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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.io.berlinModel.in;
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import java.io.File;
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import java.lang.reflect.Method;
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.util.UUID;
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import org.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport.PublishMarkerChooser;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelGeneralImportValidator;
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import eu.etaxonomy.cdm.io.common.DbImportConfiguratorBase;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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/**
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* @author a.mueller
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* @since 20.03.2008
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*/
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public class BerlinModelImportConfigurator
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extends DbImportConfiguratorBase<BerlinModelImportState>{
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private static final long serialVersionUID = 70300913255425256L;
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private static final Logger logger = LogManager.getLogger();
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public static BerlinModelImportConfigurator NewInstance(Source berlinModelSource, ICdmDataSource destination){
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return new BerlinModelImportConfigurator(berlinModelSource, destination);
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}
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private PublishMarkerChooser taxonPublishMarker = PublishMarkerChooser.ALL;
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//TODO
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private static IInputTransformer defaultTransformer = null;
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private boolean doNameStatus = true;
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private boolean doRelNames = true;
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private boolean doCommonNames = true;
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private boolean doOccurrence = true;
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private boolean doOccurrenceSources = true;
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private boolean doMarker = true;
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private boolean doUser = true;
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private boolean doFacts = true;
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private boolean doNameFacts = true;
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private boolean doAuthors = true;
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private DO_REFERENCES doReferences = DO_REFERENCES.ALL;
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private boolean doTaxonNames = true;
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private boolean doTypes = true;
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private boolean doNamedAreas = true;
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private boolean isSalvador = false;
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private boolean isEuroMed = false;
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private boolean isMcl = false;
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//taxa
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private boolean doTaxa = true;
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private boolean doRelTaxa = true;
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private boolean useSingleClassification = false;
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private boolean includeFlatClassifications = false; //concepts with no taxon relationship (even no misapplied name or synonym rel)
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private boolean includeAllNonMisappliedRelatedClassifications = true; //all concepts with any relationship except for misapplied name relationships
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private boolean useLastScrutinyAsSec = false;
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private boolean warnForDifferingSynonymReference = true; //do not warn for E+M as it uses last scrutiny
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//references
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private boolean doSourceNumber = false;
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//nullValues
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private boolean ignoreNull = false;
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//occurrences
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private boolean isSplitTdwgCodes = true;
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private boolean useEmAreaVocabulary = false;
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private boolean includesEmCode = true; // in Campanula we do not have an EMCOde
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private boolean allowInfraSpecTaxonRank = true;
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private Method namerelationshipTypeMethod;
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private Method uuidForDefTermMethod;
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private Method nameTypeDesignationStatusMethod;
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private boolean logNotMatchingOldNames = false;
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private boolean logMatchingNotExportedOldNames = true;
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private boolean checkOldNameIsSynonym = false;
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private boolean includeMANsForOldNameCheck = false;
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// NameFact stuff
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private URL mediaUrl;
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private File mediaPath;
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private int maximumNumberOfNameFacts;
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private boolean isIgnore0AuthorTeam = false;
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private boolean switchSpeciesGroup = false;
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//Term labels
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private String infrGenericRankAbbrev = null;
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private String infrSpecificRankAbbrev = null;
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private boolean removeHttpMapsAnchor = false;
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//Data Filter
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private String taxonTable = "PTaxon";
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private String classificationQuery = null;
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private String relTaxaIdQuery = null;
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private String nameIdTable = null;
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private String referenceIdTable = null;
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private String authorTeamFilter = null;
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private String authorFilter = null;
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private String factFilter = null;
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private String refDetailFilter = null;
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private String commonNameFilter = null;
