A C E F G I L N O P R S T U V W

A

apply(T) - Method in interface org.molgenis.pathways.service.RemoteFunction

applyThrows(T) - Method in interface org.molgenis.pathways.service.RemoteFunction

C

CacheFactory - Class in org.molgenis.pathways.service

Helper methods to create LoadingCaches.

CacheFactory() - Constructor for class org.molgenis.pathways.service.CacheFactory

connect(String, HttpClient) - Static method in class org.molgenis.wikipathways.utils.Utils

create(String, String) - Static method in class org.molgenis.pathways.model.Pathway

create(WSPathwayInfo) - Static method in class org.molgenis.pathways.model.Pathway

create(WSSearchResult) - Static method in class org.molgenis.pathways.model.Pathway

createPathway(String, WSAuth) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

createPathway(String, WSAuth) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

E

EFFECT_ATTRIBUTE_NAME - Static variable in class org.molgenis.pathways.WikiPathwaysController

F

findInteractions(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

findInteractions(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

findPathwaysByLiterature(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

findPathwaysByLiterature(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

findPathwaysByText(String, String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

findPathwaysByText(String, String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

findPathwaysByXref(String[], String[]) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

findPathwaysByXref(String[], String[]) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

G

getAction() - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

getAllPathways(String) - Method in class org.molgenis.pathways.service.WikiPathwaysService

Retrieves all pathways for a species.

getAllPathways() - Method in class org.molgenis.pathways.WikiPathwaysController

Retrieves all pathways.

getColor() - Method in enum org.molgenis.pathways.model.Impact

getColoredPathway(String, String) - Method in class org.molgenis.pathways.WikiPathwaysController

Retrieves a colored pathway.

getColoredPathway(String, String, String[], String[], String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getColoredPathway(String, String, String[], String[], String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getColoredPathwayImage(String, Map<String, Impact>) - Method in class org.molgenis.pathways.service.WikiPathwaysService

Retrieves a colored pathway image

getComment() - Method in class org.molgenis.wikipathways.client.WSHistoryRow

getCurationTagHistory(String, String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getCurationTagHistory(String, String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getCurationTags(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getCurationTags(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getCurationTagsByName(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getCurationTagsByName(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getDisplayName() - Method in class org.molgenis.wikipathways.client.WSCurationTag

getFields() - Method in class org.molgenis.wikipathways.client.WSSearchResult

getFields(int) - Method in class org.molgenis.wikipathways.client.WSSearchResult

getFilteredPathways(String, String) - Method in class org.molgenis.pathways.service.WikiPathwaysService

Searches pathways.

getFilteredPathways(String) - Method in class org.molgenis.pathways.WikiPathwaysController

Searches pathways.

getGpml() - Method in class org.molgenis.wikipathways.client.WSPathway

getHistory() - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

getHistory(int) - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

getId() - Method in class org.molgenis.pathways.model.Pathway

getId() - Method in class org.molgenis.wikipathways.client.WSOntologyTerm

getId() - Method in class org.molgenis.wikipathways.client.WSPathway

getId() - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

getId() - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

getId() - Method in class org.molgenis.wikipathways.client.WSSearchResult

getKey() - Method in class org.molgenis.wikipathways.client.WSAuth

getListOfPathwayNamesByGenes(String) - Method in class org.molgenis.pathways.WikiPathwaysController

Retrieves all pathways for the genes in a vcf.

getName() - Method in class org.molgenis.pathways.model.Pathway

getName() - Method in class org.molgenis.wikipathways.client.WSCurationTag

getName() - Method in class org.molgenis.wikipathways.client.WSIndexField

getName() - Method in class org.molgenis.wikipathways.client.WSOntologyTerm

getName() - Method in class org.molgenis.wikipathways.client.WSPathway

getName() - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

getName() - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

getName() - Method in class org.molgenis.wikipathways.client.WSSearchResult

getOntology() - Method in class org.molgenis.wikipathways.client.WSOntologyTerm

getOntologyTermsByPathway(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getOntologyTermsByPathway(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getPathway(String) - Method in class org.molgenis.pathways.WikiPathwaysController

Retrieves uncolored pathway image.

getPathway(String, int) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getPathway(String, int) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getPathway() - Method in class org.molgenis.wikipathways.client.WSCurationTag

getPathwayAs(String, String, int) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getPathwayAs(String, String, int) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getPathwayGPML(String) - Method in class org.molgenis.pathways.service.WikiPathwaysService

