Package org.gbif.api.model.checklistbank

Class ParsedName

java.lang.Object
org.gbif.api.model.checklistbank.ParsedName
public class ParsedName extends Object
A container of a taxon name that is atomised into its relevant, separate parts.
Hybrid formulas that consist of multiple genera, binomials or species epithets are relatively poorly represented. A simple boolean flag indicates a hybrid formula, e.g. Polygala vulgaris × Polygala epinema but not named hybrids that are have an × or notho as part of a well-formed mono/bi/trinomial e.g. ×Polygala vulgaris. In the case of hybrid formulas, i.e. isHybrid=true, the first name in the formula is tried to be kept, at least the genus.

A container of a taxon name that is only atomised into three name parts maximum plus rank and a notho property indicating the name part of named hybrids that is considered to be the hybrid. No authorship is kept. For subgenera we don't use parentheses to indicate the subgenus, but use explicit rank markers instead.

  • Field Details

  • Constructor Details

  • Method Details

    • getAuthorship

      public String getAuthorship()
      The original author of this name, e.g. basionym or recombination author

    • setAuthorship

      public void setAuthorship(String authorship)

    • getBracketAuthorship

      public String getBracketAuthorship()
      The authorship of the original name, i.e. basionym, given in brackets.

    • setBracketAuthorship

      public void setBracketAuthorship(String bracketAuthorship)

    • getBracketYear

      public String getBracketYear()
      The code relevant year of publication of the original name, i.e. basionym, given in brackets.

    • setBracketYear

      public void setBracketYear(String bracketYear)

    • getCultivarEpithet

      public String getCultivarEpithet()
      The cultivar, cultivar group or grex part of a cultivated plant name. If given the name should be of type NameType.CULTIVAR

    • setCultivarEpithet

      public void setCultivarEpithet(String cultivarEpithet)

    • getStrain

      public String getStrain()
      The strain or isolate name. Usually a capital collection code string followed by an accession number. See List of culture collection codes If given the name should be of type NameType.STRAIN

    • setStrain

      public void setStrain(String strain)

    • getGenusOrAbove

      public String getGenusOrAbove()
      The genus part of a bi/trinomial or the monomial in case of names of higher ranks

    • getInfraGeneric

      public String getInfraGeneric()
      The infrageneric part of a name, often given in parentheses between genus and species epithet, e.g. for a subgenus

    • getInfraSpecificEpithet

      public String getInfraSpecificEpithet()

    • getNomStatus

      public String getNomStatus()
      Any nomenclatoral remarks given in this name, e.g. nom. illeg.

    • setNomStatus

      public void setNomStatus(String nomStatus)

    • getNotho

      public NamePart getNotho()
      For hybrid names notho indicates which part of the name is considered a hybrid, i.e. genus, species or infraspecific epithet.

    • setNotho

      public void setNotho(NamePart notho)

    • getRemarks

      public String getRemarks()
      Any further remarks found

    • setRemarks

      public void setRemarks(String remarks)

    • getSensu

      public String getSensu()
      Taxon concept references as part of the name, e.g. "MSW2005" for Gorilla gorilla (Savage, 1847) sec. MSW2005

    • setSensu

      public void setSensu(String sensu)

    • getSpecificEpithet

      public String getSpecificEpithet()

    • getTerminalEpithet

      public String getTerminalEpithet()
      Returns:
      the terminal epithet, infraspecific epithet if existing, the species epithet or null

    • getType

      public NameType getType()
      A coarse classification of names helping to deal with different syntactical name string structures.

    • setType

      public void setType(NameType type)

    • getYear

      public String getYear()
      The year of publication as given in the authorship.

    • setYear

      public void setYear(String year)

    • hasAuthorship

      public boolean hasAuthorship()

    • setRank

      public void setRank(Rank rank)

    • getKey

      public Integer getKey()

    • setKey

      public void setKey(Integer key)

    • getScientificName

      public String getScientificName()
      The exact verbatim, full scientific name as given before parsing.

    • setScientificName

      public void setScientificName(String scientificName)

    • isParsedPartially

      public boolean isParsedPartially()
      The GBIF name parser cannot always parse the entire name. This is often the case when taxonomic, nomenclatural or identification notes are added to the end of the name. In such cases when the name was only partially parsed (NameUsageIssue.PARTIALLY_PARSABLE) this flag should be true. If the name was not parsed at all this will be false.
      Returns:
      true if name was only partially parsed, false otherwise

    • setParsedPartially

      public void setParsedPartially(boolean parsedPartially)

    • isParsed

      public boolean isParsed()
      A flag indicating if a name could not be parsed at all. If false, only the scientific name, rank and potentially the name type is given.