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private String occurrenceFilter = null;
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private String occurrenceSourceFilter = null;
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private String webMarkerFilter = null;
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//specific functions
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private Method makeUrlForTaxon = null;
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private UUID featureTreeUuid;
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private String featureTreeTitle;
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private boolean isTaxonNoteAsFeature = false;
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private boolean doPreliminaryRefDetailsWithNames = false;
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public boolean isTaxonNoteAsFeature() {return isTaxonNoteAsFeature;}
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public void setTaxonNoteAsFeature(boolean isTaxonNoteAsFeature) {this.isTaxonNoteAsFeature = isTaxonNoteAsFeature;}
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@SuppressWarnings("unchecked")
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@Override
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protected void makeIoClassList(){
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ioClassList = new Class[]{
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BerlinModelGeneralImportValidator.class
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, BerlinModelUserImport.class
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, BerlinModelAuthorImport.class
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, BerlinModelAuthorTeamImport.class
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, BerlinModelRefDetailImport.class
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, BerlinModelReferenceImport.class
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, BerlinModelTaxonNameImport.class
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, BerlinModelTaxonNameRelationImport.class
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, BerlinModelNameStatusImport.class
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, BerlinModelNameFactsImport.class
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, BerlinModelTypesImport.class
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, BerlinModelTaxonImport.class
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, BerlinModelFactsImport.class
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, BerlinModelTaxonRelationImport.class
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, BerlinModelAreaImport.class
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, BerlinModelOccurrenceImport.class
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, BerlinModelOccurrenceSourceImport.class
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, BerlinModelWebMarkerCategoryImport.class
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, BerlinModelWebMarkerImport.class
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, BerlinModelCommonNamesImport.class
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};
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}
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@Override
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public BerlinModelImportState getNewState() {
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return new BerlinModelImportState(this);
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}
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protected BerlinModelImportConfigurator(Source berlinModelSource, ICdmDataSource destination) {
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super(berlinModelSource, destination, NomenclaturalCode.ICNAFP, defaultTransformer); //default for Berlin Model
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}
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/**
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* Import name relationships yes/no?.
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*/
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public boolean isDoRelNames() {
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return doRelNames;
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}
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public void setDoRelNames(boolean doRelNames) {
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this.doRelNames = doRelNames;
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}
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public URL getMediaUrl() {
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return mediaUrl;
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}
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public void setMediaUrl(URL mediaUrl) {
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this.mediaUrl = mediaUrl;
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}
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public File getMediaPath() {
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return mediaPath;
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}
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public void setMediaPath(File mediaPath) {
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this.mediaPath = mediaPath;
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}
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public void setMediaPath(String mediaPathString){
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this.mediaPath = new File(mediaPathString);
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}
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public void setMediaUrl(String mediaUrlString) {
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try {
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this.mediaUrl = new URL(mediaUrlString);
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} catch (MalformedURLException e) {
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logger.error("Could not set mediaUrl because it was malformed: " + mediaUrlString);
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}
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}
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/**
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* @return the maximumNumberOfNameFacts
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*/
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public int getMaximumNumberOfNameFacts() {
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return maximumNumberOfNameFacts;
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}
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/**
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* set to 0 for unlimited
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*
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* @param maximumNumberOfNameFacts the maximumNumberOfNameFacts to set
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*/
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public void setMaximumNumberOfNameFacts(int maximumNumberOfNameFacts) {
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this.maximumNumberOfNameFacts = maximumNumberOfNameFacts;
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}
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/**
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* If true, no errors occur if objects are not found that should exist. This may
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* be needed e.g. when only subsets of the data are imported.
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* Default value is <cod>false</code>.
