EDIT

/**

* Copyright (C) 2009 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.io.specimen.excel.in;

import java.util.ArrayList;

import java.util.List;

import java.util.TreeMap;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.io.excel.common.ExcelRowBase;

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

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

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

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

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

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

/**

 * @author a.mueller

 * @since 08.04.2011

 * @version 1.0

 */

public class SpecimenRow extends ExcelRowBase{

	@SuppressWarnings("unused")

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

	private String basisOfRecord;

	private String country;

	private String isoCountry;

	private String locality;

	private String latitude;

	private String longitude;

	private String referenceSystem;

	private String errorRadius;

	private String altitude;

	private String altitudeMax;

	private String fieldNotes;

	private String collectingDate;

	private String collectingDateEnd;

	private String collectorsNumber;

	private String primaryCollector;

	private String language;

	private String sex;

	private String accessionNumber;

	private String barcode;

	//	private String author;

//	private String family;

//	private String genus;

//	private String specificEpithet;

	private String collectionCode;

	private String collection;

	private TreeMap<Integer, IdentifiableSource> sources = new TreeMap<Integer, IdentifiableSource>();

	private TreeMap<Integer, String> collectors = new TreeMap<Integer, String>();

	private TreeMap<Integer, String> unitNotes = new TreeMap<Integer, String>();

	private TreeMap<Integer, SpecimenTypeDesignation> types = new TreeMap<Integer, SpecimenTypeDesignation>();

	private TreeMap<Integer, DeterminationLight> determinations = new TreeMap<Integer, DeterminationLight>();

	private List<PostfixTerm> levels  = new ArrayList<PostfixTerm>();

	public SpecimenRow() {

	}

	//	may be public if necessary

	protected class DeterminationLight{

		String taxonUuid;

		String family;

		String genus;

		String rank;

		String fullName;

		String speciesEpi;

		String infraSpeciesEpi;

		String author;

		String modifier;

		String determinedBy;

		String determinedWhen;

		String notes;

		public boolean hasTaxonInformation() {

			boolean result = StringUtils.isNotBlank(taxonUuid)

			 	|| StringUtils.isNotBlank(family)

			 	|| StringUtils.isNotBlank(genus)

			 	|| StringUtils.isNotBlank(rank)

			 	|| StringUtils.isNotBlank(fullName)

			 	|| StringUtils.isNotBlank(speciesEpi)

				|| StringUtils.isNotBlank(author)

				|| StringUtils.isNotBlank(infraSpeciesEpi);

			return result;

		}

	}

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

	public void setBasisOfRecord(String basisOfRecord) {

		this.basisOfRecord = basisOfRecord;

	}

	public String getBasisOfRecord() {

		return basisOfRecord;

	}

	public void setCountry(String country) {

		this.country = country;

	}

	public String getCountry() {

		return country;

	}

	public void setIsoCountry(String isoCountry) {

		this.isoCountry = isoCountry;

	}

	public String getIsoCountry() {

		return isoCountry;

	}

	public void setLocality(String locality) {

		this.locality = locality;

	}

	public String getLocality() {

		return locality;

	}

	public void setFieldNotes(String fieldNotes) {

		this.fieldNotes = fieldNotes;

	}

	public String getFieldNotes() {

		return fieldNotes;

	}

	public void setAccessionNumber(String accessionNumber) {

		this.accessionNumber = accessionNumber;

	}

	public String getAccessionNumber() {

		return accessionNumber;

	}

	public void setBarcode(String barcode) {

		this.barcode = barcode;

	}

//

//	/**

//	 * @return the author

//	 */

//	public String getAuthor() {

//		return author;

//	}

//

//

//	/**

//	 * @param author the author to set

//	 */

//	public void setAuthor(String author) {

//		this.author = author;

//	}

	/**

	 * @return the absoluteElevation

	 */

	public String getAltitude() {

		return altitude;

	}

	/**

	 * @param absoluteElevation the absoluteElevation to set

	 */

	public void setAltitude(String altitude) {

		this.altitude = altitude;

	}

	/**

	 * @return the collectionCode

	 */

	public String getCollectionCode() {

		return collectionCode;

