A C D E F G H I K L M N O P R S T U V W

A

addAdditionalName(String, String, String, LinnaeanRankClassification) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

afdFile - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

affPattern - Static variable in class au.org.ala.checklist.lucene.CBIndexSearch

alaConcepts - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

ALAParsedName<T> - Class in au.org.ala.data.model

Stores the extra information for an ALA Parsed Phrase name.

ALAParsedName() - Constructor for class au.org.ala.data.model.ALAParsedName

ALAParsedName(ParsedName<T>) - Constructor for class au.org.ala.data.model.ALAParsedName

alaSynonyms - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

apniFile - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

au.org.ala.checklist.lucene - package au.org.ala.checklist.lucene

au.org.ala.checklist.lucene.analyzer - package au.org.ala.checklist.lucene.analyzer

au.org.ala.checklist.lucene.model - package au.org.ala.checklist.lucene.model

au.org.ala.data.model - package au.org.ala.data.model

au.org.ala.data.util - package au.org.ala.data.util

authorship - Variable in class au.org.ala.data.model.LinnaeanRankClassification

C

CBCreateLuceneIndex - Class in au.org.ala.checklist.lucene

Creates the Lucene index based on the cb_names export generated by ChecklistBankExporter

CBCreateLuceneIndex() - Constructor for class au.org.ala.checklist.lucene.CBCreateLuceneIndex

CBCreateLuceneIndex.IndexField - Enum in au.org.ala.checklist.lucene

cbExportFile - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

CBIndexSearch - Class in au.org.ala.checklist.lucene

The API used to perform a search on the CB Lucene Index.

CBIndexSearch() - Constructor for class au.org.ala.checklist.lucene.CBIndexSearch

CBIndexSearch(String) - Constructor for class au.org.ala.checklist.lucene.CBIndexSearch

Creates a new name searcher.

cfPattern - Static variable in class au.org.ala.checklist.lucene.CBIndexSearch

cid - Variable in class au.org.ala.data.model.LinnaeanRankClassification

cleanPhrase - Variable in class au.org.ala.data.model.ALAParsedName

cleanVoucher - Variable in class au.org.ala.data.model.ALAParsedName

colFile - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

commit() - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

commit(boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

create(boolean, boolean, String, String, String, String, String) - Method in class au.org.ala.checklist.lucene.DwcaNameIndexer

Creates the name matching index based on a complete list of names supplied in a single DwCA

createALAIndexDocument(String, String, String, String, LinnaeanRankClassification) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

createALAIndexDocument(String, String, String, String, String, String, String, String, LinnaeanRankClassification) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

createALAIndexDocument(String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, float) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

createALASynonymDocument(String, String, String, String, String, String, String, float, String) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

createComponents(String, Reader) - Method in class au.org.ala.checklist.lucene.analyzer.LowerCaseKeywordAnalyzer

createIndex(String, String, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

Creates the index from the specified checklist bank names usage export file into the specified index directory.

createIndex(String, String, String, String, String, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

createIndexWriter(File, Analyzer, boolean) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

Creates an index writer in the specified directory.

createIrmngIndex(String, String) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

D

dataSource - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

deleteName(String) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

Deletes the entry that has the supplied lsid.

dumpSpecies() - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Dumps a list of the species LSID's that are contained in the index.

DwcaNameIndexer - Class in au.org.ala.checklist.lucene

Create a name index from a DWCA.

DwcaNameIndexer() - Constructor for class au.org.ala.checklist.lucene.DwcaNameIndexer

E

equals(Object) - Method in class au.org.ala.data.model.LinnaeanRankClassification

ErrorType - Enum in au.org.ala.checklist.lucene.model

The error type that occurred at a lower level in the match Only used for recursive matches.

errorType - Variable in exception au.org.ala.checklist.lucene.SearchResultException

ExcludedNameException - Exception in au.org.ala.checklist.lucene

An exception that is thrown when the match is to a name that has been excluded.

