Index (vibe-core 5.1.5 API)

A B C D E F G H I L M N O P Q R S T V
All Classes All Packages

A

add(Collection<Phenotype>, int) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork
add(PhenotypeNetwork) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetworkCollection: Adds a PhenotypeNetwork to the PhenotypeNetworkCollection
add(Phenotype, int) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork: Adds a Phenotype to the PhenotypeNetwork.
add(Source) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination: Adds a Source to this gene-disease combination without an evidence URI.
add(Source, PubmedEvidence) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination
add(T3) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
addAll(Collection<? extends T3>) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
addPhenotypeToNetwork(OntClass, PhenotypeNetwork, int) - Method in class org.molgenis.vibe.core.ontology_processing.PhenotypesRetriever: Adds a OntClass representing a Phenotype to a PhenotypeNetwork.
allFieldsEquals(Object) - Method in interface org.molgenis.vibe.core.formats.AllFieldsEquals
allFieldsEquals(Object) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
allFieldsEquals(Object) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCombination
allFieldsEquals(Object) - Method in class org.molgenis.vibe.core.formats.Entity
allFieldsEquals(Object) - Method in class org.molgenis.vibe.core.formats.Gene
allFieldsEquals(Object) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination
allFieldsEquals(Object) - Method in class org.molgenis.vibe.core.formats.PubmedEvidence
AllFieldsEquals - Interface in org.molgenis.vibe.core.formats: A deep equals that compares all fields of a Class, also ones that are not used by Object.equals(Object) (for example due to design-reasons, though validity for all fields still needs to be checked in unit-tests to assess everything functions as it should).
ALTERED_EXPRESSION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType

B

BiologicalEntity - Class in org.molgenis.vibe.core.formats: Describes a biological entity (such as a Gene, Disease or Phenotype).
BiologicalEntity(String) - Constructor for class org.molgenis.vibe.core.formats.BiologicalEntity
BiologicalEntity(String, String) - Constructor for class org.molgenis.vibe.core.formats.BiologicalEntity
BiologicalEntity(URI) - Constructor for class org.molgenis.vibe.core.formats.BiologicalEntity
BiologicalEntity(URI, String) - Constructor for class org.molgenis.vibe.core.formats.BiologicalEntity
BiologicalEntityCollection<T1 extends BiologicalEntity,T2 extends BiologicalEntity,T3 extends BiologicalEntityCombination<T1,T2>> - Class in org.molgenis.vibe.core.formats: A collection of 0 or more BiologicalEntityCombinations that have the same BiologicalEntityCollection and BiologicalEntityCollection class types.
BiologicalEntityCollection() - Constructor for class org.molgenis.vibe.core.formats.BiologicalEntityCollection
BiologicalEntityCollection(Collection<? extends T3>) - Constructor for class org.molgenis.vibe.core.formats.BiologicalEntityCollection
BiologicalEntityCombination<T1 extends BiologicalEntity,T2 extends BiologicalEntity> - Class in org.molgenis.vibe.core.formats: A combination of 2 BiologicalEntity subclass objects.
BiologicalEntityCombination(T1, T2) - Constructor for class org.molgenis.vibe.core.formats.BiologicalEntityCombination
BIOMARKER - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType

C

call() - Method in class org.molgenis.vibe.core.GeneDiseaseCollectionRetrievalRunner
call() - Method in class org.molgenis.vibe.core.PhenotypesRetrievalRunner
CASUAL_MUTATION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
CHILDREN - org.molgenis.vibe.core.ontology_processing.PhenotypesRetrieverFactory
ChildrenRetriever - Class in org.molgenis.vibe.core.ontology_processing
ChildrenRetriever(OntModel, Collection<Phenotype>, int) - Constructor for class org.molgenis.vibe.core.ontology_processing.ChildrenRetriever
CHROMOSOMAL_REARRANGEMENT - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
clear() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
clear() - Method in class org.molgenis.vibe.core.formats.PhenotypeNetworkCollection: Clears the PhenotypeNetworkCollection
close() - Method in class org.molgenis.vibe.core.database_processing.QueryRunner
close() - Method in class org.molgenis.vibe.core.io.input.HdtFileReader
close() - Method in class org.molgenis.vibe.core.io.input.ModelFilesReader
close() - Method in interface org.molgenis.vibe.core.io.input.ModelReader
COMBINATION_DISEASE_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
COMBINATION_DISGENET_SCORE_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
COMBINATION_GENE_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
COMBINATION_SOURCE_COUNT_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
COMBINATION_SOURCE_NAME_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
COMBINATION_SOURCE_PUBMED_URI_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
COMBINATION_SOURCE_PUBMED_YEAR_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
COMBINATION_SOURCE_PUBMEDS_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
COMBINATION_SOURCES_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
COMBINATIONS_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
compareTo(Entity) - Method in class org.molgenis.vibe.core.formats.Entity
compareTo(Entity) - Method in class org.molgenis.vibe.core.formats.Gene
compareTo(Entity) - Method in class org.molgenis.vibe.core.formats.PubmedEvidence
compareTo(Source) - Method in class org.molgenis.vibe.core.formats.Source
contains(Object) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
contains(Phenotype) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork
containsAll(Collection<?>) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
create(OntModel, Collection<Phenotype>, int) - Method in enum org.molgenis.vibe.core.ontology_processing.PhenotypesRetrieverFactory
CURATED - org.molgenis.vibe.core.formats.Source.Level