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* @return the ignoreNull
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*/
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public boolean isIgnoreNull() {
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return ignoreNull;
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}
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public void setIgnoreNull(boolean ignoreNull) {
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this.ignoreNull = ignoreNull;
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}
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/**
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* If true, an authorTeam with authorTeamId = 0 is not imported (casus Salvador)
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* @return the isIgnore0AuthorTeam
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*/
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public boolean isIgnore0AuthorTeam() {
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return isIgnore0AuthorTeam;
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}
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/**
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* @param isIgnore0AuthorTeam the isIgnore0AuthorTeam to set
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*/
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public void setIgnore0AuthorTeam(boolean isIgnore0AuthorTeam) {
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this.isIgnore0AuthorTeam = isIgnore0AuthorTeam;
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}
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/**
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* @return the namerelationshipTypeMethod
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*/
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public Method getNamerelationshipTypeMethod() {
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return namerelationshipTypeMethod;
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}
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/**
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* @param namerelationshipTypeMethod the namerelationshipTypeMethod to set
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*/
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public void setNamerelationshipTypeMethod(Method namerelationshipTypeMethod) {
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this.namerelationshipTypeMethod = namerelationshipTypeMethod;
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}
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/**
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* @return the taxonPublishMarker
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*/
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public BerlinModelTaxonImport.PublishMarkerChooser getTaxonPublishMarker() {
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return taxonPublishMarker;
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}
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/**
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* @param taxonPublishMarker the taxonPublishMarker to set
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*/
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public void setTaxonPublishMarker(
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BerlinModelTaxonImport.PublishMarkerChooser taxonPublishMarker) {
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this.taxonPublishMarker = taxonPublishMarker;
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}
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/**
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* @return the uuidForDefTermMethod
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*/
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public Method getUuidForDefTermMethod() {
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return uuidForDefTermMethod;
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}
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/**
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* @param uuidForDefTermMethod the uuidForDefTermMethod to set
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*/
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public void setUuidForDefTermMethod(Method uuidForDefTermMethod) {
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this.uuidForDefTermMethod = uuidForDefTermMethod;
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}
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/**
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* @return the nameTypeDesignationStatusMethod
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*/
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public Method getNameTypeDesignationStatusMethod() {
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return nameTypeDesignationStatusMethod;
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}
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/**
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* @param nameTypeDesignationStatusMethod the nameTypeDesignationStatusMethod to set
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*/
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public void setNameTypeDesignationStatusMethod(
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Method nameTypeDesignationStatusMethod) {
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this.nameTypeDesignationStatusMethod = nameTypeDesignationStatusMethod;
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}
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public boolean isDoNameStatus() {
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return doNameStatus;
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}
