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c2f269f9
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Andreas Kohlbecker
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// $Id$
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25663b56
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Andreas Müller
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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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2d993c6e
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Andreas Müller
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package eu.etaxonomy.cdm.api.service;
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import java.util.List;
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24700eab
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a.babadshanjan
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import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;
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d57c0df0
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ben.clark
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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24700eab
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a.babadshanjan
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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7a931ddb
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a.babadshanjan
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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3d99737b
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Katja Luther
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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d57c0df0
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ben.clark
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import eu.etaxonomy.cdm.model.name.Rank;
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2d993c6e
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Andreas Müller
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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02cf6cb7
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Andreas Müller
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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d57c0df0
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ben.clark
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
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02cf6cb7
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Andreas Müller
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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2d993c6e
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Andreas Müller
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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d57c0df0
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ben.clark
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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3cc31c85
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Andreas Kohlbecker
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import eu.etaxonomy.cdm.persistence.dao.BeanInitializer;
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855f3dd0
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Andreas Müller
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import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
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d44277a9
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ben.clark
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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2d993c6e
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Andreas Müller
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public interface ITaxonService extends IIdentifiableEntityService<TaxonBase>{
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add8b0a9
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Andreas Müller
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643cfd14
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a.babadshanjan
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/**
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* Computes all taxon bases.
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d57c0df0
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ben.clark
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* FIXME could substitute with list(Synonym.class, limit, start)
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643cfd14
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a.babadshanjan
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* @param limit
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* @param start
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* @return
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*/
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58452b54
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Katja Luther
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public List<Synonym> getAllSynonyms(int limit, int start);
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643cfd14
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a.babadshanjan
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/**
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* Computes all taxon bases.
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d57c0df0
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ben.clark
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* FIXME could substitute with list(Taxon.class, limit,start)
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643cfd14
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a.babadshanjan
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* @param limit
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* @param start
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* @return
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*/
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58452b54
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Katja Luther
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public List<Taxon> getAllTaxa(int limit, int start);
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07eb2b2b
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a.babadshanjan
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855f3dd0
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Andreas Müller
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/**
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* Computes all Taxon instances that do not have a taxonomic parent and has at least one child.
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* @param sec The concept reference that the taxon belongs to
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* @return The List<Taxon> of root taxa.
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01c21ead
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n.hoffmann
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* @deprecated obsolete when using taxonomicTree
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855f3dd0
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Andreas Müller
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*/
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d93c0aaf
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Andreas Müller
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public List<Taxon> getRootTaxa(ReferenceBase sec);
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855f3dd0
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Andreas Müller
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/**
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* Computes all Taxon instances that do not have a taxonomic parent.
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* @param sec The concept reference that the taxon belongs to
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*
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* @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
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* @return The List<Taxon> of root taxa.
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01c21ead
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n.hoffmann
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* @deprecated obsolete when using taxonomicTree
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855f3dd0
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Andreas Müller
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*/
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58452b54
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Katja Luther
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public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, boolean onlyWithChildren);
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349fae93
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Andreas Müller
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2950108e
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Andreas Müller
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/**
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* Computes all Taxon instances that do not have a taxonomic parent.
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* @param sec The concept reference that the taxon belongs to
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* @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
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* @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are
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* the misapplied name are not returned.<Br>Default: true.
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* @return The List<Taxon> of root taxa.
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01c21ead
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n.hoffmann
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* @deprecated obsolete when using taxonomicTree
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2950108e
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Andreas Müller
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*/
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58452b54
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Katja Luther
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public List<Taxon> getRootTaxa(ReferenceBase sec, boolean onlyWithChildren, boolean withMisapplications);
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349fae93
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Andreas Müller
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7a1d87e3
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a.babadshanjan
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/**
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* Computes all Taxon instances which name is of a certain Rank.
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* @param rank The rank of the taxon name
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* @param sec The concept reference that the taxon belongs to
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* @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
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* @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are
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* the misapplied name are not returned.<Br>Default: true.
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9b62c409
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Andreas Kohlbecker
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* @param propertyPaths
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* properties to be initialized, For detailed description and
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* examples <b>please refer to:</b>
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* {@link BeanInitializer#initialize(Object, List)}. <Br>
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* Default: true.
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7a1d87e3
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a.babadshanjan
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* @return The List<Taxon> of root taxa.
