B C F G I O P R S T U

B

BestScore - Class in org.genesys2.gringlobal.taxonomy.component

BestScore helps keeping track with best scores during streaming operations.

BestScore() - Constructor for class org.genesys2.gringlobal.taxonomy.component.BestScore

C

containsGenus(String) - Method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

Case insensitive search for genus.

containsGenus(String) - Method in interface org.genesys2.gringlobal.taxonomy.component.TaxonomyDatabase

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

containsSpecies(String, String) - Method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

containsSpecies(String, String) - Method in interface org.genesys2.gringlobal.taxonomy.component.TaxonomyDatabase

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

F

findSimilarGenus(String, int) - Method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

findSimilarGenus(String, int) - Method in interface org.genesys2.gringlobal.taxonomy.component.TaxonomyDatabase

Return a list of genera close to the specified genus.

findSimilarSpecies(String, String, int) - Method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

findSimilarSpecies(String, String, int) - Method in interface org.genesys2.gringlobal.taxonomy.component.TaxonomyDatabase

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

G

GenusRow - Class in org.genesys2.gringlobal.taxonomy.model

"TAXONOMY_GENUS_ID", "CURRENT_TAXONOMY_GENUS_ID", "TAXONOMY_FAMILY_ID", "QUALIFYING_CODE", "IS_HYBRID", "GENUS_NAME", "GENUS_AUTHORITY", "SUBGENUS_NAME", "SECTION_NAME", "SUBSECTION_NAME", "SERIES_NAME", "SUBSERIES_NAME", "NOTE", "CREATED_DATE", "CREATED_BY", "MODIFIED_DATE", "MODIFIED_BY", "OWNED_DATE", "OWNED_BY" TODO Upgrade to opencsv 3.8 with @CsvDate annotation when available

GenusRow() - Constructor for class org.genesys2.gringlobal.taxonomy.model.GenusRow

getAllGenusSpecies(String) - Method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

Gets the all genus species.

getAlternateName() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the alternate name.

getBestScore() - Method in class org.genesys2.gringlobal.taxonomy.component.BestScore

Gets the best score.

getCommonFertilizationCode() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the common fertilization code.

getCreatedById() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the created by id.

getCreatedById() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the created by id.

getCreatedDate() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the created date.

getCreatedDate() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the created date.

getCurator1Id() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the curator1 id.

getCurator2Id() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the curator2 id.

getCurrentGenusId() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the current genus id.

getCurrentSpeciesId() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the current species id.

getFamilyId() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the family id.

getFormaAuthority() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the forma authority.

getFormaHybrid() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the forma hybrid.

getFormaName() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the forma name.

getFormaRankType() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the forma rank type.

getGenusAuthority() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the genus authority.

getGenusId() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the genus id.

getGenusId() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the genus id.

getGenusName() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the genus name.

getHybrid() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the hybrid.

getLifeFormCode() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the life form code.

getModifiedById() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the modified by id.

getModifiedById() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the modified by id.

getModifiedDate() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the modified date.

getModifiedDate() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the modified date.

getName() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the full scientific name.

getNameAuthority() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the name authority.

getNamePending() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the name pending.

getNameVerifiedDate() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the name verified date.

getNomenNumber() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the nomen number.

getNote() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the note.

getNote() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the note.

getOwnedById() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the owned by id.

getOwnedById() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the owned by id.

getOwnedDate() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the owned date.

getOwnedDate() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the owned date.

getPrioritySite1() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the priority site1.

getPrioritySite2() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the priority site2.

getProtologue() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the protologue.

getQualifyingCode() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the qualifying code.

getRestrictionCode() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the restriction code.

getScore() - Method in class org.genesys2.gringlobal.taxonomy.component.Suggestion

Gets the score.

getSectionName() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the section name.

getSeriesName() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the series name.

getSiteNote() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the site note.

getSpeciesAuthority(String, String) - Method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

getSpeciesAuthority(String, String) - Method in class org.genesys2.gringlobal.taxonomy.component.TaxonomyChecker

Return species authority for the genus + species.

getSpeciesAuthority(String, String) - Method in interface org.genesys2.gringlobal.taxonomy.component.TaxonomyDatabase

Return the species authority for the specified species within genus.

getSpeciesAuthority() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the species authority.

getSpeciesId() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the species id.

