Package org.molgenis.vibe.core.formats

Class GeneDiseaseCollection

java.lang.Object

org.molgenis.vibe.core.formats.BiologicalEntityCollection<Gene,Disease,GeneDiseaseCombination>

org.molgenis.vibe.core.formats.GeneDiseaseCollection

All Implemented Interfaces:

Iterable<GeneDiseaseCombination>, Collection<GeneDiseaseCombination>, AllFieldsEquals

public class GeneDiseaseCollection
extends BiologicalEntityCollection<Gene,Disease,GeneDiseaseCombination>

A collection of GeneDiseaseCombinations.

Constructor Summary

Constructors

Constructor	Description
GeneDiseaseCollection()
GeneDiseaseCollection(Set<GeneDiseaseCombination> combinationsMap)

Method Summary

Modifier and Type	Method	Description
Set<GeneDiseaseCombination>	getByDisease(Disease disease)	Get the GeneDiseaseCombinations for a single Disease.
List<GeneDiseaseCombination>	getByDiseaseOrderedByGdaScore(Disease disease)	Wrapper for getByDisease(Disease) that returns an ordered List based on GeneDiseaseCombination.getDisgenetScore() (high->low) instead of a Set.
Set<GeneDiseaseCombination>	getByGene(Gene gene)	Get the GeneDiseaseCombinations for a single Gene.
List<GeneDiseaseCombination>	getByGeneOrderedByGdaScore(Gene gene)	Wrapper for getByGene(Gene) that returns an ordered List based on GeneDiseaseCombination.getDisgenetScore() (high->low) instead of a Set.
Set<Disease>	getDiseases()
Set<GeneDiseaseCombination>	getGeneDiseaseCombinations()
List<GeneDiseaseCombination>	getGeneDiseaseCombinationsOrdered()
Set<Gene>	getGenes()

Methods inherited from class org.molgenis.vibe.core.formats.BiologicalEntityCollection

add, addAll, allFieldsEquals, clear, contains, containsAll, equals, get, getByT1, getByT2, getT1, getT2, getT3, getT3Ordered, hashCode, isEmpty, iterator, remove, removeAll, retainAll, size, toArray, toArray, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Collection

parallelStream, removeIf, spliterator, stream, toArray

Methods inherited from interface java.lang.Iterable

forEach

Constructor Detail

GeneDiseaseCollection

public GeneDiseaseCollection()

GeneDiseaseCollection

public GeneDiseaseCollection(Set<GeneDiseaseCombination> combinationsMap)

Method Detail

getGenes

public Set<Gene> getGenes()

Returns:

all Genes.

See Also:

BiologicalEntityCollection.getT1()

getDiseases

public Set<Disease> getDiseases()

Returns:

all Diseases.

See Also:

BiologicalEntityCollection.getT2()

getGeneDiseaseCombinations

public Set<GeneDiseaseCombination> getGeneDiseaseCombinations()

Returns:

all GeneDiseaseCombinations.

See Also:

BiologicalEntityCollection.getT3()

getGeneDiseaseCombinationsOrdered

public List<GeneDiseaseCombination> getGeneDiseaseCombinationsOrdered()

Returns:

all GeneDiseaseCombinations.

See Also:

BiologicalEntityCollection.getT3Ordered()

getByGene

public Set<GeneDiseaseCombination> getByGene(Gene gene)

Get the GeneDiseaseCombinations for a single Gene.

Parameters:

gene - the Gene to retrieve GeneDiseaseCombinations for

Returns:

the GeneDiseaseCombinations belonging to gene

getByDisease

public Set<GeneDiseaseCombination> getByDisease(Disease disease)

Get the GeneDiseaseCombinations for a single Disease.

Parameters:

disease - the Disease to retrieve GeneDiseaseCombinations for

Returns:

the GeneDiseaseCombinations belonging to disease

getByGeneOrderedByGdaScore

public List<GeneDiseaseCombination> getByGeneOrderedByGdaScore(Gene gene)

Wrapper for getByGene(Gene) that returns an ordered List based on GeneDiseaseCombination.getDisgenetScore() (high->low) instead of a Set.

Parameters:

gene -

Returns:

getByDisease(Disease) as ordered List based on GeneDiseaseCombination.getDisgenetScore() (high->low)

See Also:

getByGene(Gene)

getByDiseaseOrderedByGdaScore

public List<GeneDiseaseCombination> getByDiseaseOrderedByGdaScore(Disease disease)

Wrapper for getByDisease(Disease) that returns an ordered List based on GeneDiseaseCombination.getDisgenetScore() (high->low) instead of a Set.

Parameters:

disease -

Returns:

getByDisease(Disease) as ordered List based on GeneDiseaseCombination.getDisgenetScore() (high->low)

See Also:

getByDisease(Disease)