Package org.genesys.taxonomy.checker

Class InMemoryTaxonomyDatabase

java.lang.Object

org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

All Implemented Interfaces:

TaxonomyDatabase

Direct Known Subclasses:

CachingInMemoryTaxonomyDatabase

public class InMemoryTaxonomyDatabase
extends Object
implements TaxonomyDatabase

List based in-memory "database". NOT THREAD-SAFE!

Field Summary

Fields

Modifier and Type	Field	Description
static double	NONMATCH_MARGIN

Constructor Summary

Constructors

Constructor	Description
InMemoryTaxonomyDatabase()

Method Summary

Modifier and Type	Method	Description
boolean	containsGenus(String genus)	Case insensitive search for 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
protected List<IGrinSpecies>	getAllGenusSpecies(String genus)	Gets the all genus species.
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
static void	print(Object suggestion)	Prints the.
static <T> void	print(Suggestion<T> suggestion)	Prints the.
void	registerGenus(Long genusId, String genus)	Add a genus to the database.
void	registerSpecies(IGrinSpecies speciesRow)	Add species to the database.
double	similarityScore(String original, String candidate)	similarityScore returns a string similarity value in the range [0, 1.0] (where 1.0 is full match).
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

NONMATCH_MARGIN

public static final double NONMATCH_MARGIN

See Also:

Constant Field Values

Constructor Detail

InMemoryTaxonomyDatabase

public InMemoryTaxonomyDatabase()

Method Detail

registerGenus

public void registerGenus(Long genusId,
                          String genus)

Add a genus to the database.

Parameters:

genusId - the genus id

genus - the genus

registerSpecies

public void registerSpecies(IGrinSpecies speciesRow)
                     throws TaxonomyException

Add species to the database.

Parameters:

speciesRow - the species row

Throws:

TaxonomyException - the taxonomy exception

toString

public String toString()

Overrides:

toString in class Object

containsGenus

public boolean containsGenus(String genus)

Case insensitive search for genus.

Specified by:

containsGenus in interface TaxonomyDatabase

Parameters:

genus - the genus

Returns:

true, if successful

findSimilarGenus

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

Description copied from interface: TaxonomyDatabase

Return a list of genera close to the specified genus.

Specified by:

findSimilarGenus in interface TaxonomyDatabase

Parameters:

genus - genus

maxSize - TODO

Returns:

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

print

public static <T> void print(Suggestion<T> suggestion)

Prints the.

Type Parameters:

T - the generic type

Parameters:

suggestion - the suggestion

print

public static void print(Object suggestion)

Prints the.

Parameters:

suggestion - the suggestion

getAllGenusSpecies

protected List<IGrinSpecies> getAllGenusSpecies(String genus)

Gets the all genus species.

Parameters:

genus - the genus

Returns:

the all genus species

containsSpecies

public boolean containsSpecies(String genus,
                               String species)

Description copied from interface: TaxonomyDatabase

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

Specified by:

containsSpecies in interface TaxonomyDatabase

Parameters:

genus - the genus

species - the species

Returns:

true if there is at least one record

findSimilarSpecies

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

Description copied from interface: TaxonomyDatabase

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

Specified by:

findSimilarSpecies in interface TaxonomyDatabase

Parameters:

genus - valid genus

species - species

maxSize - maximum number of suggestions to return

Returns:

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

similarityScore

public double similarityScore(String original,
                              String candidate)

similarityScore returns a string similarity value in the range [0, 1.0] (where 1.0 is full match).

Specified by:

similarityScore in interface TaxonomyDatabase

Parameters:

original - the original

candidate - the candidate

Returns:

the score between 0 and 1.0 where 0 is no similarity and 1.0 is full match

getSpeciesAuthority

public String getSpeciesAuthority(String genus,
                                  String species)

Description copied from interface: TaxonomyDatabase

Return the species authority for the specified species within genus.

Specified by:

getSpeciesAuthority in interface TaxonomyDatabase

Parameters:

genus - the genus

species - the species

Returns:

the authority or null

containsSubtaxa

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

Description copied from interface: TaxonomyDatabase

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

Specified by:

containsSubtaxa in interface TaxonomyDatabase

Parameters:

genus - valid genus

species - valid species

subtaxa - subtaxa to check

Returns:

true if there is at least one record

findSimilarSubtaxa

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

Description copied from interface: TaxonomyDatabase

Suggest a list of subtaxa

Specified by:

findSimilarSubtaxa in interface TaxonomyDatabase

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

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

Description copied from interface: TaxonomyDatabase

Return the authority for the specified subtaxa

Specified by:

getSubtaxaAuthority in interface TaxonomyDatabase

Parameters:

genus - the genus

species - the species

subtaxa - subtaxa

Returns:

the authority or null

listSpecies

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

Description copied from interface: TaxonomyDatabase

Return all subtaxa for genus and species

Specified by:

listSpecies in interface TaxonomyDatabase

Parameters:

genus - valid genus

species - valid species

maxSize - maximum number of rows to return

Returns:

list of species matching genus and species name

findSpeciesRow

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

Description copied from interface: TaxonomyDatabase

Find SpeciesRows matching the definition

Specified by:

findSpeciesRow in interface TaxonomyDatabase

Parameters:

genus - the genus

species - the species

subtaxa - the MCPD subtaxa

Returns:

list of matching SpeciesRows

getSpeciesRow

public IGrinSpecies getSpeciesRow(long speciesId)

Description copied from interface: TaxonomyDatabase

Get species by speciesId

Specified by:

getSpeciesRow in interface TaxonomyDatabase

Parameters:

speciesId - duh

Returns:

SpeciesRow or null if not found

getGenus

public String getGenus(long genusId)

Description copied from interface: TaxonomyDatabase

Get genus by genusId

Specified by:

getGenus in interface TaxonomyDatabase

Parameters:

genusId - duh

Returns:

genus name or null