getSpeciesName() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the species name.

getSpecificHybrid() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the specific hybrid.

getSubGenusName() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the sub genus name.

getSubSectionName() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the sub section name.

getSubSeriesName() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Gets the sub series name.

getSubspeciesAuthority() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the subspecies authority.

getSubspeciesName() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the subspecies name.

getSubspecificHybrid() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the subspecific hybrid.

getSubvarietalHybrid() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the subvarietal hybrid.

getSubvarietyAuthority() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the subvariety authority.

getSubvarietyName() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the subvariety name.

getSuggestion() - Method in class org.genesys2.gringlobal.taxonomy.component.Suggestion

Gets the suggestion.

getSynonymCode() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the synonym code.

getVarietalHybrid() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the varietal hybrid.

getVarietyAuthority() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the variety authority.

getVarietyName() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the variety name.

getVerifierId() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Gets the verifier id.

I

InMemoryTaxonomyDatabase - Class in org.genesys2.gringlobal.taxonomy.component

List based in-memory "database".

InMemoryTaxonomyDatabase() - Constructor for class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

isCurrent() - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Is this genus record still current?.

isCurrent() - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Is this record still current?.

O

openCsvReader(Reader, int) - Static method in class org.genesys2.gringlobal.taxonomy.component.TaxonomyReader

Returns a CSVReader that properly handles GRIN-Global taxonomy files in CSV format.

org.genesys2.gringlobal.taxonomy.component - package org.genesys2.gringlobal.taxonomy.component

org.genesys2.gringlobal.taxonomy.model - package org.genesys2.gringlobal.taxonomy.model

P

print(Suggestion<T>) - Static method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

Prints the.

print(Object) - Static method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

Prints the.

R

registerGenus(Long, String) - Method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

Add a genus to the database.

registerSpecies(SpeciesRow) - Method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

Add species to the database.

S

setAlternateName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the alternate name.

setCommonFertilizationCode(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the common fertilization code.

setCreatedById(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the created by id.

setCreatedById(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the created by id.

setCreatedDate(Date) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the created date.

setCreatedDate(Date) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the created date.

setCurator1Id(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the curator1 id.

setCurator2Id(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the curator2 id.

setCurrentGenusId(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the current genus id.

setCurrentSpeciesId(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the current species id.

setFamilyId(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the family id.

setFormaAuthority(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the forma authority.

setFormaHybrid(Boolean) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the forma hybrid.

setFormaName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the forma name.

setFormaRankType(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the forma rank type.

setGenusAuthority(String) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the genus authority.

setGenusId(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the genus id.

setGenusId(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the genus id.

setGenusName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the genus name.

setHybrid(Boolean) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the hybrid.

setLifeFormCode(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the life form code.

setModifiedById(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the modified by id.

setModifiedById(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the modified by id.

setModifiedDate(Date) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the modified date.

setModifiedDate(Date) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the modified date.

setName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the name.

setNameAuthority(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the name authority.

setNamePending(Boolean) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the name pending.

setNameVerifiedDate(Date) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the name verified date.

setNomenNumber(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the nomen number.

setNote(String) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the note.

setNote(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the note.

setOwnedById(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the owned by id.

setOwnedById(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the owned by id.

setOwnedDate(Date) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the owned date.

setOwnedDate(Date) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the owned date.

setPrioritySite1(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the priority site1.

setPrioritySite2(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the priority site2.

setProtologue(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the protologue.

setQualifyingCode(String) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the qualifying code.

setRestrictionCode(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the restriction code.

setSectionName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the section name.

setSeriesName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the series name.

setSiteNote(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the site note.

setSpeciesAuthority(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the species authority.

setSpeciesId(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the species id.

setSpeciesName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the species name.

setSpecificHybrid(Boolean) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the specific hybrid.

setSubGenusName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the sub genus name.

setSubSectionName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the sub section name.

setSubSeriesName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.GenusRow

Sets the sub series name.

setSubspeciesAuthority(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the subspecies authority.

setSubspeciesName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the subspecies name.

setSubspecificHybrid(Boolean) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the subspecific hybrid.

setSubvarietalHybrid(Boolean) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the subvarietal hybrid.

setSubvarietyAuthority(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the subvariety authority.

setSubvarietyName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the subvariety name.

setSynonymCode(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the synonym code.

setTaxonomyDatabase(TaxonomyDatabase) - Method in class org.genesys2.gringlobal.taxonomy.component.TaxonomyChecker

Sets the taxonomy database.

setVarietalHybrid(Boolean) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the varietal hybrid.

setVarietyAuthority(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the variety authority.

setVarietyName(String) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the variety name.

setVerifierId(Long) - Method in class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

Sets the verifier id.