D

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionDeserializer
Disease - Class in org.molgenis.vibe.core.formats: A disease.
Disease(String) - Constructor for class org.molgenis.vibe.core.formats.Disease
Disease(String, String) - Constructor for class org.molgenis.vibe.core.formats.Disease
Disease(URI) - Constructor for class org.molgenis.vibe.core.formats.Disease
Disease(URI, String) - Constructor for class org.molgenis.vibe.core.formats.Disease
DISEASE_NAME_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
DISEASES_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
DisgenetRdfDataRetriever - Class in org.molgenis.vibe.core.database_processing: Retrieves data for further usage from the DisGeNET database.
DisgenetRdfDataRetriever(ModelReader) - Constructor for class org.molgenis.vibe.core.database_processing.DisgenetRdfDataRetriever
DISTANCE - org.molgenis.vibe.core.ontology_processing.PhenotypesRetrieverFactory

E

Entity - Class in org.molgenis.vibe.core.formats: Describes an entity.
Entity(String) - Constructor for class org.molgenis.vibe.core.formats.Entity
Entity(String, String) - Constructor for class org.molgenis.vibe.core.formats.Entity
Entity(URI) - Constructor for class org.molgenis.vibe.core.formats.Entity
Entity(URI, String) - Constructor for class org.molgenis.vibe.core.formats.Entity
EntityWithIntId - Interface in org.molgenis.vibe.core.formats
EnumTypeDefiner - Interface in org.molgenis.vibe.core.formats
equals(Object) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
equals(Object) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCombination
equals(Object) - Method in class org.molgenis.vibe.core.formats.Entity
equals(Object) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork
equals(Object) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetworkCollection
equals(Object) - Method in class org.molgenis.vibe.core.formats.Source

