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/**
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* Copyright (C) 2009 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.io.specimen.excel.in;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.TreeMap;
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import org.apache.commons.lang.StringUtils;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import eu.etaxonomy.cdm.io.excel.common.ExcelRowBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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/**
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* @author a.mueller
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* @since 08.04.2011
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* @version 1.0
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*/
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public class SpecimenRow extends ExcelRowBase{
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(SpecimenRow.class);
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private String basisOfRecord;
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private String country;
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private String isoCountry;
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private String locality;
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private String latitude;
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private String longitude;
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private String referenceSystem;
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private String errorRadius;
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private String altitude;
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private String altitudeMax;
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private String fieldNotes;
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private String collectingDate;
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private String collectingDateEnd;
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private String collectorsNumber;
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private String primaryCollector;
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private String language;
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private String sex;
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private String accessionNumber;
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private String barcode;
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// private String author;
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// private String family;
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// private String genus;
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// private String specificEpithet;
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private String collectionCode;
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private String collection;
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private TreeMap<Integer, IdentifiableSource> sources = new TreeMap<Integer, IdentifiableSource>();
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private TreeMap<Integer, String> collectors = new TreeMap<Integer, String>();
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private TreeMap<Integer, String> unitNotes = new TreeMap<Integer, String>();
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private TreeMap<Integer, SpecimenTypeDesignation> types = new TreeMap<Integer, SpecimenTypeDesignation>();
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private TreeMap<Integer, DeterminationLight> determinations = new TreeMap<Integer, DeterminationLight>();
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private List<PostfixTerm> levels = new ArrayList<PostfixTerm>();
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public SpecimenRow() {
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}
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// may be public if necessary
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protected class DeterminationLight{
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String taxonUuid;
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String family;
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String genus;
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String rank;
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String fullName;
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String speciesEpi;
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String infraSpeciesEpi;
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String author;
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String modifier;
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String determinedBy;
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String determinedWhen;
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String notes;
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public boolean hasTaxonInformation() {
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boolean result = StringUtils.isNotBlank(taxonUuid)
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|| StringUtils.isNotBlank(family)
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|| StringUtils.isNotBlank(genus)
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|| StringUtils.isNotBlank(rank)
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|| StringUtils.isNotBlank(fullName)
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|| StringUtils.isNotBlank(speciesEpi)
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|| StringUtils.isNotBlank(author)
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|| StringUtils.isNotBlank(infraSpeciesEpi);
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return result;
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}
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}
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// **************************** GETTER / SETTER *********************************/
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public void setBasisOfRecord(String basisOfRecord) {
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this.basisOfRecord = basisOfRecord;
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}
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public String getBasisOfRecord() {
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return basisOfRecord;
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}
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public void setCountry(String country) {
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this.country = country;
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}
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public String getCountry() {
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return country;
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}
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public void setIsoCountry(String isoCountry) {
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this.isoCountry = isoCountry;
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}
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public String getIsoCountry() {
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return isoCountry;
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}
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public void setLocality(String locality) {
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this.locality = locality;
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}
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public String getLocality() {
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return locality;
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}
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public void setFieldNotes(String fieldNotes) {
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this.fieldNotes = fieldNotes;
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}
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public String getFieldNotes() {
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return fieldNotes;
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}
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public void setAccessionNumber(String accessionNumber) {
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this.accessionNumber = accessionNumber;
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}
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public String getAccessionNumber() {
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return accessionNumber;
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}
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public void setBarcode(String barcode) {
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this.barcode = barcode;
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}
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//
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// /**
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// * @return the author
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// */
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// public String getAuthor() {
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// return author;
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// }
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//
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//
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// /**
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// * @param author the author to set
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// */
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// public void setAuthor(String author) {
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// this.author = author;
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// }
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/**
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* @return the absoluteElevation
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*/
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public String getAltitude() {
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return altitude;
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}
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/**
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* @param absoluteElevation the absoluteElevation to set
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*/
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public void setAltitude(String altitude) {
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this.altitude = altitude;
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}
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/**
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* @return the collectionCode
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*/
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public String getCollectionCode() {
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return collectionCode;
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}
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/**
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* @param collectionCode the collectionCode to set
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*/
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public void setCollectionCode(String collectionCode) {
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this.collectionCode = collectionCode;
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}
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/**
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* @return the collectingDate
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*/
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public String getCollectingDate() {
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return collectingDate;
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}
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/**
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* @param collectingDate the collectingDate to set
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*/
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public void setCollectingDate(String collectingDate) {
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this.collectingDate = collectingDate;
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}
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/**
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* @return the collectorsNumber
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*/
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public String getCollectorsNumber() {
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return collectorsNumber;
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}
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/**
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* @param collectorsNumber the collectorsNumber to set
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*/
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public void setCollectorsNumber(String collectorsNumber) {
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this.collectorsNumber = collectorsNumber;
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}