ExcludedNameException(String, NameSearchResult) - Constructor for exception au.org.ala.checklist.lucene.ExcludedNameException

ExcludedNameException(String, NameSearchResult, NameSearchResult) - Constructor for exception au.org.ala.checklist.lucene.ExcludedNameException

executeSqlScript(Connection, InputStream) - Static method in class org.gbif.checklistbank.utils.SqlUtils

extraALAConcepts - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

F

family - Variable in class au.org.ala.data.model.LinnaeanRankClassification

fid - Variable in class au.org.ala.data.model.LinnaeanRankClassification

FileUtils - Class in au.org.ala.data.util

FileUtils() - Constructor for class au.org.ala.data.util.FileUtils

G

genus - Variable in class au.org.ala.data.model.LinnaeanRankClassification

getAcceptedLsid() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

getAllRanksBelow(Integer) - Static method in enum au.org.ala.data.util.RankType

getAuthorship() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getBoost() - Method in enum au.org.ala.data.util.RankType

getChildResult() - Method in exception au.org.ala.checklist.lucene.ParentSynonymChildException

getCid() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getCleanName() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

getCommonNameDocument(String, String, String, float) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

getCommonNameDocument(String, String, String, float, boolean) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

getErrors() - Method in class au.org.ala.checklist.lucene.model.MetricsResultDTO

getErrors() - Method in exception au.org.ala.checklist.lucene.RecursiveSearchException

getErrorType() - Method in exception au.org.ala.checklist.lucene.SearchResultException

getExcludedName() - Method in exception au.org.ala.checklist.lucene.ExcludedNameException

getFamily() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getFid() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getForCBRank(Rank) - Static method in enum au.org.ala.data.util.RankType

getForId(Integer) - Static method in enum au.org.ala.data.util.RankType

getForName(String) - Static method in enum au.org.ala.data.util.RankType

getForStrRank(String) - Static method in enum au.org.ala.data.util.RankType

Gets the Rank Type for the supplied raw string...

getGenus() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getGid() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getId() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

getId() - Method in enum au.org.ala.checklist.lucene.model.SynonymType

getId() - Method in enum au.org.ala.data.util.RankType

getIndexDirectory() - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

getInfraspecificEpithet() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getIRMNGGenus(LinnaeanRankClassification, RankType) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Multiple genus indicate that an unresolved homonym exists for the supplied search details.

getKid() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getKingdom() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

getKingdom() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getKlass() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getLastException() - Method in class au.org.ala.checklist.lucene.model.MetricsResultDTO

getLeft() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

getLineIterator(InputStream, String) - Static method in class au.org.ala.data.util.FileUtils

getLocationPhraseDesciption() - Method in class au.org.ala.data.model.ALAParsedName

getLsid() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

Return the LSID for the result if it is not null otherwise return the id.

getLuceneSearchString(boolean) - Method in class au.org.ala.data.model.LinnaeanRankClassification

Returns the additional string that needs to be included in a search

getMatchedResult() - Method in exception au.org.ala.checklist.lucene.MisappliedException

getMatchType(String) - Method in enum au.org.ala.checklist.lucene.model.MatchType

getMatchType() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

getMisappliedResult() - Method in exception au.org.ala.checklist.lucene.MisappliedException

getNameType() - Method in class au.org.ala.checklist.lucene.model.MetricsResultDTO

getNameType() - Method in exception au.org.ala.checklist.lucene.RecursiveSearchException

getNonExcludedName() - Method in exception au.org.ala.checklist.lucene.ExcludedNameException

getOid() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getOrder() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getParentResult() - Method in exception au.org.ala.checklist.lucene.ParentSynonymChildException

getPhraseNominatingParty() - Method in class au.org.ala.data.model.ALAParsedName

getPhraseVoucher() - Method in class au.org.ala.data.model.ALAParsedName

getPhylum() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getPid() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getPrimaryLsid(String) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Returns the primary LSID for the supplied lsid.

