Class Virus

java.lang.Object

org.episteme.natural.biology.Virus

All Implemented Interfaces:

Serializable, Commented, ComprehensiveIdentification, Identified<Identification>, Named

public class Virus
extends Object
implements ComprehensiveIdentification

Represents a virus - an infectious agent that replicates inside living cells. Implements ComprehensiveIdentification to support dynamic traits and consistent identity.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	Virus.Stage	Virus lifecycle stages.

Field Summary

Fields

Modifier and Type	Field	Description
protected final Identification	id
protected final Map<String,Object>	traits

Constructor Summary

Constructors

Constructor	Description
Virus(String name, String family, VirusGenomeType genomeType, VirusMorphology morphology, BioSequence genome, double capsidDiameterNm)
Virus(String name, String family, VirusGenomeType genomeType, VirusMorphology morphology, BioSequence genome, Quantity<Length> capsidDiameter)

Method Summary

Modifier and Type	Method	Description
static Virus	bacteriophageT4()
boolean	equals(Object o)
Quantity<Length>	getCapsidDiameter()
Virus.Stage	getCurrentStage()
String	getFamily()
BioSequence	getGenome()
int	getGenomeSize()
VirusGenomeType	getGenomeType()
Identification	getId()	Returns the unique identifier of this entity.
VirusMorphology	getMorphology()
Map<String,Object>	getTraits()	Returns the traits map for this entity.
int	hashCode()
static Virus	hiv1()
static Virus	influenzaA()
boolean	isRetrovirus()
boolean	isRNAVirus()
void	nextStage()
static Virus	sarsCov2()
void	setStage(Virus.Stage stage)
String	toString()

Methods inherited from class Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface Commented

getComments, getTrait, setComments

Methods inherited from interface ComprehensiveIdentification

getName, getTrait, setName, setTrait

Field Details

id

protected final Identification id

traits

protected final Map<String,Object> traits

Constructor Details

Virus

public Virus(String name,
 String family,
 VirusGenomeType genomeType,
 VirusMorphology morphology,
 BioSequence genome,
 Quantity<Length> capsidDiameter)

Virus

public Virus(String name,
 String family,
 VirusGenomeType genomeType,
 VirusMorphology morphology,
 BioSequence genome,
 double capsidDiameterNm)

Method Details

getId

public Identification getId()

Description copied from interface: Identified

Returns the unique identifier of this entity.

Specified by:

getId in interface Identified<Identification>

Returns:

the identifier

getTraits

public Map<String,Object> getTraits()

Description copied from interface: ComprehensiveIdentification

Returns the traits map for this entity.

Specified by:

getTraits in interface Commented

Specified by:

getTraits in interface ComprehensiveIdentification

Returns:

the traits map

getFamily

public String getFamily()

getGenomeType

public VirusGenomeType getGenomeType()

getMorphology

public VirusMorphology getMorphology()

getGenome

public BioSequence getGenome()

getCapsidDiameter

public Quantity<Length> getCapsidDiameter()

getCurrentStage

public Virus.Stage getCurrentStage()

nextStage

public void nextStage()

setStage

public void setStage(Virus.Stage stage)

getGenomeSize

public int getGenomeSize()

isRNAVirus

public boolean isRNAVirus()

isRetrovirus

public boolean isRetrovirus()

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

sarsCov2

public static Virus sarsCov2()

influenzaA

public static Virus influenzaA()

hiv1

public static Virus hiv1()

bacteriophageT4

public static Virus bacteriophageT4()