Package org.molgenis.vibe.core.formats

Class GeneDiseaseCombination

java.lang.Object

org.molgenis.vibe.core.formats.BiologicalEntityCombination<Gene,Disease>

org.molgenis.vibe.core.formats.GeneDiseaseCombination

All Implemented Interfaces:

AllFieldsEquals

public class GeneDiseaseCombination
extends BiologicalEntityCombination<Gene,Disease>

A combination of a Gene and a Disease.

Constructor Summary

Constructors

Constructor	Description
GeneDiseaseCombination(Gene gene, Disease disease)	Simple constructor allowing for easy comparison of collections.
GeneDiseaseCombination(Gene gene, Disease disease, double disgenetScore)

Method Summary

Modifier and Type	Method	Description
void	add(Source source)	Adds a Source to this gene-disease combination without an evidence URI.
void	add(Source source, PubmedEvidence evidence)
boolean	allFieldsEquals(Object o)
Set<PubmedEvidence>	getAllPubmedEvidence()	The PubmedEvidence of all Sources combined.
List<PubmedEvidence>	getAllPubMedEvidenceSortedByYear()	The PubmedEvidence of all Sources combined.
int	getCountForSource(Source source)	The count for the defined Source
Disease	getDisease()
double	getDisgenetScore()
Gene	getGene()
Set<PubmedEvidence>	getPubmedEvidenceForSource(Source source)	The PubmedEvidence for the defined Source.
List<PubmedEvidence>	getPubmedEvidenceForSourceSortedByReleaseDate(Source source)	The PubmedEvidence for the defined Source.
Map<Source,Integer>	getSourcesCount()	The number of occurrences for this gene-disease combination per Source.
Set<Source>	getSourcesWithPubmedEvidence()	All Sources for this gene-disease combination that have PubmedEvidence.
String	toString()

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

equals, getT1, getT2, hashCode

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneDiseaseCombination

public GeneDiseaseCombination(Gene gene,
                              Disease disease)

Simple constructor allowing for easy comparison of collections.

Parameters:

gene -

disease -

GeneDiseaseCombination

public GeneDiseaseCombination(Gene gene,
                              Disease disease,
                              double disgenetScore)

Method Detail

getGene

public Gene getGene()

Returns:

the Gene

See Also:

BiologicalEntityCombination.getT1()

getDisease

public Disease getDisease()

Returns:

the Disease

See Also:

BiologicalEntityCombination.getT2()

getDisgenetScore

public double getDisgenetScore()

getSourcesCount

public Map<Source,Integer> getSourcesCount()

The number of occurrences for this gene-disease combination per Source.

Returns:

an unmodifiable Map

getCountForSource

public int getCountForSource(Source source)

The count for the defined Source

Parameters:

source - the Source to retrieve the count for

Returns:

an int containing the frequency of this source found (if Source is not present returns a 0)

getSourcesWithPubmedEvidence

public Set<Source> getSourcesWithPubmedEvidence()

All Sources for this gene-disease combination that have PubmedEvidence.

Returns:

an unmodifiable Set containing Sources

getPubmedEvidenceForSource

public Set<PubmedEvidence> getPubmedEvidenceForSource(Source source)

The PubmedEvidence for the defined Source.

Parameters:

source -

Returns:

an unmodifiable Set containing PubmedEvidence, or null if Source does not have any evidence

getPubmedEvidenceForSourceSortedByReleaseDate

public List<PubmedEvidence> getPubmedEvidenceForSourceSortedByReleaseDate(Source source)

The PubmedEvidence for the defined Source.

Parameters:

source -

Returns:

a List ordered through PubmedEvidence.RELEASE_YEAR_COMPARATOR containing PubmedEvidence, or null if Source does not have any evidence

getAllPubmedEvidence

public Set<PubmedEvidence> getAllPubmedEvidence()

The PubmedEvidence of all Sources combined.

Returns:

a Set containing all the PubmedEvidence

getAllPubMedEvidenceSortedByYear

public List<PubmedEvidence> getAllPubMedEvidenceSortedByYear()

The PubmedEvidence of all Sources combined.

Returns:

a List containing all the PubmedEvidence ordered through PubmedEvidence.RELEASE_YEAR_COMPARATOR

add

public void add(Source source,
                PubmedEvidence evidence)

add

public void add(Source source)

Adds a Source to this gene-disease combination without an evidence URI.

Parameters:

source -

toString

public String toString()

Overrides:

toString in class BiologicalEntityCombination<Gene,Disease>

allFieldsEquals

public boolean allFieldsEquals(Object o)

Specified by:

allFieldsEquals in interface AllFieldsEquals

Overrides:

allFieldsEquals in class BiologicalEntityCombination<Gene,Disease>