F

FUSION_GENE - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType

G

Gene - Class in org.molgenis.vibe.core.formats: A gene.
Gene(String, GeneSymbol) - Constructor for class org.molgenis.vibe.core.formats.Gene
Gene(URI, GeneSymbol) - Constructor for class org.molgenis.vibe.core.formats.Gene
GENE_DISEASE - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
GENE_SYMBOL_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
GeneDiseaseCollection - Class in org.molgenis.vibe.core.formats: A collection of GeneDiseaseCombinations.
GeneDiseaseCollection() - Constructor for class org.molgenis.vibe.core.formats.GeneDiseaseCollection
GeneDiseaseCollection(Set<GeneDiseaseCombination>) - Constructor for class org.molgenis.vibe.core.formats.GeneDiseaseCollection
GeneDiseaseCollectionDeserializer - Class in org.molgenis.vibe.core.formats
GeneDiseaseCollectionDeserializer() - Constructor for class org.molgenis.vibe.core.formats.GeneDiseaseCollectionDeserializer
GeneDiseaseCollectionJsonSerialization - Class in org.molgenis.vibe.core.formats
GeneDiseaseCollectionJsonSerialization() - Constructor for class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
GeneDiseaseCollectionRetrievalRunner - Class in org.molgenis.vibe.core
GeneDiseaseCollectionRetrievalRunner(VibeDatabase, Set<Phenotype>) - Constructor for class org.molgenis.vibe.core.GeneDiseaseCollectionRetrievalRunner
GeneDiseaseCollectionSerializer - Class in org.molgenis.vibe.core.formats: Serializers a GeneDiseaseCollection to json.
GeneDiseaseCollectionSerializer() - Constructor for class org.molgenis.vibe.core.formats.GeneDiseaseCollectionSerializer
GeneDiseaseCombination - Class in org.molgenis.vibe.core.formats: A combination of a Gene and a Disease.
GeneDiseaseCombination(Gene, Disease) - Constructor for class org.molgenis.vibe.core.formats.GeneDiseaseCombination: Simple constructor allowing for easy comparison of collections.
GeneDiseaseCombination(Gene, Disease, double) - Constructor for class org.molgenis.vibe.core.formats.GeneDiseaseCombination
GeneDiseaseCombinationType - Enum in org.molgenis.vibe.core.formats: Based on: http://semanticscience.org/ontology/sio.owl (which is licensed under http://creativecommons.org/licenses/by/4.0/) Please refer to http://www.disgenet.org/ds/DisGeNET/html/images/ontology.svg for the Ontology overview.
GenePrioritizer - Interface in org.molgenis.vibe.core.query_output_digestion.prioritization.gene: Returns a Gene priority from a GeneDiseaseCollection.
generateModel() - Method in class org.molgenis.vibe.core.io.input.ModelFilesReader: Generates a new Model using the ModelFactory.
generateModel() - Method in class org.molgenis.vibe.core.io.input.OntologyModelFilesReader
GENES_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
GenesForPhenotypeRetriever - Class in org.molgenis.vibe.core.database_processing: Retrieves all required information for further processing regarding the genes belonging to a given phenotype.
GenesForPhenotypeRetriever(ModelReader, Set<Phenotype>) - Constructor for class org.molgenis.vibe.core.database_processing.GenesForPhenotypeRetriever
GeneSymbol - Class in org.molgenis.vibe.core.formats
GeneSymbol(String) - Constructor for class org.molgenis.vibe.core.formats.GeneSymbol
GeneSymbol(URI) - Constructor for class org.molgenis.vibe.core.formats.GeneSymbol
GENETIC_VARIATION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
GENOMIC_ALTERATION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
GERMLINE_CASUAL_MUTATION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
GERMLINE_MODIFYING_MUTATION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
get(T3) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
getAllPubmedEvidence() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination: The PubmedEvidence of all Sources combined.
getAllPubMedEvidenceSortedByYear() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination: The PubmedEvidence of all Sources combined.
getByDisease(Disease) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCollection: Get the GeneDiseaseCombinations for a single Disease.
getByDiseaseOrderedByGdaScore(Disease) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCollection: Wrapper for GeneDiseaseCollection.getByDisease(Disease) that returns an ordered List based on GeneDiseaseCombination.getDisgenetScore() (high->low) instead of a Set.
getByDistance(int) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork: Retrieves all Phenotypes that have the specified distance
getByGene(Gene) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCollection: Get the GeneDiseaseCombinations for a single Gene.
getByGeneOrderedByGdaScore(Gene) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCollection: Wrapper for GeneDiseaseCollection.getByGene(Gene) that returns an ordered List based on GeneDiseaseCombination.getDisgenetScore() (high->low) instead of a Set.
getByT1(T1) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection: Get all BiologicalEntityCollection belonging to a single BiologicalEntityCollection.
getByT2(T2) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection: Get all BiologicalEntityCollection belonging to a single BiologicalEntityCollection.
getCountForSource(Source) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination: The count for the defined Source
getDescription() - Method in enum org.molgenis.vibe.core.ontology_processing.PhenotypesRetrieverFactory
getDisease() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination
getDiseases() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCollection
getDisgenetScore() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination
getDistance(Phenotype) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork: Retrieve the stored distance belonging to a Phenotype
getDistances() - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork
getFormattedId() - Method in class org.molgenis.vibe.core.formats.Entity
getFormattedId() - Method in enum org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
getFullName() - Method in class org.molgenis.vibe.core.formats.Source: Retrieves the full name.
getGene() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination
getGeneDiseaseCollection() - Method in class org.molgenis.vibe.core.database_processing.GenesForPhenotypeRetriever
getGeneDiseaseCombinations() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCollection
getGeneDiseaseCombinationsOrdered() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCollection
getGenes() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCollection
