Package org.genesys.taxonomy.checker

Class TaxonomyChecker

java.lang.Object

org.genesys.taxonomy.checker.TaxonomyChecker

public class TaxonomyChecker
extends Object

Suggest fixes to scientific names based on an in-memory list of valid taxonomies.

Constructor Summary

Constructors

Constructor	Description
TaxonomyChecker()

Method Summary

Modifier and Type	Method	Description
String	getSpeciesAuthority(String genus, String species)	Return species authority for the genus + species.
String	getSubtaxaAuthority(String genus, String species, String subtaxa)	Return authority for the genus + species + subtaxa
void	setTaxonomyDatabase(TaxonomyDatabase database)	Sets the taxonomy database.
double	similarityScore(String string1, String string2)	Get string similarity score.
List<String>	suggestGenus(String genus, int maxSize)	Find suggestions for GENUS.
List<String>	suggestSpecies(String genus, String species, int maxSize)	Find suggestions for SPECIES.
List<String>	suggestSubtaxa(String genus, String species, String subtaxa, int maxSize)	Find suggestions for SUBTAXA.

Methods inherited from class java.lang.Object

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

Constructor Detail

TaxonomyChecker

public TaxonomyChecker()

Method Detail

setTaxonomyDatabase

public void setTaxonomyDatabase(TaxonomyDatabase database)

Sets the taxonomy database.

Parameters:

database - the new taxonomy database

suggestGenus

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

Find suggestions for GENUS.

Parameters:

genus - the genus

maxSize - the max size

Returns:

suggested fixes for genus or empty list when genus is fine or when there are no suggestions.

suggestSpecies

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

Find suggestions for SPECIES.

Parameters:

genus - the genus

species - the species

maxSize - maximum number of suggestions to return

Returns:

suggested fixes for genus or empty list if species is fine or when there are no suggestions.

getSpeciesAuthority

public String getSpeciesAuthority(String genus,
                                  String species)

Return species authority for the genus + species.

Parameters:

genus - the genus

species - the species

Returns:

species authority if there's one matching record in the database

suggestSubtaxa

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

Find suggestions for SUBTAXA.

Parameters:

genus - must be valid genus in the database

species - species must be valid species within genus

subtaxa - current subtaxa, must not be null or blank

maxSize - maximum number of suggestions to return

Returns:

suggested fixes for subtaxa or empty list if there are no suggestions.

getSubtaxaAuthority

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

Return authority for the genus + species + subtaxa

Parameters:

genus - the genus

species - the species

subtaxa - subtaxa

Returns:

species authority if there's one matching record in the database

similarityScore

public double similarityScore(String string1,
                              String string2)

Get string similarity score.

Parameters:

string1 - string A

string2 - string B

Returns:

the double