Package org.molgenis.vibe.core.formats

Class PhenotypeNetwork

java.lang.Object

org.molgenis.vibe.core.formats.PhenotypeNetwork

public class PhenotypeNetwork
extends Object

A network of Phenotypes with a single source Phenotype from which the network is created.

Constructor Summary

Constructors

Constructor	Description
PhenotypeNetwork(Phenotype phenotype)

Method Summary

Modifier and Type	Method	Description
void	add(Collection<Phenotype> phenotypes, int distance)
boolean	add(Phenotype phenotype, int distance)	Adds a Phenotype to the PhenotypeNetwork.
boolean	contains(Phenotype phenotype)
boolean	equals(Object o)
Set<Phenotype>	getByDistance(int distance)	Retrieves all Phenotypes that have the specified distance
int	getDistance(Phenotype phenotype)	Retrieve the stored distance belonging to a Phenotype
Set<Integer>	getDistances()
Set<Phenotype>	getPhenotypes()
Phenotype	getSource()
int	hashCode()
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

PhenotypeNetwork

public PhenotypeNetwork(Phenotype phenotype)

Method Detail

getSource

public Phenotype getSource()

Returns:

the source phenotype (the only Phenotype with distance 0)

getPhenotypes

public Set<Phenotype> getPhenotypes()

Returns:

all stored Phenotypes

getDistances

public Set<Integer> getDistances()

Returns:

all distances for which Phenotypes are stored.

getByDistance

public Set<Phenotype> getByDistance(int distance)

Retrieves all Phenotypes that have the specified distance

Parameters:

distance - value to be used for Phenotype retrieval

Returns:

all Phenotypes with the given distance

getDistance

public int getDistance(Phenotype phenotype)

Retrieve the stored distance belonging to a Phenotype

Parameters:

phenotype - the Phenotype to retrieve the distance from

Returns:

the distance belonging to the phenotype

add

public void add(Collection<Phenotype> phenotypes,
                int distance)

add

public boolean add(Phenotype phenotype,
                   int distance)

Adds a Phenotype to the PhenotypeNetwork. If the Phenotype is already stored, compares the new distance to the currently stored one. If the already stored distance is closer or equal, nothing is done. Otherwise, the old distance is replaced with the new one. If the Phenotype is not stored yet, it is simply added.

Parameters:

phenotype - the Phenotype to be added to the network

distance - the distance the Phenotype is from the source

Returns:

true if added/distance is updated, otherwise false

contains

public boolean contains(Phenotype phenotype)

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object