getRank() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

getRank() - Method in enum au.org.ala.data.util.RankType

getRankClassification() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

getResult() - Method in class au.org.ala.checklist.lucene.model.MetricsResultDTO

getResults() - Method in exception au.org.ala.checklist.lucene.SearchResultException

getRight() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

getScientificName() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getSid() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getSpecies() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getSpecificEpithet() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getSubspecies() - Method in class au.org.ala.data.model.LinnaeanRankClassification

getSynonymLsid() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

Deprecated. Use NameSearchResult.getAcceptedLsid() instead

getSynonymType() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

getTypeFor(String) - Static method in enum au.org.ala.checklist.lucene.model.SynonymType

gid - Variable in class au.org.ala.data.model.LinnaeanRankClassification

H

hasBeenCleaned() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

hashCode() - Method in class au.org.ala.data.model.LinnaeanRankClassification

hasIdenticalClassification(LinnaeanRankClassification, RankType) - Method in class au.org.ala.data.model.LinnaeanRankClassification

checks to see if the non-null values of this classification are identical to the supplied classification This is used to determine whether classification match.

HomonymException - Exception in au.org.ala.checklist.lucene

Exception that is thrown when the result is an unresolved homonym

HomonymException(String, List<NameSearchResult>) - Constructor for exception au.org.ala.checklist.lucene.HomonymException

HomonymException(String) - Constructor for exception au.org.ala.checklist.lucene.HomonymException

HomonymException() - Constructor for exception au.org.ala.checklist.lucene.HomonymException

HomonymException(List<NameSearchResult>) - Constructor for exception au.org.ala.checklist.lucene.HomonymException

I

IGNORE_MARKERS - Static variable in class au.org.ala.data.util.PhraseNameParser

indexIrmngDwcA(IndexWriter, String) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

infraspecificEpithet - Variable in class au.org.ala.data.model.LinnaeanRankClassification

init() - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

initialOnePattern - Static variable in class au.org.ala.data.model.ALAParsedName

initialTwoPattern - Static variable in class au.org.ala.data.model.ALAParsedName

irmngDwcaDirectory - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

irmngFile - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

isHomonym() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

isSynonym() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

K

kid - Variable in class au.org.ala.data.model.LinnaeanRankClassification

kingdom - Variable in class au.org.ala.data.model.LinnaeanRankClassification

klass - Variable in class au.org.ala.data.model.LinnaeanRankClassification

L

lexFile - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

LinnaeanRankClassification - Class in au.org.ala.data.model

LinnaeanRankClassification() - Constructor for class au.org.ala.data.model.LinnaeanRankClassification

LinnaeanRankClassification(String, String, String, String, String, String, String, String, String, String, String) - Constructor for class au.org.ala.data.model.LinnaeanRankClassification

LinnaeanRankClassification(LinnaeanRankClassification) - Constructor for class au.org.ala.data.model.LinnaeanRankClassification

LinnaeanRankClassification(String, String, String, String, String, String, String) - Constructor for class au.org.ala.data.model.LinnaeanRankClassification

LinnaeanRankClassification(String, String) - Constructor for class au.org.ala.data.model.LinnaeanRankClassification

The constructor was added for convenience.