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public void setDoNameStatus(boolean doNameStatus) {
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this.doNameStatus = doNameStatus;
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}
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public boolean isDoCommonNames() {
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return doCommonNames;
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}
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/**
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* @param doCommonNames
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*/
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public void setDoCommonNames(boolean doCommonNames) {
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this.doCommonNames = doCommonNames;
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}
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public boolean isDoFacts() {
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return doFacts;
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}
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public void setDoFacts(boolean doFacts) {
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this.doFacts = doFacts;
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}
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public boolean isDoOccurrence() {
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return doOccurrence;
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}
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public void setDoOccurrence(boolean doOccurrence) {
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this.doOccurrence = doOccurrence;
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}
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public boolean isDoOccurrenceSources() {
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return doOccurrenceSources;
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}
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public void setDoOccurrenceSources(boolean doOccurrenceSources) {
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this.doOccurrenceSources = doOccurrenceSources;
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}
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public boolean isDoMarker() {
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return doMarker;
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}
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public void setDoMarker(boolean doMarker) {
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this.doMarker = doMarker;
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}
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public boolean isDoUser() {
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return doUser;
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}
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public void setDoUser(boolean doUser) {
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this.doUser = doUser;
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}
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public boolean isDoNameFacts() {
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return doNameFacts;
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}
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public void setDoNameFacts(boolean doNameFacts) {
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this.doNameFacts = doNameFacts;
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}
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public boolean isDoAuthors() {
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return doAuthors;
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}
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public void setDoAuthors(boolean doAuthors) {
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this.doAuthors = doAuthors;
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}
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public DO_REFERENCES getDoReferences() {
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return doReferences;
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}
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public void setDoReferences(DO_REFERENCES doReferences) {
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this.doReferences = doReferences;
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}
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public boolean isDoTaxonNames() {
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return doTaxonNames;
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}
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public void setDoTaxonNames(boolean doTaxonNames) {
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this.doTaxonNames = doTaxonNames;
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}
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public boolean isDoTypes() {
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return doTypes;
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}
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public void setDoTypes(boolean doTypes) {
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this.doTypes = doTypes;
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}
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public boolean isDoTaxa() {
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return doTaxa;
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}
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public void setDoTaxa(boolean doTaxa) {
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this.doTaxa = doTaxa;
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}
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public boolean isDoRelTaxa() {