	}

	/**

	 * @param collectionCode the collectionCode to set

	 */

	public void setCollectionCode(String collectionCode) {

		this.collectionCode = collectionCode;

	}

	/**

	 * @return the collectingDate

	 */

	public String getCollectingDate() {

		return collectingDate;

	}

	/**

	 * @param collectingDate the collectingDate to set

	 */

	public void setCollectingDate(String collectingDate) {

		this.collectingDate = collectingDate;

	}

	/**

	 * @return the collectorsNumber

	 */

	public String getCollectorsNumber() {

		return collectorsNumber;

	}

	/**

	 * @param collectorsNumber the collectorsNumber to set

	 */

	public void setCollectorsNumber(String collectorsNumber) {

		this.collectorsNumber = collectorsNumber;

	}

	/**

	 * @return the barcode

	 */

	public String getBarcode() {

		return barcode;

	}

	/**

	 * @return the collectingDateEnd

	 */

	public String getCollectingDateEnd() {

		return collectingDateEnd;

	}

	/**

	 * @param collectingDateEnd the collectingDateEnd to set

	 */

	public void setCollectingDateEnd(String collectingDateEnd) {

		this.collectingDateEnd = collectingDateEnd;

	}

	/**

	 * @return the latitude

	 */

	public String getLatitude() {

		return latitude;

	}

	/**

	 * @param latitude the latitude to set

	 */

	public void setLatitude(String latitude) {

		this.latitude = latitude;

	}

	/**

	 * @return the longitude

	 */

	public String getLongitude() {

		return longitude;

	}

	/**

	 * @param longitude the longitude to set

	 */

	public void setLongitude(String longitude) {

		this.longitude = longitude;

	}

	@Override

    public void putIdInSource(int key, String id){

		IdentifiableSource source = getOrMakeSource(key, OriginalSourceType.Import);

		source.setIdInSource(id);

	}

	@Override

    public void putSourceReference(int key, Reference reference){

		IdentifiableSource source = getOrMakeSource(key, OriginalSourceType.Unknown);

		source.setCitation(reference);

	}

	@Override

    public List<IdentifiableSource> getSources() {

		return getOrdered(sources);

	}

	public void setCollectors(String value) {

		//TODO better parse somewhere else? Quick and dirty implementation

		List<String> authors = new ArrayList<String>();

		String[] splits = value.split("&");

		for (String split: splits){

			split = split.trim();

			authors.add(split);

		}

		int index = 1;

		for (int i = 0; i < authors.size() ; i++){

			String author = authors.get(i);

			if (i < authors.size()-1){

				String[] internalSplits = author.split(",");

				for (String internal : internalSplits){

					internal = internal.trim();

					this.collectors.put(index++, internal);

				}

			}else{

				this.collectors.put(index++, author);

			}

		}

	}

	public void putCollector(int key, String collector){

		this.collectors.put(key, collector);

	}

	public List<String> getCollectors() {

		return getOrdered(collectors);

	}

	public void putUnitNote(int key, String unitNote){

		this.unitNotes.put(key, unitNote);

	}

	public List<String> getUnitNotes() {

		return getOrdered(unitNotes);

	}

	/**

	 * @param key

	 * @return

	 */

	private IdentifiableSource getOrMakeSource(int key, OriginalSourceType type) {

		IdentifiableSource  source = sources.get(key);

		if (source == null){

			source = IdentifiableSource.NewInstance(type);

			sources.put(key, source);

		}

		return source;

	}

	@Override

    public void putTypeCategory(int key, SpecimenTypeDesignationStatus status){

		SpecimenTypeDesignation designation = getOrMakeTypeDesignation(key);

		designation.setTypeStatus(status);

	}

	@Override

    public void putTypifiedName(int key, TaxonName name){

		if (name != null){

			SpecimenTypeDesignation designation = getOrMakeTypeDesignation(key);

			name.addTypeDesignation(designation, false);

		}

	}

	@Override

    public List<SpecimenTypeDesignation> getTypeDesignations() {

		return getOrdered(types);