LOCATION_OR_DESCR - Static variable in class au.org.ala.data.util.PhraseNameParser

locationPhraseDescription - Variable in class au.org.ala.data.model.ALAParsedName

log - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

log - Variable in class au.org.ala.checklist.lucene.CBIndexSearch

log - Variable in class au.org.ala.checklist.lucene.DwcaNameIndexer

log - Static variable in class org.gbif.checklistbank.utils.SqlUtils

LowerCaseKeywordAnalyzer - Class in au.org.ala.checklist.lucene.analyzer

A custom KeywordAnalyzer that converts the text to lowercase before tokenizing the complete string as one token

LowerCaseKeywordAnalyzer() - Constructor for class au.org.ala.checklist.lucene.analyzer.LowerCaseKeywordAnalyzer

ltrim(String) - Static method in class au.org.ala.data.util.TaxonNameSoundEx

M

main(String[]) - Static method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

Generates the Lucene index required for the name matching API.

main(String[]) - Static method in class au.org.ala.checklist.lucene.DwcaNameIndexer

main(String[]) - Static method in class au.org.ala.data.model.ALAParsedName

main(String[]) - Static method in class au.org.ala.data.model.LinnaeanRankClassification

main(String[]) - Static method in class au.org.ala.data.util.PhraseNameParser

MatchType - Enum in au.org.ala.checklist.lucene.model

MetricsResultDTO - Class in au.org.ala.checklist.lucene.model

Stores the data the data that makes up a name match includes metrics such as name types and errors Allows a metrics to be returned even when a match is not found.

MetricsResultDTO() - Constructor for class au.org.ala.checklist.lucene.model.MetricsResultDTO

MisappliedException - Exception in au.org.ala.checklist.lucene

Indicates that the matched name has been misapplied in the past.

MisappliedException(NameSearchResult) - Constructor for exception au.org.ala.checklist.lucene.MisappliedException

Constructor to use of the first result is misapplied.

MisappliedException(NameSearchResult, NameSearchResult) - Constructor for exception au.org.ala.checklist.lucene.MisappliedException

Constructor to use if the first result is accepted and second result is a misapplied synonym

multipleSpaces - Static variable in class au.org.ala.data.model.ALAParsedName

N

NameIndexField - Enum in au.org.ala.checklist.lucene

An Enum for all the fields that are indexed for the name matching

NameSearchResult - Class in au.org.ala.checklist.lucene.model

A model to store the required information in a search result This includes the type of match that was used to get the result

NameSearchResult(String, String, MatchType) - Constructor for class au.org.ala.checklist.lucene.model.NameSearchResult

NameSearchResult(Document, MatchType) - Constructor for class au.org.ala.checklist.lucene.model.NameSearchResult

normalize(String) - Static method in class au.org.ala.data.util.TaxonNameSoundEx

O

oid - Variable in class au.org.ala.data.model.LinnaeanRankClassification

order - Variable in class au.org.ala.data.model.LinnaeanRankClassification

org.gbif.checklistbank.utils - package org.gbif.checklistbank.utils

P

ParentSynonymChildException - Exception in au.org.ala.checklist.lucene

An exception that is thrown when the result represents a situation where the parent is a synonym of the child concept.

ParentSynonymChildException(NameSearchResult, NameSearchResult) - Constructor for exception au.org.ala.checklist.lucene.ParentSynonymChildException

parse(String) - Method in class au.org.ala.data.util.PhraseNameParser

PHRASE - Static variable in class au.org.ala.data.util.PhraseNameParser

PHRASE_PATTERN - Static variable in class au.org.ala.data.util.PhraseNameParser

PHRASE_RANKS - Static variable in class au.org.ala.data.util.PhraseNameParser

phraseBlacklist - Static variable in class au.org.ala.data.model.ALAParsedName

PhraseNameParser - Class in au.org.ala.data.util

A Parser that can be used to parse a "Phrase" name.

PhraseNameParser() - Constructor for class au.org.ala.data.util.PhraseNameParser

phraseNominatingParty - Variable in class au.org.ala.data.model.ALAParsedName

phrasePunctuationRemoval - Static variable in class au.org.ala.data.model.ALAParsedName

phraseVoucher - Variable in class au.org.ala.data.model.ALAParsedName

phylum - Variable in class au.org.ala.data.model.LinnaeanRankClassification

pid - Variable in class au.org.ala.data.model.LinnaeanRankClassification

POTENTIAL_SPECIES_PATTERN - Static variable in class au.org.ala.data.util.PhraseNameParser

potentialVoucherId - Static variable in class au.org.ala.data.model.ALAParsedName

R

RANK_MARKER - Static variable in class au.org.ala.data.util.PhraseNameParser

RankType - Enum in au.org.ala.data.util

An enumeration of the rank types available in ALA.

