Package org.gbif.api.model.checklistbank

Class NameUsage

  • All Implemented Interfaces:
    LinneanClassification, LinneanClassificationKeys
    Direct Known Subclasses:
    NameUsageContainer
    @Deprecated
public class NameUsage
extends Object
implements LinneanClassification, LinneanClassificationKeys
    Deprecated.
    A usage of a scientific name according to one particular Checklist including the GBIF Taxonomic Backbone, the NUB. It is shown as species in the portal and API.
    Backbone (NUB) usages have key==nubKey. Backbone usages can also be detected by either the NameUsage.isNub() method or by manually comparing the datasetKey with the fixed backbone datasetKey, see Constants.NUB_DATASET_KEY.
    Name usages from other checklists with names that also exist in the backbone will have a nubKey that points to the related usage in the NUB.
    To store not eagerly loaded subresources such as vernacular names or synonyms with a usage please use the NameUsageContainer class.

    • Method Detail

      • getNameKey

        public Integer getNameKey()
        Deprecated.
        Returns:
        the name key for retrieving a parsed name object

      • getSourceTaxonKey

        @Nullable
public Integer getSourceTaxonKey()
        Deprecated.
        For backbone taxa the source taxon key refers to the original name usage that was used during backbone building and is the primary reason that this taxon exists in the backbone.
        All backbone name usages are built from several underlying checklist usages, but these are sorted by priority and the usage key for the highest priority one becomes the sourceTaxonKey for a backbone usage.
        Some backbone usages do not have any source record altogether. For example if there is a subspecies found, but no matching parent species, the missing species will be created nevertheless and has no primary source.
        Returns:
        The key of the name usage this backbone taxon is derived from.

      • getAccepted

        public String getAccepted()
        Deprecated.
        Returns:
        the scientific name of the accepted name

      • setAccepted

        public void setAccepted​(String accepted)
        Deprecated.
        Sets the scientific name of the basionym, i.e. original name usage.

      • getAcceptedKey

        public Integer getAcceptedKey()
        Deprecated.
        Returns:
        the name usage key of the accepted name

      • setAcceptedKey

        public void setAcceptedKey​(Integer acceptedKey)
        Deprecated.
        Sets the usage key for the accepted name.

      • getAccordingTo

        @Nullable
public String getAccordingTo()
        Deprecated.
        The taxon concept reference is usually a reference to some publication or author and year.
        The dwc:taxonAccordingTo reference is usually appended to the scientific name to further qualify the concept with "sensu" or "sec." being used for concatenation. E.g. "Acer nigrum sec. Gleason Cronquist 1991".
        In the case of backbone taxa this refers to the primary checklist the name was found in.
        Returns:
        the taxon concept reference

      • setAccordingTo

        public void setAccordingTo​(String accordingTo)
        Deprecated.
        Parameters:
        accordingTo - the accordingTo to set

      • getAuthorship

        @Nullable
public String getAuthorship()
        Deprecated.
        Returns the authorship information for the scientific name.
        Returns:
        the authorship

      • setAuthorship

        public void setAuthorship​(String authorship)
        Deprecated.
        Parameters:
        authorship - the authorship to set

      • getBasionym

        public String getBasionym()
        Deprecated.
        Returns:
        the scientific name of the basionym

      • setBasionym

        public void setBasionym​(String basionym)
        Deprecated.
        sets the basionym name.

      • getBasionymKey

        @Nullable
public Integer getBasionymKey()
        Deprecated.
        Returns the earlier name (basionym) for this scientific name. Return null if the basionym does not exist.
        Returns:
        the basionymKey

      • setBasionymKey

        public void setBasionymKey​(Integer basionymKey)
        Deprecated.
        Parameters:
        basionymKey - the basionymKey to set

      • setCanonicalName

        public void setCanonicalName​(String canonicalName)
        Deprecated.
        Parameters:
        canonicalName - the canonicalName to set

      • getDatasetKey

        @NotNull
public @NotNull UUID getDatasetKey()
        Deprecated.
        Returns the key of the checklist that "hosts" this name usage.
        Returns:
        the datasetKey

      • setDatasetKey

        public void setDatasetKey​(UUID datasetKey)
        Deprecated.
        Parameters:
        datasetKey - the datasetKey to set

      • getKey

        @NotNull
public @NotNull Integer getKey()
        Deprecated.
        Return the key that uniquely identifies this name usage.
        Returns:
        the key

      • setKey

        public void setKey​(Integer key)
        Deprecated.
        Parameters:
        key - the key to set

      • getNameType

        public NameType getNameType()
        Deprecated.
        Returns:
        the type of name string classified by CLB.

      • setNameType

        public void setNameType​(NameType nameType)
        Deprecated.
        Parameters:
        nameType - the type of name string

      • getNubKey

        @Nullable
public Integer getNubKey()
        Deprecated.
        Returns:
        the taxon key of the matching backbone name usage

      • setNubKey

        public void setNubKey​(Integer nubKey)
        Deprecated.
        Parameters:
        nubKey - the nubKey to set

      • getNumDescendants

        public int getNumDescendants()
        Deprecated.
        The number of all accepted taxonomic elements under this usage.
        Returns:
        the number of descendants

      • setNumDescendants

        public void setNumDescendants​(int numDescendants)
        Deprecated.
        Parameters:
        numDescendants - the n umber of descendants to set

      • getOrigin

        @NotNull
public @NotNull Origin getOrigin()
        Deprecated.
        The origin of this name usage record, i.e. the reason why it exists. In most cases this is because the record existed explicitly in the checklist sources, but some usages are created de novo because they exist implicitly in the data.
        Returns:
        the name usage origin
        See Also:
        Origin