	}

	private SpecimenTypeDesignation getOrMakeTypeDesignation(int key) {

		SpecimenTypeDesignation designation = types.get(key);

		if (designation == null){

			designation = SpecimenTypeDesignation.NewInstance();

			types.put(key, designation);

		}

		return designation;

	}

	public void putDeterminationFamily(int key, String family){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.family = family;

	}

	public void putDeterminationFullName(int key, String fullName){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.fullName = fullName;

	}

	public void putDeterminationTaxonUuid(int key, String taxonUuid){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.taxonUuid = taxonUuid;

	}

	public void putDeterminationRank(int key, String rank){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.rank = rank;

	}

	public void putDeterminationGenus(int key, String genus){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.genus = genus;

	}

	public void putDeterminationSpeciesEpi(int key, String speciesEpi){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.speciesEpi = speciesEpi;

	}

	public void putDeterminationInfraSpeciesEpi(int key, String infraSpeciesEpi){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.infraSpeciesEpi = infraSpeciesEpi;

	}

	public void putDeterminationAuthor(int key, String author){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.author = author;

	}

	public void putDeterminationDeterminedBy(int key, String determinedBy){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.determinedBy = determinedBy;

	}

	public void putDeterminationDeterminedWhen(int key, String determinedWhen){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.determinedWhen = determinedWhen;

	}

	public void putDeterminationDeterminationNotes(int key, String notes){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.notes = notes;

	}

	public void putDeterminationDeterminationModifier(int key, String modifier){

		DeterminationLight determinationEvent = getOrMakeDetermination(key);

		determinationEvent.modifier = modifier;

	}

	public List<DeterminationLight> getDetermination() {

		List<DeterminationLight> result = getOrdered(determinations);

		if (determinations.size() > 1 && getCommonDetermination()!= null ){

			result.remove(getCommonDetermination());

		}

		return result;

	}

	/**

	 * Returns the determination with key "0".

	 * @return

	 */

	public DeterminationLight getCommonDetermination() {

		if (determinations.get(0) != null){

			return determinations.get(0);

		}

		return null;

	}

	private DeterminationLight getOrMakeDetermination(int key) {

		DeterminationLight determination = this.determinations.get(key);

		if (determination == null){

			determination = new DeterminationLight();

			this.determinations.put(key, determination);

		}

		return determination;

	}

	private<T extends Object> List<T> getOrdered(TreeMap<?, T> tree) {

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

		for (T value : tree.values()){

			result.add(value);

		}

		return result;

	}

	public void setSex(String sex) {

		this.sex = sex;

	}

	public String getSex() {

		return sex;

	}

	/**

	 * @return the referenceSystem

	 */

	public String getReferenceSystem() {

		return referenceSystem;

	}

	/**

	 * @param referenceSystem the referenceSystem to set

	 */

	public void setReferenceSystem(String referenceSystem) {

		this.referenceSystem = referenceSystem;

	}

	/**

	 * @return the errorRadius

	 */

	public String getErrorRadius() {

		return errorRadius;

	}

	/**

	 * @param errorRadius the errorRadius to set

	 */

	public void setErrorRadius(String errorRadius) {

		this.errorRadius = errorRadius;

	}

	public void setCollection(String collection) {

		this.collection = collection;

	}

	public String getCollection() {

		return collection;

	}

	public void addLeveledArea(String levelPostfix, String value) {

		PostfixTerm area = new PostfixTerm();

		area.term = value;

		area.postfix = levelPostfix;

		this.levels.add(area);

	}

	public List<PostfixTerm> getLeveledAreas(){

		return levels;

	}

	public void setAltitudeMax(String altitudeMax) {

		this.altitudeMax = altitudeMax;

	}

	public String getAltitudeMax() {

		return altitudeMax;

	}

	/**

	 * @param primaryCollector the primaryCollector to set

	 */

	public void setPrimaryCollector(String primaryCollector) {

		this.primaryCollector = primaryCollector;

	}

	/**

	 * @return the primaryCollector

	 */

	public String getPrimaryCollector() {

		return primaryCollector;

	}

	public String getLanguage() {

		return language;

	}

	public void setLanguage(String language) {

		this.language = language;

	}

}