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/**
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* @return the barcode
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*/
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public String getBarcode() {
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return barcode;
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}
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/**
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* @return the collectingDateEnd
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*/
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public String getCollectingDateEnd() {
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return collectingDateEnd;
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}
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/**
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* @param collectingDateEnd the collectingDateEnd to set
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*/
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public void setCollectingDateEnd(String collectingDateEnd) {
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this.collectingDateEnd = collectingDateEnd;
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}
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/**
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* @return the latitude
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*/
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public String getLatitude() {
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return latitude;
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}
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/**
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* @param latitude the latitude to set
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*/
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public void setLatitude(String latitude) {
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this.latitude = latitude;
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}
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/**
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* @return the longitude
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*/
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public String getLongitude() {
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return longitude;
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}
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/**
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* @param longitude the longitude to set
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*/
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public void setLongitude(String longitude) {
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this.longitude = longitude;
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}
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@Override
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public void putIdInSource(int key, String id){
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IdentifiableSource source = getOrMakeSource(key, OriginalSourceType.Import);
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source.setIdInSource(id);
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}
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@Override
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public void putSourceReference(int key, Reference reference){
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IdentifiableSource source = getOrMakeSource(key, OriginalSourceType.Unknown);
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source.setCitation(reference);
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}
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@Override
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public List<IdentifiableSource> getSources() {
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return getOrdered(sources);
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}
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public void setCollectors(String value) {
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//TODO better parse somewhere else? Quick and dirty implementation
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List<String> authors = new ArrayList<String>();
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String[] splits = value.split("&");
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for (String split: splits){
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split = split.trim();
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authors.add(split);
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}
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int index = 1;
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for (int i = 0; i < authors.size() ; i++){
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String author = authors.get(i);
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if (i < authors.size()-1){
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String[] internalSplits = author.split(",");
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for (String internal : internalSplits){
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internal = internal.trim();
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this.collectors.put(index++, internal);
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}
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}else{
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this.collectors.put(index++, author);
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}
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}
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}
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public void putCollector(int key, String collector){
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this.collectors.put(key, collector);
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}
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public List<String> getCollectors() {
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return getOrdered(collectors);
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}
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public void putUnitNote(int key, String unitNote){
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this.unitNotes.put(key, unitNote);
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}
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public List<String> getUnitNotes() {
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return getOrdered(unitNotes);
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}
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/**
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* @param key
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* @return
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*/
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private IdentifiableSource getOrMakeSource(int key, OriginalSourceType type) {
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IdentifiableSource source = sources.get(key);
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if (source == null){
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source = IdentifiableSource.NewInstance(type);
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sources.put(key, source);
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}
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return source;
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}
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@Override
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public void putTypeCategory(int key, SpecimenTypeDesignationStatus status){
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SpecimenTypeDesignation designation = getOrMakeTypeDesignation(key);
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designation.setTypeStatus(status);
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}
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@Override
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public void putTypifiedName(int key, TaxonName name){
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if (name != null){
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SpecimenTypeDesignation designation = getOrMakeTypeDesignation(key);
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name.addTypeDesignation(designation, false);
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}
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}
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@Override
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public List<SpecimenTypeDesignation> getTypeDesignations() {
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return getOrdered(types);
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}
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private SpecimenTypeDesignation getOrMakeTypeDesignation(int key) {
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SpecimenTypeDesignation designation = types.get(key);
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if (designation == null){
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designation = SpecimenTypeDesignation.NewInstance();
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types.put(key, designation);
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}
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return designation;
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}
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public void putDeterminationFamily(int key, String family){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.family = family;
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}
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public void putDeterminationFullName(int key, String fullName){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.fullName = fullName;
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}
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public void putDeterminationTaxonUuid(int key, String taxonUuid){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.taxonUuid = taxonUuid;
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}
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public void putDeterminationRank(int key, String rank){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.rank = rank;
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}
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public void putDeterminationGenus(int key, String genus){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.genus = genus;
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}
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public void putDeterminationSpeciesEpi(int key, String speciesEpi){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.speciesEpi = speciesEpi;
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}
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public void putDeterminationInfraSpeciesEpi(int key, String infraSpeciesEpi){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.infraSpeciesEpi = infraSpeciesEpi;
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}
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public void putDeterminationAuthor(int key, String author){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.author = author;
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}
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public void putDeterminationDeterminedBy(int key, String determinedBy){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.determinedBy = determinedBy;
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}
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public void putDeterminationDeterminedWhen(int key, String determinedWhen){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.determinedWhen = determinedWhen;
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}
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public void putDeterminationDeterminationNotes(int key, String notes){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.notes = notes;
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}
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public void putDeterminationDeterminationModifier(int key, String modifier){
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DeterminationLight determinationEvent = getOrMakeDetermination(key);
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determinationEvent.modifier = modifier;
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}
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public List<DeterminationLight> getDetermination() {
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List<DeterminationLight> result = getOrdered(determinations);
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if (determinations.size() > 1 && getCommonDetermination()!= null ){
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result.remove(getCommonDetermination());
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}
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return result;
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}
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/**
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* Returns the determination with key "0".