RecursiveSearchException - Exception in au.org.ala.checklist.lucene

Represents an exception that occurs during a recursive match.

RecursiveSearchException(Set<ErrorType>, NameType) - Constructor for exception au.org.ala.checklist.lucene.RecursiveSearchException

reopenReaders() - Method in class au.org.ala.checklist.lucene.CBIndexSearch

resolveIRMNGHomonym(LinnaeanRankClassification, RankType) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Attempt to resolve the homonym using the IRMNG index.

results - Variable in exception au.org.ala.checklist.lucene.SearchResultException

rtrim(String) - Static method in class au.org.ala.data.util.TaxonNameSoundEx

S

scientificName - Variable in class au.org.ala.data.model.LinnaeanRankClassification

searchForAcceptedLsidDefaultHandling(LinnaeanRankClassification, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Returns the accepted LSID for the supplied classification.

searchForAcceptedLsidDefaultHandling(LinnaeanRankClassification, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

searchForAcceptedRecordDefaultHandling(LinnaeanRankClassification, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Returns the accepted result for the supplied classification.

searchForAcceptedRecordDefaultHandling(LinnaeanRankClassification, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

searchForCommonName(String) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Performs a search on the supplied common name returning a NameSearchResult.

searchForLSID(String, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches the index for the supplied name with or without fuzzy name matching.

searchForLSID(String, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

searchForLSID(String) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches for the name without using fuzzy name matching...

searchForLSID(String, RankType, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches the index for the supplied name of the specified rank with or without fuzzy name matching.

searchForLSID(String, RankType, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches for the supplied name of the specified rank with or without fuzzy name matching.

searchForLSID(String, RankType) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches for an LSID of the supplied name and rank without a fuzzy match...

searchForLSID(String, String, String, RankType) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Deprecated. Use #searchForLSID(java.lang.String, au.org.ala.data.model.LinnaeanRankClassification, au.org.ala.data.util.RankType, boolean) instead. It is more extensible to supply a classification object then a list of higher classification

searchForLSID(String, LinnaeanRankClassification, RankType, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Search for an LSID based on the supplied name, classification and rank with or without fuzzy name matching.

searchForLSID(LinnaeanRankClassification, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Search for an LSID with the supplied classification without a fuzzy match.

searchForLSID(String, LinnaeanRankClassification, RankType) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Search for an LSID based on suppled name, classification and rank without a fuzzy match...

searchForLsidById(String) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Gets the LSID for the record that has the supplied checklist bank id.

searchForLSIDCommonName(String) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Performs a search on the common name index for the supplied name.

searchForRecord(LinnaeanRankClassification, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

searchForRecord(LinnaeanRankClassification, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

searchForRecord(LinnaeanRankClassification, boolean, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Search for an LSID with the supplied classification without a fuzzy match.

searchForRecord(String, RankType, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches the index for the supplied name of the specified rank.

searchForRecord(String, RankType) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches index for the supplied name and rank without a fuzzy match.

searchForRecord(String, String, String, RankType) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Deprecated. Use CBIndexSearch.searchForRecord(java.lang.String, au.org.ala.data.model.LinnaeanRankClassification, au.org.ala.data.util.RankType, boolean) instead. It is more extensible to supply a classification object then a list of higher classification

searchForRecord(String, LinnaeanRankClassification, RankType, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

searchForRecord(String, LinnaeanRankClassification, RankType, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches for a record based on the supplied name, rank and classification with or without fuzzy name matching.

