Index (taxonomy-checker 3.5 API)

B C D F G I L M N O P R S T U
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

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

CachingInMemoryTaxonomyDatabase - Class in org.genesys.taxonomy.checker: Guava cache supported in-memory taxonomy database.
CachingInMemoryTaxonomyDatabase() - Constructor for class org.genesys.taxonomy.checker.CachingInMemoryTaxonomyDatabase
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?.
containsSpecies(String, String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase
containsSpecies(String, 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?.
containsSubtaxa(String, String, String, String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase
containsSubtaxa(String, String, 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

findSimilar(String, String, String, String, String, int) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase
findSimilar(String, String, String, String, String, int) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker: Suggest a list of matches.
findSimilar(String, String, String, String, String, int) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase: Suggest a list of matches.
findSimilarGenera(String, int) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase: Find similar genera.
findSimilarGenus(String, int) - Method in class org.genesys.taxonomy.checker.CachingInMemoryTaxonomyDatabase: Find similar genus.
findSimilarGenus(String, int) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase: If genus is registered return empty list, otherwise search for similar genera.
findSimilarGenus(String, int) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase: Return a list of genera close to the specified genus.
findSimilarSpecies(String, String, String, int) - Method in class org.genesys.taxonomy.checker.CachingInMemoryTaxonomyDatabase: Find similar species.
findSimilarSpecies(String, String, String, int) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase
findSimilarSpecies(String, 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
findSimilarSubtaxa(String, String, String, String, String, int) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase
findSimilarSubtaxa(String, String, 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
findSpeciesRows(String, String, String, String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase
findSpeciesRows(String, String, String, String, String) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase: Find SpeciesRows matching the definition
findTaxa(String, String, String, String, String, int) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase
findTaxa(String, String, String, String, String, int) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker: Suggest a list of matches.
findTaxa(String, String, String, String, String, int) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase

G

getAllGenusSpecies(String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase: Get all species for one genus
getAllGenusSpecies(List<String>) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase: Gets the all species for specified genera.
getAllGenusSpecies(String) - Method in class org.genesys.taxonomy.checker.CachingInMemoryTaxonomyDatabase: 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: Get Levenshtein coefficient of two strings
getMostFreqKSimilarity(int[], int[]) - Static method in class org.genesys.taxonomy.checker.MostFrequentKChars: Calculate the similarity of the two hashes.
getMostFreqKSimilarity(String, String) - 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.
getSpeciesAuthority(String, String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase
getSpeciesAuthority(String, String, String) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker: Return species authority for the genus + species.
getSpeciesAuthority(String, 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 interface org.genesys.taxonomy.checker.TaxonomyDatabase: Return the authority for the specified subtaxa
getSubtaxaAuthority(String, String, String, String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase
getSubtaxaAuthority(String, String, String, String, String) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker: Return authority for the genus + species + subtaxa
getSubtaxaAuthority(String, String, 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.
getTaxon(String, String, String, String, String) - Method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase
getTaxon(String, String, String, String, String) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker: Get exact match.
getTaxon(String, String, String, String, String) - Method in interface org.genesys.taxonomy.checker.TaxonomyDatabase: Get exact match.

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) - Static method in class org.genesys.taxonomy.checker.MostFrequentKChars: Most freq ksdf.
mostFreqKSDF(String, String, int, int) - Static method in class org.genesys.taxonomy.checker.MostFrequentKChars: Wrapper function.
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: Percentage margin from best score.

O

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

P

print(Object) - Static method in class org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase: Prints the.
print(Suggestion<T>) - 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(IGrinSpecies) - 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.
suggestSpecies(String, 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.
suggestSubtaxa(String, String, String, String, String, int) - Method in class org.genesys.taxonomy.checker.TaxonomyChecker: Find suggestions for SUBTAXA.

T

Taxon() - Constructor for class org.genesys.taxonomy.checker.TaxonomyChecker.Taxon: Blank
Taxon(String, String, String, String, String) - Constructor for class org.genesys.taxonomy.checker.TaxonomyChecker.Taxon: Create Taxon from data.
Taxon(IGrinSpecies, Function<Long, IGrinSpecies>, Function<Long, String>) - Constructor for class org.genesys.taxonomy.checker.TaxonomyChecker.Taxon: Create Taxon from IGrinSpecies.
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
TaxonomyChecker.Taxon - Class in org.genesys.taxonomy.checker: Taxon record
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 best score.

B C D F G I L M N O P R S T U
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form