Retrieves the GPML of the current version of a pathway

getPathwayHistory(String, String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getPathwayHistory(String, String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getPathwayId() - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

getPathwayInfo(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getPathwayInfo(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getPathwaysByOntologyTerm(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getPathwaysByOntologyTerm(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getPathwaysByParentOntologyTerm(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getPathwaysByParentOntologyTerm(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getPathwaysForGene(String, String) - Method in class org.molgenis.pathways.service.WikiPathwaysService

Retrieves pathways according to gene, filtered for a certain species.

getRecentChanges(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getRecentChanges(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getRevision() - Method in class org.molgenis.wikipathways.client.WSCurationTag

getRevision() - Method in class org.molgenis.wikipathways.client.WSHistoryRow

getRevision() - Method in class org.molgenis.wikipathways.client.WSPathway

getRevision() - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

getRevision() - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

getRevision() - Method in class org.molgenis.wikipathways.client.WSSearchResult

getScore() - Method in class org.molgenis.wikipathways.client.WSSearchResult

getSpecies() - Method in class org.molgenis.wikipathways.client.WSPathway

getSpecies() - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

getSpecies() - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

getSpecies() - Method in class org.molgenis.wikipathways.client.WSSearchResult

getTagName() - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

getText() - Method in class org.molgenis.wikipathways.client.WSCurationTag

getText() - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

getTime() - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

getTimeModified() - Method in class org.molgenis.wikipathways.client.WSCurationTag

getTimestamp() - Method in class org.molgenis.wikipathways.client.WSHistoryRow

getUncoloredPathwayImage(String) - Method in class org.molgenis.pathways.service.WikiPathwaysService

Retrieves an uncolored pathway image

getUrl() - Method in class org.molgenis.wikipathways.client.WSPathway

getUrl() - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

getUrl() - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

getUrl() - Method in class org.molgenis.wikipathways.client.WSSearchResult

getUser() - Method in class org.molgenis.wikipathways.client.WSAuth

getUser() - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

getUser() - Method in class org.molgenis.wikipathways.client.WSHistoryRow

getUserByOrcid(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getUserByOrcid(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

getUserModified() - Method in class org.molgenis.wikipathways.client.WSCurationTag

getValues() - Method in class org.molgenis.wikipathways.client.WSIndexField

getValues(int) - Method in class org.molgenis.wikipathways.client.WSIndexField

getXrefList(String, String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

getXrefList(String, String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

I

Impact - Enum in org.molgenis.pathways.model

Impact of a variant in a VCF file.

init(Model) - Method in class org.molgenis.pathways.WikiPathwaysController

Shows the start screen.

L

listOrganisms() - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

listOrganisms() - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

listPathways(String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

listPathways(String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

loadingCache(RemoteFunction<K, V>) - Static method in class org.molgenis.pathways.service.CacheFactory

Creates a LoadingCache for a FunctionalInterface that may throw a RemoteException

loadingPathwayCache(RemoteFunction<Params, Result[]>, BiPredicate<Params, Result>, Function<Result, Pathway>) - Static method in class org.molgenis.pathways.service.CacheFactory

Creates a LoadingCache for Pathways

login(String, String) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

login(String, String) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

N

NS1 - Static variable in class org.molgenis.wikipathways.client.WSNamespaces

NS2 - Static variable in class org.molgenis.wikipathways.client.WSNamespaces

O

org.molgenis.pathways - package org.molgenis.pathways

org.molgenis.pathways.model - package org.molgenis.pathways.model

org.molgenis.pathways.service - package org.molgenis.pathways.service

org.molgenis.wikipathways.client - package org.molgenis.wikipathways.client

org.molgenis.wikipathways.utils - package org.molgenis.wikipathways.utils

P

parseCurationTag(Element) - Static method in class org.molgenis.wikipathways.utils.Utils

parseCurationTagHistory(Element) - Static method in class org.molgenis.wikipathways.utils.Utils

parseHistoryRow(Element) - Static method in class org.molgenis.wikipathways.utils.Utils

parseOntologyTerm(Element) - Static method in class org.molgenis.wikipathways.utils.Utils

parsePathway(Element) - Static method in class org.molgenis.wikipathways.utils.Utils

parsePathwayHistory(Element) - Static method in class org.molgenis.wikipathways.utils.Utils

parseWSIndexField(Element) - Static method in class org.molgenis.wikipathways.utils.Utils

parseWSPathwayInfo(Element) - Static method in class org.molgenis.wikipathways.utils.Utils

parseWSSearchResult(Element) - Static method in class org.molgenis.wikipathways.utils.Utils