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return doRelTaxa;
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}
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public void setDoRelTaxa(boolean doRelTaxa) {
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this.doRelTaxa = doRelTaxa;
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}
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public String getTaxonTable() {
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return this.taxonTable ;
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}
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public void setTaxonTable(String taxonTable) {
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this.taxonTable = taxonTable;
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}
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public String getClassificationQuery() {
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return this.classificationQuery ;
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}
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public void setClassificationQuery(String classificationQuery) {
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this.classificationQuery = classificationQuery;
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}
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public void setRelTaxaIdQuery(String relTaxaIdQuery) {
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this.relTaxaIdQuery = relTaxaIdQuery;
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}
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public String getRelTaxaIdQuery() {
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return this.relTaxaIdQuery ;
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}
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public String getNameIdTable() {
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return nameIdTable;
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}
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public void setNameIdTable(String nameIdTable) {
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this.nameIdTable = nameIdTable;
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}
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public String getReferenceIdTable() {
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return referenceIdTable;
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}
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public void setReferenceIdTable(String referenceIdTable) {
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this.referenceIdTable = referenceIdTable;
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}
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public String getFactFilter() {
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return factFilter;
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}
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public void setFactFilter(String factFilter) {
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this.factFilter = factFilter;
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}
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public String getRefDetailFilter() {
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return refDetailFilter;
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}
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public void setRefDetailFilter(String refDetailFilter) {
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this.refDetailFilter = refDetailFilter;
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}
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|
483
|
|
484
|
|
485
|
public String getOccurrenceFilter() {
|
486
|
return occurrenceFilter;
|
487
|
}
|
488
|
public void setOccurrenceFilter(String occurrenceFilter) {
|
489
|
this.occurrenceFilter = occurrenceFilter;
|
490
|
}
|
491
|
|
492
|
|
493
|
|
494
|
public String getCommonNameFilter() {
|
495
|
return commonNameFilter;
|
496
|
}
|
497
|
public void setCommonNameFilter(String commonNameFilter) {
|
498
|
this.commonNameFilter = commonNameFilter;
|
499
|
}
|
500
|
|
501
|
|
502
|
|
503
|
public String getOccurrenceSourceFilter() {
|
504
|
return occurrenceSourceFilter;
|
505
|
}
|
506
|
public void setOccurrenceSourceFilter(String occurrenceSourceFilter) {
|
507
|
this.occurrenceSourceFilter = occurrenceSourceFilter;
|
508
|
}
|
509
|
|
510
|
|
511
|
|
512
|
public String getWebMarkerFilter() {
|
513
|
return webMarkerFilter;
|
514
|
}
|
515
|
public void setWebMarkerFilter(String webMarkerFilter) {
|
516
|
this.webMarkerFilter = webMarkerFilter;
|
517
|
}
|
518
|
|
519
|
|
520
|
public boolean isUseSingleClassification() {
|
521
|
return useSingleClassification;
|
522
|
}
|
523
|
public void setUseSingleClassification(boolean useSingleClassification) {
|
524
|
this.useSingleClassification = useSingleClassification;
|
525
|
}
|
526
|
|
527
|
public String getAuthorTeamFilter() {
|
528
|
return authorTeamFilter;
|
529
|
}
|
530
|
public void setAuthorTeamFilter(String authorTeamFilter) {
|
531
|
this.authorTeamFilter = authorTeamFilter;
|
532
|
}
|
533
|
|
534
|
public String getAuthorFilter() {
|
535
|
return authorFilter;
|
536
|
}
|
537
|
public void setAuthorFilter(String authorFilter) {
|
538
|
this.authorFilter = authorFilter;
|
539
|
}
|
540
|
|
541
|
public boolean isSwitchSpeciesGroup() {
|
542
|
return switchSpeciesGroup;
|
543
|
}
|
544
|
/**
|
545
|
* If true, the rankId for speicesGroup is changed from 59 to 57 and
|
546
|
* 59 is used for coll. species instead
|
547
|
* @param switchSpeciesGroup
|
548
|
*/
|
549
|
public void setSwitchSpeciesGroup(boolean switchSpeciesGroup) {
|
550
|
this.switchSpeciesGroup = switchSpeciesGroup;
|
551
|
}
|
552
|
|
553
|
|
554
|
public boolean isSplitTdwgCodes() {
|
555
|
return isSplitTdwgCodes;