getGenesForPhenotypes(Set<Phenotype>) - Static method in class org.molgenis.vibe.core.database_processing.query_string_creation.QueryStringGenerator
getId() - Method in class org.molgenis.vibe.core.formats.Entity
getId() - Method in interface org.molgenis.vibe.core.formats.EnumTypeDefiner
getId() - Method in enum org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
getId() - Method in enum org.molgenis.vibe.core.ontology_processing.PhenotypesRetrieverFactory
getIdInt() - Method in interface org.molgenis.vibe.core.formats.EntityWithIntId
getIdInt() - Method in class org.molgenis.vibe.core.formats.Gene
getIdInt() - Method in class org.molgenis.vibe.core.formats.PubmedEvidence
getIdPrefix() - Method in class org.molgenis.vibe.core.formats.Disease
getIdPrefix() - Method in class org.molgenis.vibe.core.formats.Entity: The entity prefix.
getIdPrefix() - Method in class org.molgenis.vibe.core.formats.Gene
getIdPrefix() - Method in class org.molgenis.vibe.core.formats.GeneSymbol
getIdPrefix() - Method in class org.molgenis.vibe.core.formats.Phenotype
getIdPrefix() - Method in class org.molgenis.vibe.core.formats.PubmedEvidence
getIdRegex() - Method in class org.molgenis.vibe.core.formats.Disease
getIdRegex() - Method in class org.molgenis.vibe.core.formats.Entity: A regular expression an input String should adhere to when deriving the Entity from it.
getIdRegex() - Method in class org.molgenis.vibe.core.formats.Gene
getIdRegex() - Method in class org.molgenis.vibe.core.formats.GeneSymbol
getIdRegex() - Method in class org.molgenis.vibe.core.formats.Phenotype
getIdRegex() - Method in class org.molgenis.vibe.core.formats.PubmedEvidence
getInputPhenotypes() - Method in class org.molgenis.vibe.core.ontology_processing.PhenotypesRetriever
getLevel() - Method in class org.molgenis.vibe.core.formats.Source
getMaxDistance() - Method in class org.molgenis.vibe.core.ontology_processing.PhenotypesRetriever
getModel() - Method in class org.molgenis.vibe.core.io.input.HdtFileReader
getModel() - Method in class org.molgenis.vibe.core.io.input.ModelFilesReader
getModel() - Method in interface org.molgenis.vibe.core.io.input.ModelReader
getModel() - Method in class org.molgenis.vibe.core.io.input.OntologyModelFilesReader
getModelReader() - Method in class org.molgenis.vibe.core.database_processing.DisgenetRdfDataRetriever
getModelReader() - Method in class org.molgenis.vibe.core.io.input.VibeDatabase
getName() - Method in class org.molgenis.vibe.core.formats.Entity
getName() - Method in class org.molgenis.vibe.core.formats.Source: Retrieves the short name (first word only).
getPhenotypeNetworkBySource(Phenotype) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetworkCollection: Retrieve a PhenotypeNetwork based on its PhenotypeNetwork.getSource().
getPhenotypeNetworkCollection() - Method in class org.molgenis.vibe.core.ontology_processing.PhenotypesRetriever
getPhenotypes() - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork
getPhenotypes() - Method in class org.molgenis.vibe.core.formats.PhenotypeNetworkCollection
getPubmedEvidenceForSource(Source) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination: The PubmedEvidence for the defined Source.
getPubmedEvidenceForSourceSortedByReleaseDate(Source) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination: The PubmedEvidence for the defined Source.
getQuery() - Method in class org.molgenis.vibe.core.database_processing.query_string_creation.QueryString
getRangeString() - Method in class org.molgenis.vibe.core.database_processing.query_string_creation.QueryStringPathRange
getReadableString() - Method in enum org.molgenis.vibe.core.formats.Source.Level
getRegexIdGroup() - Method in class org.molgenis.vibe.core.formats.Disease
getRegexIdGroup() - Method in class org.molgenis.vibe.core.formats.Entity: The group within the regular expression the actual Entity.id is stored in.
getRegexIdGroup() - Method in class org.molgenis.vibe.core.formats.Gene
getRegexIdGroup() - Method in class org.molgenis.vibe.core.formats.GeneSymbol
getRegexIdGroup() - Method in class org.molgenis.vibe.core.formats.Phenotype
getRegexIdGroup() - Method in class org.molgenis.vibe.core.formats.PubmedEvidence
getReleaseYear() - Method in class org.molgenis.vibe.core.formats.PubmedEvidence
getResultSet() - Method in class org.molgenis.vibe.core.database_processing.QueryRunner: Retrieve the output from the Model based on the given queryString.
getSource() - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork
getSources() - Method in class org.molgenis.vibe.core.database_processing.DisgenetRdfDataRetriever: Requires DisgenetRdfDataRetriever.retrieveSources() to be run first!
getSources() - Static method in class org.molgenis.vibe.core.database_processing.query_string_creation.QueryStringGenerator
getSourcesCount() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination: The number of occurrences for this gene-disease combination per Source.
getSourcesWithPubmedEvidence() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination: All Sources for this gene-disease combination that have PubmedEvidence.
getSymbol() - Method in class org.molgenis.vibe.core.formats.Gene
getSyntax() - Method in class org.molgenis.vibe.core.database_processing.query_string_creation.QueryString
getSyntax() - Method in class org.molgenis.vibe.core.database_processing.query_string_creation.QueryStringPathRange
getT1() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
getT1() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCombination
getT2() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
getT2() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCombination
getT3() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
getT3Ordered() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection: Uses BiologicalEntityCollection.getT3() to create an ordered List first ordered based on BiologicalEntityCollection and then ordered based on BiologicalEntityCollection.
getUri() - Method in class org.molgenis.vibe.core.formats.Entity
getUri() - Method in interface org.molgenis.vibe.core.formats.ResourceUri
getUri() - Method in class org.molgenis.vibe.core.formats.Source
getUriPrefix() - Method in class org.molgenis.vibe.core.formats.Disease
getUriPrefix() - Method in class org.molgenis.vibe.core.formats.Entity: The String describing the URI prefix it should match with.
getUriPrefix() - Method in class org.molgenis.vibe.core.formats.Gene
getUriPrefix() - Method in class org.molgenis.vibe.core.formats.GeneSymbol
getUriPrefix() - Method in class org.molgenis.vibe.core.formats.Phenotype
getUriPrefix() - Method in class org.molgenis.vibe.core.formats.PubmedEvidence