Pathway - Class in org.molgenis.pathways.model

Name and ID of a Pathway

Pathway() - Constructor for class org.molgenis.pathways.model.Pathway

PathwaysConfig - Class in org.molgenis.pathways

PathwaysConfig() - Constructor for class org.molgenis.pathways.PathwaysConfig

R

RemoteFunction<T,R> - Interface in org.molgenis.pathways.service

FunctionalInterface for a Function that can throw a RemoteException.

removeCurationTag(String, String, WSAuth) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

removeCurationTag(String, String, WSAuth) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

removeOntologyTag(String, String, WSAuth) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

removeOntologyTag(String, String, WSAuth) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

S

saveCurationTag(String, String, String, int, WSAuth) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

saveCurationTag(String, String, String, int, WSAuth) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

saveOntologyTag(String, String, String, WSAuth) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

saveOntologyTag(String, String, String, WSAuth) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

service() - Method in class org.molgenis.pathways.PathwaysConfig

setAction(String) - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

setComment(String) - Method in class org.molgenis.wikipathways.client.WSHistoryRow

setDisplayName(String) - Method in class org.molgenis.wikipathways.client.WSCurationTag

setFields(WSIndexField[]) - Method in class org.molgenis.wikipathways.client.WSSearchResult

setFields(int, WSIndexField) - Method in class org.molgenis.wikipathways.client.WSSearchResult

setGpml(String) - Method in class org.molgenis.wikipathways.client.WSPathway

setHistory(WSHistoryRow[]) - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

setHistory(int, WSHistoryRow) - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

setId(String) - Method in class org.molgenis.wikipathways.client.WSOntologyTerm

setId(String) - Method in class org.molgenis.wikipathways.client.WSPathway

setId(String) - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

setId(String) - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

setId(String) - Method in class org.molgenis.wikipathways.client.WSSearchResult

setKey(String) - Method in class org.molgenis.wikipathways.client.WSAuth

setName(String) - Method in class org.molgenis.wikipathways.client.WSCurationTag

setName(String) - Method in class org.molgenis.wikipathways.client.WSIndexField

setName(String) - Method in class org.molgenis.wikipathways.client.WSOntologyTerm

setName(String) - Method in class org.molgenis.wikipathways.client.WSPathway

setName(String) - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

setName(String) - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

setName(String) - Method in class org.molgenis.wikipathways.client.WSSearchResult

setOntology(String) - Method in class org.molgenis.wikipathways.client.WSOntologyTerm

setPathway(WSPathwayInfo) - Method in class org.molgenis.wikipathways.client.WSCurationTag

setPathwayId(String) - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

setRevision(String) - Method in class org.molgenis.wikipathways.client.WSCurationTag

setRevision(String) - Method in class org.molgenis.wikipathways.client.WSHistoryRow

setRevision(String) - Method in class org.molgenis.wikipathways.client.WSPathway

setRevision(String) - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

setRevision(String) - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

setRevision(String) - Method in class org.molgenis.wikipathways.client.WSSearchResult

setScore(double) - Method in class org.molgenis.wikipathways.client.WSSearchResult

setSpecies(String) - Method in class org.molgenis.wikipathways.client.WSPathway

setSpecies(String) - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

setSpecies(String) - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

setSpecies(String) - Method in class org.molgenis.wikipathways.client.WSSearchResult

setTagName(String) - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

setText(String) - Method in class org.molgenis.wikipathways.client.WSCurationTag

setText(String) - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

setTime(String) - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

setTimeModified(long) - Method in class org.molgenis.wikipathways.client.WSCurationTag

setTimestamp(String) - Method in class org.molgenis.wikipathways.client.WSHistoryRow

setUrl(String) - Method in class org.molgenis.wikipathways.client.WSPathway

setUrl(String) - Method in class org.molgenis.wikipathways.client.WSPathwayHistory

setUrl(String) - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

setUrl(String) - Method in class org.molgenis.wikipathways.client.WSSearchResult

setUser(String) - Method in class org.molgenis.wikipathways.client.WSAuth

setUser(String) - Method in class org.molgenis.wikipathways.client.WSCurationTagHistory

setUser(String) - Method in class org.molgenis.wikipathways.client.WSHistoryRow

setUserModified(String) - Method in class org.molgenis.wikipathways.client.WSCurationTag

setValues(String[]) - Method in class org.molgenis.wikipathways.client.WSIndexField

setValues(int, String) - Method in class org.molgenis.wikipathways.client.WSIndexField

