B C D F G I L M N O P R S T U

B

BestScore - Class in org.genesys.taxonomy.checker

BestScore helps keeping track with best scores during streaming operations.

BestScore() - Constructor for class org.genesys.taxonomy.checker.BestScore

C

containsGenus(String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

Case insensitive search for genus.

containsGenus(String) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

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

containsSpecies(String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

containsSpecies(String, String) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

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

containsSubtaxa(String, String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

containsSubtaxa(String, String, String) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

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

D

diceCoefficientOptimized(String, String) - Static method in class org.genesys.taxonomy.checker.StringSimilarity

Retrieved from https://en.wikibooks.org/wiki/Algorithm_Implementation/Strings/Dice's_coefficient#Java Here's an optimized version of the dice coefficient calculation.

F

findSimilarGenus(String, int) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

findSimilarGenus(String, int) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

Return a list of genera close to the specified genus.

findSimilarSpecies(String, String, int) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

findSimilarSpecies(String, String, int) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

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

findSimilarSubtaxa(String, String, String, int) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

findSimilarSubtaxa(String, String, String, int) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

Suggest a list of subtaxa

findSpeciesRow(String, String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

findSpeciesRow(String, String, String) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

Find SpeciesRows matching the definition

G

getAllGenusSpecies(String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

Gets the all genus species.

getBestScore() - Method in class org.genesys.taxonomy.checker.BestScore

Gets the best score.

getGenus(long) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

getGenus(long) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

Get genus by genusId

getLevenshteinCoefficient(String, String) - Static method in class org.genesys.taxonomy.checker.StringSimilarity

getMostFreqKSimilarity(String, String) - Static method in class org.genesys.taxonomy.checker.MostFrequentKChars

Calculate the similarity of the two hashes.

getMostFreqKSimilarity(int[], int[]) - Static method in class org.genesys.taxonomy.checker.MostFrequentKChars

Calculate the similarity of the two hashes.

getMostFrequentKHash(String, int) - Static method in class org.genesys.taxonomy.checker.MostFrequentKChars

Get the hash for an input string with at most K most frequent characters.

getScore() - Method in class org.genesys.taxonomy.checker.Suggestion

Gets the score.

getSpeciesAuthority(String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

getSpeciesAuthority(String, String) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker

Return species authority for the genus + species.

getSpeciesAuthority(String, String) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

Return the species authority for the specified species within genus.

getSpeciesRow(long) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

getSpeciesRow(long) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

Get species by speciesId

getSubtaxaAuthority(String, String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

getSubtaxaAuthority(String, String, String) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker

Return authority for the genus + species + subtaxa

getSubtaxaAuthority(String, String, String) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

Return the authority for the specified subtaxa

getSuggestion() - Method in class org.genesys.taxonomy.checker.Suggestion

Gets the suggestion.

I

InMemoryTaxonomyDatabase - Class in org.genesys.taxonomy.checker

List based in-memory "database".

InMemoryTaxonomyDatabase() - Constructor for class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

L

listSpecies(String, String, int) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

listSpecies(String, String, int) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

Return all subtaxa for genus and species

M

mostFreqKSDF(String, String, int, int) - Static method in class org.genesys.taxonomy.checker.MostFrequentKChars

Wrapper function.

mostFreqKSDF(String, String, int) - Static method in class org.genesys.taxonomy.checker.MostFrequentKChars

Most freq ksdf.

MostFrequentKChars - Class in org.genesys.taxonomy.checker

Based on pseudocode at https://en.wikipedia.org/wiki/Most_frequent_k_characters and http://rosettacode.org/wiki/Most_frequent_k_chars_distance Does not handle digits [0-9] for obvious reasons.

MostFrequentKChars() - Constructor for class org.genesys.taxonomy.checker.MostFrequentKChars

N

NONMATCH_MARGIN - Static variable in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

O

org.genesys.taxonomy.checker - package org.genesys.taxonomy.checker

P

print(Suggestion<T>) - Static method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

Prints the.

print(Object) - Static method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

Prints the.

R

registerGenus(Long, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

Add a genus to the database.

registerSpecies(SpeciesRow) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

Add species to the database.

S

setScore(double) - Method in class org.genesys.taxonomy.checker.Suggestion

Update the score

setTaxonomyDatabase(TaxonomyDatabase) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker

Sets the taxonomy database.

similarityScore(String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

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

similarityScore(String, String) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker

Get string similarity score

similarityScore(String, String) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

Get string similarity score

StringSimilarity - Class in org.genesys.taxonomy.checker

Code from https://en.wikibooks.org/wiki/Algorithm_Implementation/Strings/Dice's_coefficient#Java

StringSimilarity() - Constructor for class org.genesys.taxonomy.checker.StringSimilarity

suggestGenus(String, int) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker

Find suggestions for GENUS.

Suggestion<T> - Class in org.genesys.taxonomy.checker

The Class Suggestion.

suggestSpecies(String, String, int) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker

Find suggestions for SPECIES.

suggestSubtaxa(String, String, String, int) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker

Find suggestions for SUBTAXA.

T

TaxonomyChecker - Class in org.genesys.taxonomy.checker

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

TaxonomyChecker() - Constructor for class org.genesys.taxonomy.checker.TaxonomyChecker

TaxonomyDatabase - Interface in org.genesys.taxonomy.checker

Defines searches possible against a database of taxonomic data.

TaxonomyException - Exception in org.genesys.taxonomy.checker

The Class TaxonomyException.

TaxonomyException(String) - Constructor for exception org.genesys.taxonomy.checker.TaxonomyException

Instantiates a new taxonomy exception.

toHashString(int[]) - Static method in class org.genesys.taxonomy.checker.MostFrequentKChars

Encode a hash array to String.

toString() - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase

toString() - Method in class org.genesys.taxonomy.checker.Suggestion

U

update(double) - Method in class org.genesys.taxonomy.checker.BestScore

Update.

B C D F G I L M N O P R S T U