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* @return
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*/
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public DeterminationLight getCommonDetermination() {
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if (determinations.get(0) != null){
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return determinations.get(0);
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}
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return null;
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}
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494
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private DeterminationLight getOrMakeDetermination(int key) {
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DeterminationLight determination = this.determinations.get(key);
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if (determination == null){
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determination = new DeterminationLight();
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this.determinations.put(key, determination);
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}
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return determination;
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}
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private<T extends Object> List<T> getOrdered(TreeMap<?, T> tree) {
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507
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List<T> result = new ArrayList<T>();
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for (T value : tree.values()){
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result.add(value);
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}
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return result;
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}
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513
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public void setSex(String sex) {
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this.sex = sex;
|
516
|
}
|
517
|
|
518
|
|
519
|
public String getSex() {
|
520
|
return sex;
|
521
|
}
|
522
|
|
523
|
|
524
|
/**
|
525
|
* @return the referenceSystem
|
526
|
*/
|
527
|
public String getReferenceSystem() {
|
528
|
return referenceSystem;
|
529
|
}
|
530
|
|
531
|
|
532
|
/**
|
533
|
* @param referenceSystem the referenceSystem to set
|
534
|
*/
|
535
|
public void setReferenceSystem(String referenceSystem) {
|
536
|
this.referenceSystem = referenceSystem;
|
537
|
}
|
538
|
|
539
|
|
540
|
/**
|
541
|
* @return the errorRadius
|
542
|
*/
|
543
|
public String getErrorRadius() {
|
544
|
return errorRadius;
|
545
|
}
|
546
|
|
547
|
|
548
|
/**
|
549
|
* @param errorRadius the errorRadius to set
|
550
|
*/
|
551
|
public void setErrorRadius(String errorRadius) {
|
552
|
this.errorRadius = errorRadius;
|
553
|
}
|
554
|
|
555
|
|
556
|
public void setCollection(String collection) {
|
557
|
this.collection = collection;
|
558
|
}
|
559
|
|
560
|
|
561
|
public String getCollection() {
|
562
|
return collection;
|
563
|
}
|
564
|
|
565
|
|
566
|
public void addLeveledArea(String levelPostfix, String value) {
|
567
|
PostfixTerm area = new PostfixTerm();
|
568
|
area.term = value;
|
569
|
area.postfix = levelPostfix;
|
570
|
this.levels.add(area);
|
571
|
}
|
572
|
|
573
|
public List<PostfixTerm> getLeveledAreas(){
|
574
|
return levels;
|
575
|
}
|
576
|
|
577
|
public void setAltitudeMax(String altitudeMax) {
|
578
|
this.altitudeMax = altitudeMax;
|
579
|
}
|
580
|
|
581
|
|
582
|
public String getAltitudeMax() {
|
583
|
return altitudeMax;
|
584
|
}
|
585
|
|
586
|
|
587
|
/**
|
588
|
* @param primaryCollector the primaryCollector to set
|
589
|
*/
|
590
|
public void setPrimaryCollector(String primaryCollector) {
|
591
|
this.primaryCollector = primaryCollector;
|
592
|
}
|
593
|
|
594
|
|
595
|
/**
|
596
|
* @return the primaryCollector
|
597
|
*/
|
598
|
public String getPrimaryCollector() {
|
599
|
return primaryCollector;
|
600
|
}
|
601
|
|
602
|
|
603
|
public String getLanguage() {
|
604
|
return language;
|
605
|
}
|
606
|
|
607
|
|
608
|
public void setLanguage(String language) {
|
609
|
this.language = language;
|
610
|
}
|
611
|
|
612
|
}
|