T

toString() - Method in class org.molgenis.wikipathways.client.WSAuth

toString() - Method in class org.molgenis.wikipathways.client.WSOntologyTerm

toString() - Method in class org.molgenis.wikipathways.client.WSPathwayInfo

U

update(String, HttpClient, Map<String, String>) - Static method in class org.molgenis.wikipathways.utils.Utils

updatePathway(String, String, String, int, WSAuth) - Method in interface org.molgenis.wikipathways.client.WikiPathwaysPortType

updatePathway(String, String, String, int, WSAuth) - Method in class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

URI - Static variable in class org.molgenis.pathways.WikiPathwaysController

Utils - Class in org.molgenis.wikipathways.utils

Utils() - Constructor for class org.molgenis.wikipathways.utils.Utils

V

valueOf(String) - Static method in enum org.molgenis.pathways.model.Impact

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.molgenis.pathways.model.Impact

Returns an array containing the constants of this enum type, in the order they are declared.

W

WikiPathwaysController - Class in org.molgenis.pathways

WikiPathwaysController(WikiPathwaysService) - Constructor for class org.molgenis.pathways.WikiPathwaysController

WikiPathwaysPortType - Interface in org.molgenis.wikipathways.client

WikiPathwaysRESTBindingStub - Class in org.molgenis.wikipathways.client

connects to the new WikiPathways REST webservice

WikiPathwaysRESTBindingStub(HttpClient, String) - Constructor for class org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

WikiPathwaysService - Class in org.molgenis.pathways.service

Interacts with WikiPathways.

WikiPathwaysService(WikiPathwaysPortType) - Constructor for class org.molgenis.pathways.service.WikiPathwaysService

Creates a new WikiPathwaysService.

WSAuth - Class in org.molgenis.wikipathways.client

authentication object needed for updating and saving data to WP

WSAuth(String, String) - Constructor for class org.molgenis.wikipathways.client.WSAuth

WSCurationTag - Class in org.molgenis.wikipathways.client

curation tag data object

WSCurationTag(String, String, WSPathwayInfo, String, String, long, String) - Constructor for class org.molgenis.wikipathways.client.WSCurationTag

WSCurationTagHistory - Class in org.molgenis.wikipathways.client

curation tag history object

WSCurationTagHistory(String, String, String, String, String, String) - Constructor for class org.molgenis.wikipathways.client.WSCurationTagHistory

WSHistoryRow - Class in org.molgenis.wikipathways.client

contains one point in the history of a pathway

WSHistoryRow(String, String, String, String) - Constructor for class org.molgenis.wikipathways.client.WSHistoryRow

WSIndexField - Class in org.molgenis.wikipathways.client

one field in a WP Index

WSIndexField(String, String[]) - Constructor for class org.molgenis.wikipathways.client.WSIndexField

WSNamespaces - Class in org.molgenis.wikipathways.client

WP namespaces

WSNamespaces() - Constructor for class org.molgenis.wikipathways.client.WSNamespaces

WSOntologyTerm - Class in org.molgenis.wikipathways.client

ontology term object

WSOntologyTerm(String, String, String) - Constructor for class org.molgenis.wikipathways.client.WSOntologyTerm

WSPathway - Class in org.molgenis.wikipathways.client

contains all information about a pathway

WSPathway(String, String, String, String, String, String) - Constructor for class org.molgenis.wikipathways.client.WSPathway

WSPathwayHistory - Class in org.molgenis.wikipathways.client

contains the history of a pathway

WSPathwayHistory(WSHistoryRow[], String, String, String, String, String) - Constructor for class org.molgenis.wikipathways.client.WSPathwayHistory

WSPathwayInfo - Class in org.molgenis.wikipathways.client

contains basic information about a pathway

WSPathwayInfo(String, String, String, String, String) - Constructor for class org.molgenis.wikipathways.client.WSPathwayInfo

WSSearchResult - Class in org.molgenis.wikipathways.client

contains a search result from the WP webservice

WSSearchResult() - Constructor for class org.molgenis.wikipathways.client.WSSearchResult

WSSearchResult(double, WSIndexField[], String, String, String, String, String) - Constructor for class org.molgenis.wikipathways.client.WSSearchResult

A C E F G I L N O P R S T U V W