|
556
|
}
|
557
|
public void setSplitTdwgCodes(boolean isSplitTdwgCodes) {
|
558
|
this.isSplitTdwgCodes = isSplitTdwgCodes;
|
559
|
}
|
560
|
|
561
|
|
562
|
public Method getMakeUrlForTaxon() {
|
563
|
return makeUrlForTaxon;
|
564
|
}
|
565
|
public void setMakeUrlForTaxon(Method makeUrlForTaxon) {
|
566
|
this.makeUrlForTaxon = makeUrlForTaxon;
|
567
|
}
|
568
|
|
569
|
|
570
|
public String getInfrGenericRankAbbrev() {
|
571
|
return infrGenericRankAbbrev;
|
572
|
}
|
573
|
public void setInfrGenericRankAbbrev(String infrGenericRankAbbrev) {
|
574
|
this.infrGenericRankAbbrev = infrGenericRankAbbrev;
|
575
|
}
|
576
|
|
577
|
|
578
|
public String getInfrSpecificRankAbbrev() {
|
579
|
return infrSpecificRankAbbrev;
|
580
|
}
|
581
|
public void setInfrSpecificRankAbbrev(String infrSpecificRankAbbrev) {
|
582
|
this.infrSpecificRankAbbrev = infrSpecificRankAbbrev;
|
583
|
}
|
584
|
|
585
|
|
586
|
public boolean isRemoveHttpMapsAnchor() {
|
587
|
return removeHttpMapsAnchor;
|
588
|
}
|
589
|
public void setRemoveHttpMapsAnchor(boolean removeHttpMapsAnchor) {
|
590
|
this.removeHttpMapsAnchor = removeHttpMapsAnchor;
|
591
|
}
|
592
|
|
593
|
|
594
|
public boolean isIncludeFlatClassifications() {
|
595
|
return includeFlatClassifications;
|
596
|
}
|
597
|
public void setIncludeFlatClassifications(boolean includeFlatClassifications) {
|
598
|
this.includeFlatClassifications = includeFlatClassifications;
|
599
|
}
|
600
|
|
601
|
|
602
|
public boolean isIncludesAreaEmCode() {
|
603
|
return includesEmCode;
|
604
|
}
|
605
|
public void setIncludesEmCode(boolean includesEmCode) {
|
606
|
this.includesEmCode = includesEmCode;
|
607
|
|
608
|
}
|
609
|
|
610
|
|
611
|
public boolean isAllowInfraSpecTaxonRank() {
|
612
|
return allowInfraSpecTaxonRank ;
|
613
|
}
|
614
|
public void setAllowInfraSpecTaxonRank(boolean allowInfraSpecTaxonRank) {
|
615
|
this.allowInfraSpecTaxonRank = allowInfraSpecTaxonRank;
|
616
|
}
|
617
|
|
618
|
|
619
|
public boolean isIncludeAllNonMisappliedRelatedClassifications() {
|
620
|
return includeAllNonMisappliedRelatedClassifications;
|
621
|
}
|
622
|
public void setIncludeAllNonMisappliedRelatedClassifications(boolean includeAllNonMisappliedRelatedClassifications) {
|
623
|
this.includeAllNonMisappliedRelatedClassifications = includeAllNonMisappliedRelatedClassifications;
|
624
|
}
|
625
|
|
626
|
|
627
|
public boolean isUseEmAreaVocabulary() {
|
628
|
return useEmAreaVocabulary;
|
629
|
}
|
630
|
public void setUseEmAreaVocabulary(boolean useEmAreaVocabulary) {
|
631
|
this.useEmAreaVocabulary = useEmAreaVocabulary;
|
632
|
}
|
633
|
|
634
|
|
635
|
public boolean isSalvador() {return isSalvador;}
|
636
|
public void setSalvador(boolean isSalvador) {this.isSalvador = isSalvador;}
|
637
|
|
638
|
public boolean isEuroMed() {return isEuroMed;}
|
639
|
public void setEuroMed(boolean isEuroMed) {this.isEuroMed = isEuroMed;}
|
640
|
|
641
|
public boolean isMcl() {return isMcl;}
|
642
|
public void setMcl(boolean isMcl) {this.isMcl = isMcl;}
|
643
|
|
644
|
public UUID getFeatureTreeUuid() {
|
645
|
return featureTreeUuid;
|
646
|
}
|
647
|
public void setFeatureTreeUuid(UUID featureTreeUuid) {
|
648
|
this.featureTreeUuid = featureTreeUuid;
|
649
|
}
|
650
|
|
651
|
@Override
|
652
|
public String getFeatureTreeTitle() {
|
653
|
return featureTreeTitle;
|
654
|
}
|
655
|
@Override
|
656
|
public void setFeatureTreeTitle(String featureTreeTitle) {
|
657
|
this.featureTreeTitle = featureTreeTitle;
|
658
|
}
|
659
|
|
660
|
public boolean isUseLastScrutinyAsSec() {
|
661
|
return useLastScrutinyAsSec;
|
662
|
}
|
663
|
public void setUseLastScrutinyAsSec(boolean useLastScrutinyAsSec) {
|
664
|
this.useLastScrutinyAsSec = useLastScrutinyAsSec;
|
665
|
}
|
666
|
|
667
|
|
668
|
public boolean isDoPreliminaryRefDetailsWithNames() {
|
669
|
return doPreliminaryRefDetailsWithNames;
|
670
|
}
|
671
|
public void setDoPreliminaryRefDetailsWithNames(boolean doPreliminaryRefDetailsWithNames) {
|
672
|
this.doPreliminaryRefDetailsWithNames = doPreliminaryRefDetailsWithNames;
|
673
|
}
|
674
|
|
675
|
public boolean isWarnForDifferingSynonymReference() {
|
676
|
return warnForDifferingSynonymReference;
|
677
|
}
|
678
|
public void setWarnForDifferingSynonymReference(boolean warnForDifferingSynonymReference) {
|
679
|
this.warnForDifferingSynonymReference = warnForDifferingSynonymReference;
|
680
|
}
|
681
|
|
682
|
public boolean isLogNotMatchingOldNames() {
|
683
|
return logNotMatchingOldNames;
|
684
|
}
|
685
|
public void setLogNotMatchingOldNames(boolean logNotMatchingOldNames) {
|
686
|
this.logNotMatchingOldNames = logNotMatchingOldNames;
|
687
|
}
|
688
|
|
689
|
public boolean isCheckOldNameIsSynonym() {
|
690
|
return checkOldNameIsSynonym;
|
691
|
}
|
692
|
public void setCheckOldNameIsSynonym(boolean checkOldNameIsSynonym) {
|
693
|
this.checkOldNameIsSynonym = checkOldNameIsSynonym;
|
694
|
}
|
695
|
|
696
|
public boolean isLogMatchingNotExportedOldNames() {
|
697
|
return logMatchingNotExportedOldNames;
|
698
|
}
|
699
|
public void setLogMatchingNotExportedOldNames(boolean logMatchingNotExportedOldNames) {
|
700
|
this.logMatchingNotExportedOldNames = logMatchingNotExportedOldNames;
|
701
|
}
|
702
|
|
703
|
public boolean isDoSourceNumber() {
|
704
|
return doSourceNumber;
|
705
|
}
|
706
|
public void setDoSourceNumber(boolean doSourceNumber) {
|
707
|
this.doSourceNumber = doSourceNumber;
|
708
|
}
|
709
|
public boolean isDoNamedAreas() {
|
710
|
return doNamedAreas;
|
711
|
}
|
712
|
public void setDoNamedAreas(boolean doNamedAreas) {
|
713
|
this.doNamedAreas = doNamedAreas;
|
714
|
}
|
715
|
|
716
|
public boolean isIncludeMANsForOldNameCheck() {
|
717
|
return includeMANsForOldNameCheck;
|
718
|
}
|
719
|
public void setIncludeMANsForOldNameCheck(boolean includeMANsForOldNameCheck) {
|
720
|
this.includeMANsForOldNameCheck = includeMANsForOldNameCheck;
|
721
|
}
|
722
|
|
723
|
}
|