Uses of Class
org.episteme.natural.biology.taxonomy.Species

Packages that use Species

Package	Description
org.episteme.natural.biology
org.episteme.natural.biology.ecology
org.episteme.natural.biology.evolution
org.episteme.natural.biology.loaders
org.episteme.natural.biology.loaders.itis	Biological taxonomy, genetics, and physiological modeling.
org.episteme.natural.biology.loaders.phyloxml	PhyloXML loader for phylogenetic tree data.
org.episteme.natural.biology.phylogeny	Biological modeling, genetics, and life science simulations.
org.episteme.natural.biology.taxonomy
org.episteme.natural.medicine	Provides the org.episteme.social.medicine module.
org.episteme.social.economics	Provides comprehensive mathematical models for economic systems, agent-based modeling, and financial analysis.
org.episteme.social.psychology.social	Provides the org.episteme.social.psychology.social module.

Uses of Species in org.episteme.natural.biology

Fields in org.episteme.natural.biology declared as Species

Modifier and Type	Field	Description
static final Species	HomoSapiens.SPECIES	The human species

Methods in org.episteme.natural.biology that return Species

Modifier and Type	Method	Description
static Species	CommonSpecies.arabidopsisThaliana()
static Species	CommonSpecies.caenorhabditisElegans()
static Species	CommonSpecies.canisLupusFamiliaris()
static Species	CommonSpecies.danioRerio()
static Species	CommonSpecies.drosophilaMelanogaster()
static Species	CommonSpecies.escherichiaColiK12()
static Species	CommonSpecies.felisCatus()
Species	Individual.getSpecies()
static Species	CommonSpecies.musMusculus()
static Species	CommonSpecies.panTroglodytes()
static Species	CommonSpecies.saccharomycesCerevisiae()

Methods in org.episteme.natural.biology that return types with arguments of type Species

Modifier and Type	Method	Description
static List<Species>	CommonSpecies.modelOrganisms()	Returns list of all common model organisms.

Constructors in org.episteme.natural.biology with parameters of type Species

Modifier	Constructor	Description
	Individual(String id, Species species, BiologicalSex sex)
	Individual(String id, Species species, BiologicalSex sex, LocalDate birthDate)	Helper constructor for String IDs.
	Individual(Identification id, Species species, BiologicalSex sex)
	Individual(Identification id, Species species, BiologicalSex sex, LocalDate birthDate, EventDrivenEngine engine)	Creates a new individual organism with an associated simulation engine.

Uses of Species in org.episteme.natural.biology.ecology

Methods in org.episteme.natural.biology.ecology that return Species

Modifier and Type	Method	Description
Species	Population.getSpecies()

Constructors in org.episteme.natural.biology.ecology with parameters of type Species

Modifier	Constructor	Description
	Population(String name, Species species, Place territory)
	Population(Identification id, String name, Species species, Place territory)
	Population(Identification id, String name, Species species, Place territory, EventDrivenEngine engine)
	Population(Species species)

Uses of Species in org.episteme.natural.biology.evolution

Methods in org.episteme.natural.biology.evolution that return Species

Modifier and Type	Method	Description
Species	Clade.getSpecies()

Methods in org.episteme.natural.biology.evolution with parameters of type Species

Modifier and Type	Method	Description
void	Clade.setSpecies(Species species)

Method parameters in org.episteme.natural.biology.evolution with type arguments of type Species

Modifier and Type	Method	Description
static Clade	PhylogeneticTree.buildUPGMA(Real[][] distanceMatrix, List<Species> speciesList)

Uses of Species in org.episteme.natural.biology.loaders

Subclasses with type arguments of type Species in org.episteme.natural.biology.loaders

Modifier and Type	Class	Description
class	NCBITaxonomyReader	Loader for NCBI Taxonomy database.

Methods in org.episteme.natural.biology.loaders that return Species

Modifier and Type	Method	Description
protected Species	NCBITaxonomyReader.loadFromSource(String resourceId)

Methods in org.episteme.natural.biology.loaders that return types with arguments of type Species

Modifier and Type	Method	Description
Optional<Species>	NCBITaxonomyReader.fetchByTaxId(long taxId)	Fetches taxonomy by NCBI taxon ID.
Class<Species>	NCBITaxonomyReader.getResourceType()
List<Species>	NCBITaxonomyReader.loadFromResource(String resourcePath)	Loads species from a specific resource path (JSON).

Uses of Species in org.episteme.natural.biology.loaders.itis

Methods in org.episteme.natural.biology.loaders.itis that return Species

Modifier and Type	Method	Description
Species	ITISBridge.toSpecies(ITISTaxon itisTaxon)	Converts ITIS taxon record to Episteme Species.

