Package org.genesys.taxonomy.checker

Interface TaxonomyDatabase

All Known Implementing Classes:

CachingInMemoryTaxonomyDatabase, InMemoryTaxonomyDatabase

public interface TaxonomyDatabase

Defines searches possible against a database of taxonomic data.

Method Summary

Modifier and Type	Method	Description
boolean	containsGenus(String genus)	Does the database contain at least one record that exactly matches specified genus?.
boolean	containsSpecies(String genus, String species)	Does the database contain at least one record that exactly matches specified genus and species?.
boolean	containsSubtaxa(String genus, String species, String subtaxa)	Does the database contain at least one record that exactly matches specified genus, species and subtaxa?.
List<String>	findSimilarGenus(String genus, int maxSize)	Return a list of genera close to the specified genus.
List<String>	findSimilarSpecies(String genus, String species, int maxSize)	Return a list of species close to the specified genus and species.
List<String>	findSimilarSubtaxa(String genus, String species, String subtaxa, int maxSize)	Suggest a list of subtaxa
List<IGrinSpecies>	findSpeciesRow(String genus, String species, String subtaxa)	Find SpeciesRows matching the definition
String	getGenus(long genusId)	Get genus by genusId
String	getSpeciesAuthority(String genus, String species)	Return the species authority for the specified species within genus.
IGrinSpecies	getSpeciesRow(long speciesId)	Get species by speciesId
String	getSubtaxaAuthority(String genus, String species, String subtaxa)	Return the authority for the specified subtaxa
List<IGrinSpecies>	listSpecies(String genus, String species, int maxSize)	Return all subtaxa for genus and species
double	similarityScore(String string1, String string2)	Get string similarity score.

Method Detail

containsGenus

boolean containsGenus(String genus)

Does the database contain at least one record that exactly matches specified genus?.

Parameters:

genus - the genus

Returns:

true if there is at least one record

findSimilarGenus

List<String> findSimilarGenus(String genus,
                              int maxSize)

Return a list of genera close to the specified genus.

Parameters:

genus - genus

maxSize - TODO

Returns:

list of suggestions, ordered by preference (best first), never null.

containsSpecies

boolean containsSpecies(String genus,
                        String species)

Does the database contain at least one record that exactly matches specified genus and species?.

Parameters:

genus - the genus

species - the species

Returns:

true if there is at least one record

findSimilarSpecies

List<String> findSimilarSpecies(String genus,
                                String species,
                                int maxSize)

Return a list of species close to the specified genus and species.

Parameters:

genus - valid genus

species - species

maxSize - maximum number of suggestions to return

Returns:

list of suggestions, ordered by preference (best first), never null.

getSpeciesAuthority

String getSpeciesAuthority(String genus,
                           String species)

Return the species authority for the specified species within genus.

Parameters:

genus - the genus

species - the species

Returns:

the authority or null

containsSubtaxa

boolean containsSubtaxa(String genus,
                        String species,
                        String subtaxa)

Does the database contain at least one record that exactly matches specified genus, species and subtaxa?.

Parameters:

genus - valid genus

species - valid species

subtaxa - subtaxa to check

Returns:

true if there is at least one record

findSimilarSubtaxa

List<String> findSimilarSubtaxa(String genus,
                                String species,
                                String subtaxa,
                                int maxSize)

Suggest a list of subtaxa

Parameters:

genus - valid genus

species - valid species

subtaxa - current subtaxa

maxSize - maximum number of suggestions to return

Returns:

list of suggestions, ordered by preference, never null

getSubtaxaAuthority

String getSubtaxaAuthority(String genus,
                           String species,
                           String subtaxa)

Return the authority for the specified subtaxa

Parameters:

genus - the genus

species - the species

subtaxa - subtaxa

Returns:

the authority or null

listSpecies

List<IGrinSpecies> listSpecies(String genus,
                               String species,
                               int maxSize)

Return all subtaxa for genus and species

Parameters:

genus - valid genus

species - valid species

maxSize - maximum number of rows to return

Returns:

list of species matching genus and species name

findSpeciesRow

List<IGrinSpecies> findSpeciesRow(String genus,
                                  String species,
                                  String subtaxa)

Find SpeciesRows matching the definition

Parameters:

genus - the genus

species - the species

subtaxa - the MCPD subtaxa

Returns:

list of matching SpeciesRows

getSpeciesRow

IGrinSpecies getSpeciesRow(long speciesId)

Get species by speciesId

Parameters:

speciesId - duh

Returns:

SpeciesRow or null if not found

getGenus

String getGenus(long genusId)

Get genus by genusId

Parameters:

genusId - duh

Returns:

genus name or null

similarityScore

double similarityScore(String string1,
                       String string2)

Get string similarity score.

Parameters:

string1 - the string 1

string2 - the string 2

Returns:

the double