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01c21ead
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n.hoffmann
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* @deprecated obsolete when using taxonomicTree
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7a1d87e3
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a.babadshanjan
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*/
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58452b54
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Katja Luther
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public List<Taxon> getRootTaxa(Rank rank, ReferenceBase sec, boolean onlyWithChildren, boolean withMisapplications, List<String> propertyPaths);
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101 |
2d993c6e
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Andreas Müller
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7a931ddb
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a.babadshanjan
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/**
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* Computes all relationships.
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* @param limit
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* @param start
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* @return
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*/
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58452b54
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Katja Luther
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public List<RelationshipBase> getAllRelationships(int limit, int start);
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7a931ddb
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a.babadshanjan
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24700eab
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a.babadshanjan
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/**
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* Returns TaxonRelationshipType vocabulary
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* @return
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f3ba008a
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n.hoffmann
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* @deprecated use TermService#getVocabulary(VocabularyType) instead
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24700eab
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a.babadshanjan
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*/
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public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary();
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/** */
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58452b54
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Katja Luther
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public List<TaxonBase> searchTaxaByName(String name, ReferenceBase sec);
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a400a105
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m.doering
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bb4f5701
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n.hoffmann
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/**
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* Changes an accepted taxon to a synonym of another taxon.
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*
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* @param oldTaxon
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* the accepted taxon that will be changed into a synonym
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* @param newAcceptedTaxon
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* the accepted taxon, the old taxon will become a synonym of
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* @param synonymType
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af8f90fb
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n.hoffmann
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* <code>SynonymRelationshipType</code> to indicate whether hetero or homotypic
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bb4f5701
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n.hoffmann
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* @param citation
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* the reference for this assumption
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* @param citationMicroReference
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* the micro citation
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* @return
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* the newly created synonym
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*/
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02cf6cb7
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Andreas Müller
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public Synonym makeTaxonSynonym (Taxon oldTaxon, Taxon newAcceptedTaxon, SynonymRelationshipType synonymType, ReferenceBase citation, String citationMicroReference);
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137 |
2d993c6e
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Andreas Müller
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f4cfc931
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n.hoffmann
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/**
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af8f90fb
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n.hoffmann
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* Swaps given synonym and accepted taxon.
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* In particular:
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* <ul>
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* <li>A new accepted taxon with the synonyms name is created</li>
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* <li>The synonym is deleted from the old accepted taxons synonym list</li>
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* <li>A new synonym with the name of the old accepted taxon is created</li>
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* <li>The newly created synonym get related to the newly created accepted taxon</li>
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* </ul>
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f4cfc931
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n.hoffmann
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*
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* @param synonym
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* @param acceptedTaxon
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* @param synonymRelationshipType the relationship type the newly created synonym will have. Defaults to SYNONYM_OF
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*/
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2b72538e
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n.hoffmann
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public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, SynonymRelationshipType synonymRelationshipType );
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f4cfc931
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n.hoffmann
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af8f90fb
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n.hoffmann
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/**
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* Change a synonym into an accepted taxon and removes existing synonym relationship to the given accepted taxon.
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*
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* @param synonym
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* the synonym to change into an accepted taxon
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* @param acceptedTaxon
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* an accepted taxon, the synonym had a relationship to
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* @return
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* the newly created accepted taxon
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*/
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public Taxon makeSynonymAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
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d57c0df0
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ben.clark
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/**
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167 |
d40f8755
|
Andreas Kohlbecker
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* Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
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d57c0df0
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ben.clark
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* where the supplied taxon is relatedTo.
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*
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* @param taxon The taxon that is relatedTo
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* @param type The type of TaxonRelationship (can be null)
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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d44277a9
|
ben.clark
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* @param orderHints Properties to order by
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* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
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d40f8755
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Andreas Kohlbecker
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* @return a List of TaxonRelationship instances
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*/
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public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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f4cfc931
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n.hoffmann
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d40f8755
|
Andreas Kohlbecker
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/**
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f4cfc931
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n.hoffmann
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* Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied)
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d40f8755
|
Andreas Kohlbecker
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* where the supplied taxon is relatedTo.
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*
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* @param taxon The taxon that is relatedTo
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* @param type The type of TaxonRelationship (can be null)
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param orderHints Properties to order by
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* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
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* @return a Pager of TaxonRelationship instances
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*/
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public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
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* where the supplied taxon is relatedFrom.
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*
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* @param taxon The taxon that is relatedFrom
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* @param type The type of TaxonRelationship (can be null)
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param orderHints Properties to order by
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* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
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* @return a List of TaxonRelationship instances
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*/
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public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
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* where the supplied taxon is relatedFrom.