searchForRecord(String, LinnaeanRankClassification, RankType) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches for a record based on the supplied name, classification and rank without fuzzy name matching

searchForRecordByID(String) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Returns the records that has the supplied checklist bank id

searchForRecordByLsid(String) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

searchForRecordMetrics(LinnaeanRankClassification, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

searchForRecordMetrics(LinnaeanRankClassification, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

searchForRecordMetrics(LinnaeanRankClassification, boolean, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Search for a specific name returning extra metrics that can be reported as name match quality...

searchForRecordMetrics(LinnaeanRankClassification, boolean, boolean, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

searchForRecords(String, RankType, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches for records with the specified name and rank with or without fuzzy name matching

searchForRecords(String, RankType, LinnaeanRankClassification, int) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches for a list of results for the supplied name, classification and rank without fuzzy match

searchForRecords(String, RankType, LinnaeanRankClassification, int, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Searches for the records that satisfy the given conditions using the algorithm outlined in the class description.

searchForRecords(String, RankType, LinnaeanRankClassification, int, boolean, boolean) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

SearchResultException - Exception in au.org.ala.checklist.lucene

SearchResultException(String) - Constructor for exception au.org.ala.checklist.lucene.SearchResultException

SearchResultException(String, List<NameSearchResult>) - Constructor for exception au.org.ala.checklist.lucene.SearchResultException

setAuthorship(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setCid(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setCleanName(String) - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

setErrors(Set<ErrorType>) - Method in class au.org.ala.checklist.lucene.model.MetricsResultDTO

setExcludedName(NameSearchResult) - Method in exception au.org.ala.checklist.lucene.ExcludedNameException

setFamily(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setFid(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setGenus(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setGid(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setIndexDirectory(String) - Method in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

setInfraspecificEpithet(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setKid(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setKingdom(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setKlass(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setLastException(SearchResultException) - Method in class au.org.ala.checklist.lucene.model.MetricsResultDTO

setLeft(String) - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

setLocationPhraseDescription(String) - Method in class au.org.ala.data.model.ALAParsedName

setMatchedResult(NameSearchResult) - Method in exception au.org.ala.checklist.lucene.MisappliedException

setMatchType(MatchType) - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

setMisappliedResult(NameSearchResult) - Method in exception au.org.ala.checklist.lucene.MisappliedException

setNameType(NameType) - Method in class au.org.ala.checklist.lucene.model.MetricsResultDTO

setNonExcludedName(NameSearchResult) - Method in exception au.org.ala.checklist.lucene.ExcludedNameException

setOid(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setOrder(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setPhraseNominatingParty(String) - Method in class au.org.ala.data.model.ALAParsedName

setPhraseVoucher(String) - Method in class au.org.ala.data.model.ALAParsedName

setPhylum(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setPid(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setRank(RankType) - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

setResult(NameSearchResult) - Method in class au.org.ala.checklist.lucene.model.MetricsResultDTO

setResults(List<NameSearchResult>) - Method in exception au.org.ala.checklist.lucene.HomonymException

setRight(String) - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

setScientificName(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setSid(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setSpecies(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setSpecificEpithet(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

setSubspecies(String) - Method in class au.org.ala.data.model.LinnaeanRankClassification

sid - Variable in class au.org.ala.data.model.LinnaeanRankClassification

soundEx(String) - Method in class au.org.ala.data.util.TaxonNameSoundEx

Returns the SoundEx for the source string

SOURCE_AUTHORITY - Static variable in class au.org.ala.data.util.PhraseNameParser

species - Variable in class au.org.ala.data.model.LinnaeanRankClassification

SPECIES_PATTERN - Static variable in class au.org.ala.data.util.PhraseNameParser

specificEpithet - Variable in class au.org.ala.data.model.LinnaeanRankClassification

SPPException - Exception in au.org.ala.checklist.lucene

The exception to be thrown when a Genus spp.