SpeciesRow - Class in org.genesys2.gringlobal.taxonomy.model

"TAXONOMY_SPECIES_ID", "CURRENT_TAXONOMY_SPECIES_ID", "NOMEN_NUMBER", "IS_SPECIFIC_HYBRID", "SPECIES_NAME", "SPECIES_AUTHORITY", "IS_SUBSPECIFIC_HYBRID", "SUBSPECIES_NAME", "SUBSPECIES_AUTHORITY", "IS_VARIETAL_HYBRID", "VARIETY_NAME", "VARIETY_AUTHORITY", "IS_SUBVARIETAL_HYBRID", "SUBVARIETY_NAME", "SUBVARIETY_AUTHORITY", "IS_FORMA_HYBRID", "FORMA_RANK_TYPE", "FORMA_NAME", "FORMA_AUTHORITY", "TAXONOMY_GENUS_ID", "PRIORITY1_SITE_ID", "PRIORITY2_SITE_ID", "CURATOR1_COOPERATOR_ID", "CURATOR2_COOPERATOR_ID", "RESTRICTION_CODE", "LIFE_FORM_CODE", "COMMON_FERTILIZATION_CODE", "IS_NAME_PENDING", "SYNONYM_CODE", "VERIFIER_COOPERATOR_ID", "NAME_VERIFIED_DATE", "NAME", "NAME_AUTHORITY", "PROTOLOGUE", "NOTE", "SITE_NOTE", "ALTERNATE_NAME", "CREATED_DATE", "CREATED_BY", "MODIFIED_DATE", "MODIFIED_BY", "OWNED_DATE", "OWNED_BY" TODO Upgrade to opencsv 3.8 with @CsvDate annotation when available

SpeciesRow() - Constructor for class org.genesys2.gringlobal.taxonomy.model.SpeciesRow

suggestGenus(String, int) - Method in class org.genesys2.gringlobal.taxonomy.component.TaxonomyChecker

Find suggestions for GENUS.

Suggestion<T> - Class in org.genesys2.gringlobal.taxonomy.component

The Class Suggestion.

suggestSpecies(String, String, int) - Method in class org.genesys2.gringlobal.taxonomy.component.TaxonomyChecker

Find suggestions for SPECIES.

T

TaxonomyChecker - Class in org.genesys2.gringlobal.taxonomy.component

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

TaxonomyChecker() - Constructor for class org.genesys2.gringlobal.taxonomy.component.TaxonomyChecker

TaxonomyDatabase - Interface in org.genesys2.gringlobal.taxonomy.component

Defines searches possible against a database of taxonomic data.

TaxonomyException - Exception in org.genesys2.gringlobal.taxonomy.component

The Class TaxonomyException.

TaxonomyException(String) - Constructor for exception org.genesys2.gringlobal.taxonomy.component.TaxonomyException

Instantiates a new taxonomy exception.

TaxonomyReader - Class in org.genesys2.gringlobal.taxonomy.component

The CSV file reader for GRIN-Global taxonomy.

TaxonomyReader() - Constructor for class org.genesys2.gringlobal.taxonomy.component.TaxonomyReader

toDate(String) - Static method in class org.genesys2.gringlobal.taxonomy.component.TaxonomyReader

Convert a string in agreed format (yyyy-MM-dd HH:mm:ss) to Date.

toGenus(String[]) - Static method in class org.genesys2.gringlobal.taxonomy.component.TaxonomyReader

Convert row to GenusRow.

toSpecies(String[]) - Static method in class org.genesys2.gringlobal.taxonomy.component.TaxonomyReader

Convert row to SpeciesRow.

toString() - Method in class org.genesys2.gringlobal.taxonomy.component.InMemoryTaxonomyDatabase

U

update(float) - Method in class org.genesys2.gringlobal.taxonomy.component.BestScore

Update.

B C F G I O P R S T U