H

hashCode() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
hashCode() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCombination
hashCode() - Method in class org.molgenis.vibe.core.formats.Entity
hashCode() - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork
hashCode() - Method in class org.molgenis.vibe.core.formats.PhenotypeNetworkCollection
hashCode() - Method in class org.molgenis.vibe.core.formats.Source
hasNext() - Method in class org.molgenis.vibe.core.database_processing.QueryRunner
HDT - org.molgenis.vibe.core.io.input.ModelReaderFactory
HdtFileReader - Class in org.molgenis.vibe.core.io.input: Reader for a HDT file.
HdtFileReader(String) - Constructor for class org.molgenis.vibe.core.io.input.HdtFileReader
HdtFileReader(Path) - Constructor for class org.molgenis.vibe.core.io.input.HdtFileReader
HighestSingleDisgenetScoreGenePrioritizer - Class in org.molgenis.vibe.core.query_output_digestion.prioritization.gene: A Gene priority for a GeneDiseaseCollection that is based on the highest GeneDiseaseCombination.getDisgenetScore() per Gene.
HighestSingleDisgenetScoreGenePrioritizer() - Constructor for class org.molgenis.vibe.core.query_output_digestion.prioritization.gene.HighestSingleDisgenetScoreGenePrioritizer

I

ID_PREFIX - Static variable in class org.molgenis.vibe.core.formats.Disease
ID_PREFIX - Static variable in class org.molgenis.vibe.core.formats.Gene
ID_PREFIX - Static variable in class org.molgenis.vibe.core.formats.GeneSymbol
ID_PREFIX - Static variable in class org.molgenis.vibe.core.formats.Phenotype
ID_PREFIX - Static variable in class org.molgenis.vibe.core.formats.PubmedEvidence
InvalidStringFormatException - Exception in org.molgenis.vibe.core.exceptions: Thrown to indicate that a method has been given a String that is formatted in an inappropriate/unexpected way.
InvalidStringFormatException() - Constructor for exception org.molgenis.vibe.core.exceptions.InvalidStringFormatException: Constructs an InvalidStringFormatException with null as its error detail message.
InvalidStringFormatException(String) - Constructor for exception org.molgenis.vibe.core.exceptions.InvalidStringFormatException
InvalidStringFormatException(String, Throwable) - Constructor for exception org.molgenis.vibe.core.exceptions.InvalidStringFormatException
InvalidStringFormatException(Throwable) - Constructor for exception org.molgenis.vibe.core.exceptions.InvalidStringFormatException
isEmpty() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
iterator() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection

L

LITERATURE - org.molgenis.vibe.core.formats.Source.Level

M

MaxDistanceRetriever - Class in org.molgenis.vibe.core.ontology_processing
MaxDistanceRetriever(OntModel, Collection<Phenotype>, int) - Constructor for class org.molgenis.vibe.core.ontology_processing.MaxDistanceRetriever
MODEL - org.molgenis.vibe.core.formats.Source.Level
ModelFilesReader - Class in org.molgenis.vibe.core.io.input: Creates an (Ontology) Model from RDF files.
ModelFilesReader(String) - Constructor for class org.molgenis.vibe.core.io.input.ModelFilesReader
ModelFilesReader(String, Lang) - Constructor for class org.molgenis.vibe.core.io.input.ModelFilesReader
ModelReader - Interface in org.molgenis.vibe.core.io.input: Interface describing a Class that reads in a Model.
ModelReaderFactory - Enum in org.molgenis.vibe.core.io.input
MODIFYING_MUTATION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType

N

next() - Method in class org.molgenis.vibe.core.database_processing.QueryRunner

O

OntologyModelFilesReader - Class in org.molgenis.vibe.core.io.input: Generates an OntModel using OntModelSpec.OWL_MEM.
OntologyModelFilesReader(String) - Constructor for class org.molgenis.vibe.core.io.input.OntologyModelFilesReader
org.molgenis.vibe.core - package org.molgenis.vibe.core
org.molgenis.vibe.core.database_processing - package org.molgenis.vibe.core.database_processing
org.molgenis.vibe.core.database_processing.query_string_creation - package org.molgenis.vibe.core.database_processing.query_string_creation
org.molgenis.vibe.core.exceptions - package org.molgenis.vibe.core.exceptions
org.molgenis.vibe.core.formats - package org.molgenis.vibe.core.formats
org.molgenis.vibe.core.io.input - package org.molgenis.vibe.core.io.input
org.molgenis.vibe.core.ontology_processing - package org.molgenis.vibe.core.ontology_processing
org.molgenis.vibe.core.query_output_digestion.prioritization - package org.molgenis.vibe.core.query_output_digestion.prioritization
org.molgenis.vibe.core.query_output_digestion.prioritization.gene - package org.molgenis.vibe.core.query_output_digestion.prioritization.gene

P

Phenotype - Class in org.molgenis.vibe.core.formats: Defines a phenotype.
Phenotype(String) - Constructor for class org.molgenis.vibe.core.formats.Phenotype
Phenotype(URI) - Constructor for class org.molgenis.vibe.core.formats.Phenotype
PhenotypeNetwork - Class in org.molgenis.vibe.core.formats: A network of Phenotypes with a single source Phenotype from which the network is created.
PhenotypeNetwork(Phenotype) - Constructor for class org.molgenis.vibe.core.formats.PhenotypeNetwork
PhenotypeNetworkCollection - Class in org.molgenis.vibe.core.formats: A collection of PhenotypeNetworks.
PhenotypeNetworkCollection() - Constructor for class org.molgenis.vibe.core.formats.PhenotypeNetworkCollection
PhenotypesRetrievalRunner - Class in org.molgenis.vibe.core: Class containing all required logic for retrieving related Phenotypes for the input Phenotypes.
PhenotypesRetrievalRunner(Path, PhenotypesRetrieverFactory, Collection<Phenotype>, Integer) - Constructor for class org.molgenis.vibe.core.PhenotypesRetrievalRunner
PhenotypesRetriever - Class in org.molgenis.vibe.core.ontology_processing: For one or more Phenotypes within an OntModel, retrieves other Phenotypes that are linked to it.
PhenotypesRetriever(OntModel, Collection<Phenotype>, int) - Constructor for class org.molgenis.vibe.core.ontology_processing.PhenotypesRetriever
PhenotypesRetrieverFactory - Enum in org.molgenis.vibe.core.ontology_processing
POST_TRANSLATIONAL_MODIFICATION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
Prioritizer<T1 extends BiologicalEntity,T2 extends BiologicalEntityCollection> - Interface in org.molgenis.vibe.core.query_output_digestion.prioritization: Returns a priority of T1 from T2.
PubmedEvidence - Class in org.molgenis.vibe.core.formats
PubmedEvidence(String, int) - Constructor for class org.molgenis.vibe.core.formats.PubmedEvidence
PubmedEvidence(URI, int) - Constructor for class org.molgenis.vibe.core.formats.PubmedEvidence