SPPException() - Constructor for exception au.org.ala.checklist.lucene.SPPException

SqlUtils - Class in org.gbif.checklistbank.utils

Copied this class from Checklist bank code to remove some of the dependencies.

SqlUtils() - Constructor for class org.gbif.checklistbank.utils.SqlUtils

streamToSet(InputStream, Set<String>, boolean) - Static method in class au.org.ala.data.util.FileUtils

subspecies - Variable in class au.org.ala.data.model.LinnaeanRankClassification

SynonymType - Enum in au.org.ala.checklist.lucene.model

Stores the Synonym type information TODO: Get a correct description for the synonym types.

T

taxonConeptName - Variable in class au.org.ala.checklist.lucene.CBCreateLuceneIndex

TaxonNameSoundEx - Class in au.org.ala.data.util

A Java implementation of the sound ex algorithm supplied by Tony Rees

TaxonNameSoundEx() - Constructor for class au.org.ala.data.util.TaxonNameSoundEx

testParse(String) - Method in class au.org.ala.data.util.PhraseNameParser

tnse - Variable in class au.org.ala.checklist.lucene.CBIndexSearch

toCSV(char) - Method in class au.org.ala.data.model.LinnaeanRankClassification

toString() - Method in enum au.org.ala.checklist.lucene.CBCreateLuceneIndex.IndexField

toString() - Method in enum au.org.ala.checklist.lucene.model.ErrorType

toString() - Method in enum au.org.ala.checklist.lucene.model.MatchType

toString() - Method in class au.org.ala.checklist.lucene.model.NameSearchResult

toString() - Method in enum au.org.ala.checklist.lucene.NameIndexField

toString() - Method in class au.org.ala.data.model.LinnaeanRankClassification

treatWord(String, String) - Static method in class au.org.ala.data.util.TaxonNameSoundEx

U

updateClassificationWithGUID(LinnaeanRankClassification) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Updates the supplied classification so that the supplied ID's are substituted with GUIDs.

V

VALID_PHRASE_RANKS - Static variable in class au.org.ala.data.util.PhraseNameParser

validateHomonymByAuthor(List<NameSearchResult>, String, LinnaeanRankClassification) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

validateHomonyms(List<NameSearchResult>, String, LinnaeanRankClassification) - Method in class au.org.ala.checklist.lucene.CBIndexSearch

Takes a result set that contains a homonym and then either throws a HomonymException or returns the first result that matches the supplied taxa.

valueOf(String) - Static method in enum au.org.ala.checklist.lucene.CBCreateLuceneIndex.IndexField

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum au.org.ala.checklist.lucene.model.ErrorType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum au.org.ala.checklist.lucene.model.MatchType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum au.org.ala.checklist.lucene.model.SynonymType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum au.org.ala.checklist.lucene.NameIndexField

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum au.org.ala.data.util.RankType

Returns the enum constant of this type with the specified name.

values() - Static method in enum au.org.ala.checklist.lucene.CBCreateLuceneIndex.IndexField

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum au.org.ala.checklist.lucene.model.ErrorType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum au.org.ala.checklist.lucene.model.MatchType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum au.org.ala.checklist.lucene.model.SynonymType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum au.org.ala.checklist.lucene.NameIndexField

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum au.org.ala.data.util.RankType

Returns an array containing the constants of this enum type, in the order they are declared.

virusStopPattern - Static variable in class au.org.ala.checklist.lucene.CBIndexSearch

VOUCHER - Static variable in class au.org.ala.data.util.PhraseNameParser

voucherBlacklist - Static variable in class au.org.ala.data.model.ALAParsedName

voucherRemovePattern - Static variable in class au.org.ala.checklist.lucene.CBIndexSearch

voucherRemovePattern - Static variable in class au.org.ala.data.model.ALAParsedName

W

WRONG_CASE_INFRAGENERIC - Static variable in class au.org.ala.data.util.PhraseNameParser

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