    • setParsed

      public void setParsed(boolean parsed)

    • authorshipComplete

      public String authorshipComplete()
      Returns:
      The full concatenated authorship or null if it is a hybrid

    • buildName

      public String buildName(boolean hybridMarker, boolean rankMarker, boolean authorship, boolean infrageneric, boolean genusForInfrageneric, boolean abbreviateGenus, boolean decomposition, boolean asciiOnly, boolean showIndet, boolean nomNote, boolean remarks, boolean showSensu, boolean showCultivar, boolean showStrain)
      build a name controlling all available flags for name parts to be included in the resulting name.
      Parameters:
      hybridMarker - include the hybrid marker with the name if existing
      rankMarker - include the infraspecific or infrageneric rank marker with the name if existing
      authorship - include the names authorship (authorteam and year)
      infrageneric - include the infrageneric name in brackets for species or infraspecies
      genusForInfrageneric - include the genus name in front of an infrageneric name (not a species)
      abbreviateGenus - if true abreviate the genus with its first character
      decomposition - decompose unicode ligatures into their corresponding ascii ones, e.g. æ beomes ae
      asciiOnly - transform unicode letters into their corresponding ascii ones, e.g. ø beomes o and ü u
      showIndet - if true include the rank marker for incomplete determinations, for example Puma spec.
      nomNote - include nomenclatural notes
      remarks - include informal remarks

    • canonicalName

      public String canonicalName()
      The canonical name sensu strictu with nothing else but 3 name parts at max (genus, species, infraspecific). No rank or hybrid markers and no authorship, cultivar or strain information. Infrageneric names are represented without a leading genus. Unicode characters will be replaced by their matching ASCII characters.

      For example: Abies alba Abies alba alpina Abies Bracteata Heucherella tiarelloides

      Returns:
      the 1, 2 or 3 parted name as a single string

    • canonicalNameWithMarker

      public String canonicalNameWithMarker()
      The code-compliant, canonical name with three name parts at max (genus, species, infraspecific), a rank marker for infraspecific names and cultivar or strain epithets. The canonical name can be a 1, 2 or 3 parted name, but does not include any informal notes or authorships. Notho taxa will have the hybrid marker. Unicode characters will be replaced by their matching ASCII characters.

      For example: Abies alba Abies alba subsp. alpina Abies sect. Bracteata ×Heucherella tiarelloides

      Returns:
      the 1,2 or 3 parted name as a single string

    • canonicalNameComplete

      public String canonicalNameComplete()
      The code-compliant, canonical name with rank and hybrid marker, authorship and cultivar or strain name included. Informal or nomenclatoral notes, concept references, subgenus and non-terminal authorships are removed.
      Returns:
      the 1,2 or 3 parted name as a single string

    • canonicalSpeciesName

      public String canonicalSpeciesName()
      Returns:
      the species binomial if this parsed name is a species or below. Or null in case its superspecific

    • fullName

      public String fullName()
      Returns:
      the name with all details that exist.

    • getBracketYearInt

      public Integer getBracketYearInt()

    • getRank

      public Rank getRank()
      Returns:
      rank as enumeration or null

    • getYearInt

      public Integer getYearInt()

    • isAutonym

      public boolean isAutonym()

    • isBinomial

      public boolean isBinomial()

    • isHybridFormula

      public boolean isHybridFormula()

    • isIndetermined

      public boolean isIndetermined()
      Returns:
      true for names with an infraspecifc rank but missing lowest name part. E.g. Coccyzuz americanus ssp. or Asteraceae spec. but not Maxillaria sect. Acaules

    • isParsableType

      public boolean isParsableType()

    • isQualified

      public boolean isQualified()

    • isRecombination

      public boolean isRecombination()
      Returns:
      true if a bracket authorship is given, indicating that the name has been subsequently recombined.

    • setGenusOrAbove

      public void setGenusOrAbove(String genusOrAbove)

    • setHybridFormula

      public void setHybridFormula(boolean hybrid)

    • setInfraGeneric

      public void setInfraGeneric(String infraGeneric)

    • setInfraSpecificEpithet

      public void setInfraSpecificEpithet(String infraSpecies)

    • setSpecificEpithet

      public void setSpecificEpithet(String species)

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object