Methods in org.episteme.natural.biology.loaders.itis that return types with arguments of type Species

Modifier and Type	Method	Description
List<Species>	ITISBridge.toSpeciesList(List<ITISTaxon> taxa)	Converts multiple ITIS taxa to Species list.

Method parameters in org.episteme.natural.biology.loaders.itis with type arguments of type Species

Modifier and Type	Method	Description
void	ITISBridge.buildHierarchy(List<Species> speciesList)	Builds parent-child relationships between Species based on ITIS TSN hierarchy.

Uses of Species in org.episteme.natural.biology.loaders.phyloxml

Methods in org.episteme.natural.biology.loaders.phyloxml that return Species

Modifier and Type	Method	Description
Species	PhyloXMLBridge.convertTaxonomy(PhyloXMLTaxonomy dto)	Converts PhyloXML taxonomy DTO to Episteme Species.

Methods in org.episteme.natural.biology.loaders.phyloxml that return types with arguments of type Species

Modifier and Type	Method	Description
List<Species>	PhyloXMLBridge.extractSpecies(PhylogeneticTree tree)	Extracts all species from a PhyloXML tree.

Uses of Species in org.episteme.natural.biology.phylogeny

Fields in org.episteme.natural.biology.phylogeny declared as Species

Modifier and Type	Field	Description
final Species	PhylogeneticTree.Node.species

Method parameters in org.episteme.natural.biology.phylogeny with type arguments of type Species

Modifier and Type	Method	Description
static PhylogeneticTree.Node	PhylogeneticTree.buildNeighborJoining(Real[][] distanceMatrix, List<Species> speciesList)
static PhylogeneticTree.Node	PhylogeneticTree.buildUPGMA(Real[][] distanceMatrix, List<Species> speciesList)

Constructors in org.episteme.natural.biology.phylogeny with parameters of type Species

Modifier	Constructor	Description
	Node(Species species)	Leaf node constructor from Species

Uses of Species in org.episteme.natural.biology.taxonomy

Fields in org.episteme.natural.biology.taxonomy declared as Species

Modifier and Type	Field	Description
static final Species	Species.HUMAN

Methods in org.episteme.natural.biology.taxonomy that return Species

Modifier and Type	Method	Description
Species	Species.getAncestor()
static Species	TaxonomyReader.getSpecies(String name)

Methods in org.episteme.natural.biology.taxonomy with parameters of type Species

Modifier and Type	Method	Description
void	Species.setAncestor(Species ancestor)

Uses of Species in org.episteme.natural.medicine

Methods in org.episteme.natural.medicine that return types with arguments of type Species

Modifier and Type	Method	Description
Set<Species>	Disease.getTargets()
Set<Species>	Disease.getVectors()

Methods in org.episteme.natural.medicine with parameters of type Species

Modifier and Type	Method	Description
void	Disease.addTarget(Species species)
void	Disease.addVector(Species species)
void	Disease.removeTarget(Species species)
void	Disease.removeVector(Species species)

Uses of Species in org.episteme.social.economics

Constructors in org.episteme.social.economics with parameters of type Species

Modifier	Constructor	Description
	Community(Identification id, String name, Species species, Place place)
	Community(Identification id, Species species, Place place)
	Community(Species species, Set<Individual> individuals, Place place)	Creates a new Community with initial members.
	Community(Species species, Place place)	Creates a new empty Community at a specific place.
	EarthEcosource(Species species)	Creates a new EarthEcosource object for a specific species.

Uses of Species in org.episteme.social.psychology.social

Constructors in org.episteme.social.psychology.social with parameters of type Species

Modifier	Constructor	Description
	Crowd(Species species, String motive)	Creates a new Crowd with a specific motive.
	PsychologicalFamily(Species species)	Creates a new PsychologicalFamily for a specific species.
	PsychologicalFamily(Species species, Place formalTerritory)	Creates a new PsychologicalFamily with a designated home territory.
	PsychologicalGroup(String name, Species species, Place territory)	Default Constructor with ID generation.
	PsychologicalGroup(String name, Species species, Place territory, EventDrivenEngine engine)
	PsychologicalGroup(Identification id, String name, Species species, Place territory)	Constructor used by subclasses or for explicit ID.
	PsychologicalGroup(Identification id, String name, Species species, Place territory, EventDrivenEngine engine)
	PsychologicalGroup(Species species)	Legacy/Convenience constructor.
	PsychologicalGroup(Species species, Place formalTerritory)	Legacy/Convenience constructor.