Geo-Political Entity)
     */ 
    private String type;
    
    private String source;

    /** Reference to different occurrences of the same named entity in the document (at least one required) */
    private List> references;

    /** External references (optional) */
    private List externalReferences;

    Entity(String id, List> references) {
	super(id);
	if (references.size() < 1) {
	    throw new IllegalStateException("Entities must contain at least one reference span");
	}
	if (references.get(0).size() < 1) {
	    throw new IllegalStateException("Entities' reference's spans must contain at least one target");
	}
	this.references = references;
	this.externalReferences = new ArrayList();
    }

    Entity(Entity entity, HashMap terms) {
	super(entity.getId());
	this.type = entity.type;
	/* Copy references */
	String id = entity.getId();
	this.references = new ArrayList>();
	for (Span span : entity.getSpans()) {
	    /* Copy span */
	    List targets = span.getTargets();
	    List copiedTargets = new ArrayList();
	    for (Term term : targets) {
		Term copiedTerm = terms.get(term.getId());
		if (copiedTerm == null) {
		    throw new IllegalStateException("Term not found when copying " + id);
		}
		copiedTargets.add(copiedTerm);
	    }
	    if (span.hasHead()) {
		Term copiedHead = terms.get(span.getHead().getId());
		this.references.add(new Span(copiedTargets, copiedHead));
	    }
	    else {
		this.references.add(new Span(copiedTargets));
	    }
	}
	/* Copy external references */
	this.externalReferences = new ArrayList();
	for (ExternalRef externalRef : entity.getExternalRefs()) {
	    this.externalReferences.add(new ExternalRef(externalRef));
	}
    }

    public boolean hasType() {
	return type != null;
    }

    public String getType() {
	return type;
    }

    public void setType(String type) {
	this.type = type;
    }

    public boolean hasSource() {
	return source != null;
    }

    public String getSource() {
	return source;
    }

    public void setSource(String source) {
	this.source = source;
    }

    /** Returns the term targets of the first span. When targets of other spans are needed getReferences() method should be used. */ 
    public List getTerms() {
	return this.references.get(0).getTargets();
    }

    /** Adds a term to the first span. */
    public void addTerm(Term term) {
	this.references.get(0).addTarget(term);
    }

    /** Adds a term to the first span. */
    public void addTerm(Term term, boolean isHead) {
	this.references.get(0).addTarget(term, isHead);
    }

    public List> getSpans() {
	return this.references;
    }

    public void addSpan(Span span) {
	this.references.add(span);
    }

    public List getExternalRefs() {
	return externalReferences;
    }

    public void addExternalRef(ExternalRef externalRef) {
	externalReferences.add(externalRef);
    }

    public void addExternalRefs(List externalRefs) {
	externalReferences.addAll(externalRefs);
    }

    public String getSpanStr(Span span) {
	String str = "";
	for (Term term : span.getTargets()) {
	    if (!str.isEmpty()) {
		str += " ";
	    }
	    str += term.getStr();
	}
	return str;
    }

    public String getStr() {
	return getSpanStr(this.getSpans().get(0));
    }
    
    Map> getReferencedAnnotations() {
	Map> referenced = new HashMap>();
	List terms = new ArrayList();
	for (Span span : this.getSpans()) {
	    terms.addAll((List)(List) span.getTargets());
	}
	referenced.put(AnnotationType.TERM, terms);
	return referenced;
    }
    
    public Integer getSent() {
	return this.getSpans().get(0).getFirstTarget().getSent();
    }
    
    public Integer getPara() {
	return this.getSpans().get(0).getFirstTarget().getPara();
    }

    /** Deprecated */
    public List> getReferences() {
	List> list = new ArrayList>();
	for (Span span : this.references) {
	    list.add(span.getTargets());
	}
	return list;
    }

    /** Deprecated */
    public void addReference(List span) {
	this.references.add(KAFDocument.list2Span(span));
    }    
    
    /*
    @Override
    public boolean equals(Object o) {
	if (this == o) return true;
	if (!(o instanceof Entity)) return false;
	Entity ann = (Entity) o;
	return Utils.areEquals(this.type, ann.type) &&
		Utils.areEquals(this.source, ann.source) &&
		Utils.areEquals(this.references, ann.references) &&
		Utils.areEquals(this.externalReferences, ann.externalReferences);
    }
    */

}