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*
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* @param taxon The taxon that is relatedFrom
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* @param type The type of TaxonRelationship (can be null)
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param orderHints Properties to order by
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* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
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d57c0df0
|
ben.clark
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* @return a Pager of TaxonRelationship instances
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*/
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220 |
d40f8755
|
Andreas Kohlbecker
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public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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d57c0df0
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ben.clark
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222 |
219ab499
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ben.clark
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/**
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* Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
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* where the supplied synonym is relatedFrom.
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*
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* @param taxon The synonym that is relatedFrom
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* @param type The type of SynonymRelationship (can be null)
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* * @param orderHints Properties to order by
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* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
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* @return a Pager of SynonymRelationship instances
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*/
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public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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d57c0df0
|
ben.clark
|
/**
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237 |
d40f8755
|
Andreas Kohlbecker
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* Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
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d57c0df0
|
ben.clark
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* where the supplied taxon is relatedTo.
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*
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* @param taxon The taxon that is relatedTo
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* @param type The type of SynonymRelationship (can be null)
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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244 |
d44277a9
|
ben.clark
|
* * @param orderHints Properties to order by
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245 |
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* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
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246 |
d57c0df0
|
ben.clark
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* @return a Pager of SynonymRelationship instances
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*/
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248 |
d44277a9
|
ben.clark
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public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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249 |
d57c0df0
|
ben.clark
|
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250 |
9b62c409
|
Andreas Kohlbecker
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public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
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public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths);
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254 |
d57c0df0
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ben.clark
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/**
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255 |
aba8d6ad
|
ben.clark
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* Returns a Paged List of TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
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256 |
d57c0df0
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ben.clark
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*
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257 |
aba8d6ad
|
ben.clark
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* @param clazz filter the results by class (or pass null to return all TaxonBase instances)
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258 |
d57c0df0
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ben.clark
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* @param queryString
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* @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
261 |
aba8d6ad
|
ben.clark
|
* @param orderHints
|
262 |
|
|
* Supports path like <code>orderHints.propertyNames</code> which
|
263 |
|
|
* include *-to-one properties like createdBy.username or
|
264 |
|
|
* authorTeam.persistentTitleCache
|
265 |
|
|
* @param propertyPaths properties to be initialized
|
266 |
d57c0df0
|
ben.clark
|
* @return a Pager Taxon instances
|
267 |
|
|
* @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
|
268 |
|
|
*/
|
269 |
aba8d6ad
|
ben.clark
|
public Pager<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
270 |
d57c0df0
|
ben.clark
|
|
271 |
|
|
/**
|
272 |
a9e5cd74
|
ben.clark
|
* Returns a list of TaxonBase instances where the
|
273 |
d57c0df0
|
ben.clark
|
* taxon.name properties match the parameters passed.
|
274 |
|
|
*
|
275 |
a9e5cd74
|
ben.clark
|
* @param clazz optionally filter by class
|
276 |
d57c0df0
|
ben.clark
|
* @param uninomial
|
277 |
|
|
* @param infragenericEpithet
|
278 |
|
|
* @param specificEpithet
|
279 |
|
|
* @param infraspecificEpithet
|
280 |
|
|
* @param rank
|
281 |
|
|
* @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
|
282 |
|
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
283 |
|
|
* @return a Pager of TaxonBase instances
|
284 |
|
|
*/
|
285 |
a9e5cd74
|
ben.clark
|
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
|
286 |
24700eab
|
a.babadshanjan
|
|
287 |
|
|
/**
|
288 |
|
|
* Returns a list of IdentifiableEntity instances (in particular, TaxonNameBase and TaxonBase instances)
|
289 |
|
|
* that match the properties specified in the configurator.
|
290 |
|
|
* @param configurator
|
291 |
|
|
* @return
|
292 |
|
|
*/
|
293 |
|
|
public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator);
|
294 |
18e91500
|
n.hoffmann
|
|
295 |
|
|
/**
|
296 |
|
|
*
|
297 |
3d99737b
|
Katja Luther
|
* @param taxon
|
298 |
01c21ead
|
n.hoffmann
|
* @param size
|
299 |
|
|
* @param height
|
300 |
|
|
* @param widthOrDuration
|
301 |
|
|
* @param mimeTypes
|
302 |
|
|
* @return
|
303 |
3d99737b
|
Katja Luther
|
*/
|
304 |
a4e49cfa
|
Katja Luther
|
public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes);
|
305 |
2d993c6e
|
Andreas Müller
|
}
|