      • setOrigin

        public void setOrigin​(Origin origin)
        Deprecated.
        Parameters:
        origin - the origin to set

      • getParent

        public String getParent()
        Deprecated.
        The scientific name of the parent.
        Returns:
        the parent name

      • setParent

        public void setParent​(String parent)
        Deprecated.
        Parameters:
        parent - the parent name to set

      • getParentKey

        @Nullable
public Integer getParentKey()
        Deprecated.
        Returns the immediate parent. If this usage if for the highest taxonomic level, return null.
        Returns:
        the parentKey

      • setParentKey

        public void setParentKey​(Integer parentKey)
        Deprecated.
        Parameters:
        parentKey - the parentKey to set

      • getProParteKey

        public Integer getProParteKey()
        Deprecated.
        Pro parte synonyms, i.e. a synonym with multiple accepted names, are grouped by a single, primary name usage key.
        Returns:
        the primary name usage key for a pro parte synonym or null

      • setProParteKey

        public void setProParteKey​(Integer proParteKey)
        Deprecated.
        Sets the pro parte usage key.

      • getPublishedIn

        @Nullable
public String getPublishedIn()
        Deprecated.
        Original publication for this name usage.
        Returns:
        the publishedIn

      • setPublishedIn

        public void setPublishedIn​(String publishedIn)
        Deprecated.
        Parameters:
        publishedIn - the publishedIn to set

      • getRank

        @Nullable
public Rank getRank()
        Deprecated.
        Returns the rank for this usage.

        Example: "Kingdom", "Genus"

        Returns:
        the rank

      • setRank

        public void setRank​(Rank rank)
        Deprecated.
        Parameters:
        rank - the rank to set

      • getScientificName

        @NotNull
public @NotNull String getScientificName()
        Deprecated.
        The scientific name (with date and authorship information if applicable).

        Example: "Coleoptera" (order), "Vespertilionidae" (family), "Manis" (genus), "Ctenomys sociabilis" (genus + specific name), "Ambystoma tigrinum diaboli" (genus + specific name + infraspecific name), "Quercus agrifolia var. oxyadenia (Torr.)"

        Returns:
        the scientificName

      • setScientificName

        public void setScientificName​(String scientificName)
        Deprecated.
        Parameters:
        scientificName - the scientificName to set

      • getConstituentKey

        @Nullable
public UUID getConstituentKey()
        Deprecated.
        Return the optional sub dataset key for this usage.
        Returns:
        the subDatasetKey or null

      • setConstituentKey

        public void setConstituentKey​(UUID constituentKey)
        Deprecated.
        Parameters:
        constituentKey - to set

      • getVernacularName

        @Nullable
public String getVernacularName()
        Deprecated.
        A common or vernacular name for this usage.

        Example: Andean Condor", "Condor Andino", "American Eagle", "Gänsegeier".

        Returns:
        the vernacularName

      • setVernacularName

        public void setVernacularName​(String vernacularName)
        Deprecated.
        Parameters:
        vernacularName - the vernacularName to set

      • getReferences

        @Nullable
public URI getReferences()
        Deprecated.
        A URI link or reference to the source of this record, the record's "homepage".

        Example: https://www.catalogueoflife.org/data/taxon/4R5YN

        Returns:
        the link

      • getHigherRank

        public String getHigherRank​(Rank rank)
        Deprecated.
        Description copied from interface: LinneanClassification
        Gets a higher taxon property by passing the rank of it. Only Linnean ranks are supported.
        Specified by:
        getHigherRank in interface LinneanClassification
        Parameters:
        rank - the higher linnean rank to retrieve
        Returns:
        the name of the higher taxon or null if rank doesnt exist

      • getHigherClassificationMap

        @NotNull
public @NotNull LinkedHashMap<Integer,​String> getHigherClassificationMap()
        Deprecated.
        An ordered map with entries for all higher Linnean ranks down to the actual direct parent of this usage. The map starts with the highest rank, e.g. the kingdom and maps the name usage key to its canonical name. The name usage itself is never included, even though a higher rank might point to the usage itself.
        Returns:
        map of higher ranks

      • getTaxonID

        @Nullable
public String getTaxonID()
        Deprecated.
        The original taxonID of the name usage as found in the source. For backbone taxa and name usages with an origin different to SOURCE this is null.

      • getTaxonomicStatus

        @Nullable
public TaxonomicStatus getTaxonomicStatus()
        Deprecated.
        The taxonomic status of the name usage. Can be null, but for all synonyms with an accepted name usage it is guaranteed to exist.
        Returns:
        the taxonomicStatus, can be null

      • getModified

        @Nullable
public Date getModified()
        Deprecated.
        The interpreted dc:modified from the verbatim source data. Ideally indicating when a record was last modified in the source.

      • getDeleted

        @Nullable
public Date getDeleted()
        Deprecated.
        The date this record was deleted. Logical deletions only occur for backbone usages!

      • getLastCrawled

        @Nullable
public Date getLastCrawled()
        Deprecated.
        The date this record was last crawled during clb indexing.

      • getLastInterpreted

        @Nullable
public Date getLastInterpreted()
        Deprecated.
        The date this record was last interpreted during indexing. This includes matching to the backbone.

      • isNub

        public boolean isNub()
        Deprecated.

      • isProParte

        public boolean isProParte()
        Deprecated.
        True for pro parte synonyms with multiple accepted usages.
        Returns:
        true if proParte, false otherwise

      • isSynonym

        public boolean isSynonym()
        Deprecated.
        Convenience method using the taxonomicStatus field.
        Returns:
        true if it's a synonym