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A

addNode(ConceptCoordinates) - Method in class de.julielab.concepts.db.creators.Forest

Adds a new node with the given ID if there is not yet a node with that ID.

addNode(ConceptCoordinates, Node) - Method in class de.julielab.concepts.db.creators.Forest

addNode(ConceptCoordinates, ConceptCoordinates) - Method in class de.julielab.concepts.db.creators.Forest

addNode(ConceptCoordinates, Iterable<ConceptCoordinates>) - Method in class de.julielab.concepts.db.creators.Forest

addNode(ImportConcept) - Method in class de.julielab.concepts.db.creators.Forest

addParent(Node) - Method in class de.julielab.concepts.db.creators.Node

addToOriginalCluster(String, String) - Method in class de.julielab.concepts.db.creators.GeneOrthologyCluster

This method is used to build the original gene_orthology information where one gene is associated with a set of other genes in the "Ortholog" relation.

B

BASEPATH - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

C

convertGeneInfoToTerms(File, Set<String>, File) - Method in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

createConcepts(HierarchicalConfiguration<ImmutableNode>) - Method in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

geneInfo Original gene_info file download from the NCBI.

D

de.julielab.concepts.db.creators - package de.julielab.concepts.db.creators

E

exposeParameters(String, HierarchicalConfiguration<ImmutableNode>) - Method in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

F

Forest - Class in de.julielab.concepts.db.creators

Forest() - Constructor for class de.julielab.concepts.db.creators.Forest

G

GENE_GROUP - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

GENE_GROUP_PREFIX - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

"gene_group" is the name of the file specifying the ortholog relationships between genes.

GENE_INFO - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

GENEDESCRIPTIONS - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

GeneOrthologyCluster - Class in de.julielab.concepts.db.creators

GeneOrthologyCluster() - Constructor for class de.julielab.concepts.db.creators.GeneOrthologyCluster

getConcept() - Method in class de.julielab.concepts.db.creators.Node

getGeneCoordinates(String) - Static method in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

getId() - Method in class de.julielab.concepts.db.creators.Node

getName() - Method in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

getParents() - Method in class de.julielab.concepts.db.creators.Node

getRoot(ConceptCoordinates) - Method in class de.julielab.concepts.db.creators.Forest

getRoots(ConceptCoordinates) - Method in class de.julielab.concepts.db.creators.Forest

H

HOMOLOGENE_PREFIX - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

M

mergeOverlappingClusters() - Method in class de.julielab.concepts.db.creators.GeneOrthologyCluster

N

NCBI_GENE_SOURCE - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

NCBIGeneConceptCreator - Class in de.julielab.concepts.db.creators

NCBIGeneConceptCreator() - Constructor for class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

Node - Class in de.julielab.concepts.db.creators

Node(ConceptCoordinates) - Constructor for class de.julielab.concepts.db.creators.Node

O

ORGANISMLIST - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

ORGANISMNAMES - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

S

SEMEDICO_RESOURCE_MANAGEMENT_SOURCE - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

setConcept(ImportConcept) - Method in class de.julielab.concepts.db.creators.Node

setId(ConceptCoordinates) - Method in class de.julielab.concepts.db.creators.Node

setParents(Set<Node>) - Method in class de.julielab.concepts.db.creators.Node

T

TOP_HOMOLOGY_PREFIX - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

TOP_ORTHOLOGY_PREFIX - Static variable in class de.julielab.concepts.db.creators.NCBIGeneConceptCreator

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