Q

QueryRunner - Class in org.molgenis.vibe.core.database_processing: Is able to run a SPARQL query on a Model.
QueryRunner(Model, QueryString) - Constructor for class org.molgenis.vibe.core.database_processing.QueryRunner
QueryString - Class in org.molgenis.vibe.core.database_processing.query_string_creation: A String that can be used for SPARQL querying.
QueryString(String) - Constructor for class org.molgenis.vibe.core.database_processing.query_string_creation.QueryString
QueryString(String, Syntax) - Constructor for class org.molgenis.vibe.core.database_processing.query_string_creation.QueryString
QueryStringGenerator - Class in org.molgenis.vibe.core.database_processing.query_string_creation: Generates SPARQL queries specific for the DisGeNET RDF dataset.
QueryStringPathRange - Class in org.molgenis.vibe.core.database_processing.query_string_creation: A String defining the path which should be used in the RDF graph.
QueryStringPathRange(int) - Constructor for class org.molgenis.vibe.core.database_processing.query_string_creation.QueryStringPathRange
QueryStringPathRange(int, boolean) - Constructor for class org.molgenis.vibe.core.database_processing.query_string_creation.QueryStringPathRange
QueryStringPathRange(int, int) - Constructor for class org.molgenis.vibe.core.database_processing.query_string_creation.QueryStringPathRange

R

read(String) - Method in class org.molgenis.vibe.core.io.input.ModelFilesReader: Adds the file to the existing Model
read(String, Lang) - Method in class org.molgenis.vibe.core.io.input.ModelFilesReader: Adds the file to the existing Model
readDatabase(Path) - Method in enum org.molgenis.vibe.core.io.input.ModelReaderFactory
RELEASE_YEAR_COMPARATOR - Static variable in class org.molgenis.vibe.core.formats.PubmedEvidence: Sorts PubmedEvidence first on PubmedEvidence.getReleaseYear() (most recent first) and then by ID (as int, lowest to highest).
remove(Object) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
remove(Phenotype) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetworkCollection: Removes a PhenotypeNetwork from the PhenotypeNetworkCollection.
remove(PhenotypeNetwork) - Method in class org.molgenis.vibe.core.formats.PhenotypeNetworkCollection: Removes a PhenotypeNetwork from the PhenotypeNetworkCollection.
removeAll(Collection<?>) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
ResourceUri - Interface in org.molgenis.vibe.core.formats: An Object that also contains a reference to the unique ID within an RDF database (and this reference is an URI).
retainAll(Collection<?>) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
retrieve(String) - Static method in enum org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
retrieve(String) - Static method in enum org.molgenis.vibe.core.ontology_processing.PhenotypesRetrieverFactory
retrieve(String, Class<T>) - Static method in interface org.molgenis.vibe.core.formats.EnumTypeDefiner: Retrieves Enum type based on a given String (using EnumTypeDefiner.getId() for comparison).
retrieveIdFromString(String) - Method in class org.molgenis.vibe.core.formats.Entity: Validates and retrieves the ID from a String describing an id (that also includes other information such as a prefix).
retrieveLevelByString(String) - Static method in enum org.molgenis.vibe.core.formats.Source.Level: Retrieves the Source.Level based on a String.
retrievePhenotypeFromModel(Phenotype) - Method in class org.molgenis.vibe.core.ontology_processing.PhenotypesRetriever
retrieveSources() - Method in class org.molgenis.vibe.core.database_processing.DisgenetRdfDataRetriever: Retrieves sources from the database.
ROOT - Static variable in enum org.molgenis.vibe.core.formats.GeneDiseaseCombinationType: The root GeneDiseaseCombinationType of all association types available in this enum
run() - Method in class org.molgenis.vibe.core.database_processing.DisgenetRdfDataRetriever
run() - Method in class org.molgenis.vibe.core.database_processing.GenesForPhenotypeRetriever
run() - Method in class org.molgenis.vibe.core.ontology_processing.ChildrenRetriever
run() - Method in class org.molgenis.vibe.core.ontology_processing.MaxDistanceRetriever
run() - Method in class org.molgenis.vibe.core.ontology_processing.PhenotypesRetriever

S

serialize(GeneDiseaseCollection, Type, JsonSerializationContext) - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionSerializer
setName(String) - Method in class org.molgenis.vibe.core.formats.Entity
size() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
skippableUri(OntClass) - Method in class org.molgenis.vibe.core.ontology_processing.PhenotypesRetriever: Checks whether an URI is skippable.
SOMATIC_CASUAL_MUTATION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
SOMATIC_MODIFYING_MUTATION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
sort(GeneDiseaseCollection) - Method in interface org.molgenis.vibe.core.query_output_digestion.prioritization.gene.GenePrioritizer
sort(GeneDiseaseCollection) - Method in class org.molgenis.vibe.core.query_output_digestion.prioritization.gene.HighestSingleDisgenetScoreGenePrioritizer
sort(T2) - Method in interface org.molgenis.vibe.core.query_output_digestion.prioritization.Prioritizer: Sorts the given list.
Source - Class in org.molgenis.vibe.core.formats: Describes the source (the database) for a specific piece of information.
Source(URI, String, String) - Constructor for class org.molgenis.vibe.core.formats.Source: A constructor for describing a source with an URI id from an RDF database.
Source(URI, String, Source.Level) - Constructor for class org.molgenis.vibe.core.formats.Source: A constructor for describing a source with an URI id from an RDF database.
SOURCE_FULL_NAME_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
SOURCE_LEVEL_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
SOURCE_URI_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
Source.Level - Enum in org.molgenis.vibe.core.formats: The possible Source levels.
SOURCES_KEY - Static variable in class org.molgenis.vibe.core.formats.GeneDiseaseCollectionJsonSerialization
SUSCEPTIBILITY_MUTATION - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType

T

THERAPEUTIC - org.molgenis.vibe.core.formats.GeneDiseaseCombinationType
toArray() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
toArray(T[]) - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
toString() - Method in class org.molgenis.vibe.core.database_processing.query_string_creation.QueryStringPathRange
toString() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCollection
toString() - Method in class org.molgenis.vibe.core.formats.BiologicalEntityCombination
toString() - Method in class org.molgenis.vibe.core.formats.Disease
toString() - Method in class org.molgenis.vibe.core.formats.Entity: While uniqueness is based on the Entity.id (as each Entity.id should only occur once and data belonging to it should be consistent), Entity.toString() can be used for testing whether data retrieval from external sources yielded the expected results.
toString() - Method in class org.molgenis.vibe.core.formats.Gene: While uniqueness is based on the Entity.id (as each Entity.id should only occur once and data belonging to it should be consistent), Entity.toString() can be used for testing whether data retrieval from external sources yielded the expected results.
toString() - Method in class org.molgenis.vibe.core.formats.GeneDiseaseCombination
toString() - Method in class org.molgenis.vibe.core.formats.GeneSymbol
toString() - Method in class org.molgenis.vibe.core.formats.Phenotype
toString() - Method in class org.molgenis.vibe.core.formats.PhenotypeNetwork
toString() - Method in class org.molgenis.vibe.core.formats.PhenotypeNetworkCollection
toString() - Method in class org.molgenis.vibe.core.formats.PubmedEvidence
toString() - Method in class org.molgenis.vibe.core.formats.Source

V

valueOf(String) - Static method in enum org.molgenis.vibe.core.formats.GeneDiseaseCombinationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.vibe.core.formats.Source.Level: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.vibe.core.io.input.ModelReaderFactory: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.vibe.core.ontology_processing.PhenotypesRetrieverFactory: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.molgenis.vibe.core.formats.GeneDiseaseCombinationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.vibe.core.formats.Source.Level: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.vibe.core.io.input.ModelReaderFactory: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.vibe.core.ontology_processing.PhenotypesRetrieverFactory: Returns an array containing the constants of this enum type, in the order they are declared.
VibeDatabase - Class in org.molgenis.vibe.core.io.input: A vibe database that can be accessed through retrieving the ModelReader.
VibeDatabase(Path, ModelReaderFactory) - Constructor for class org.molgenis.vibe.core.io.input.VibeDatabase

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