A C D E G H I M O S U V W

A

add(ModuleConfig) - Method in class org.molgenis.dataexplorer.controller.ModulesConfigResponse

AggregateRequest - Class in org.molgenis.dataexplorer.controller

AggregateRequest() - Constructor for class org.molgenis.dataexplorer.controller.AggregateRequest

AggregateResponse - Class in org.molgenis.dataexplorer.controller

AggregateResponse(List<List<Long>>, Set<String>, Set<String>) - Constructor for class org.molgenis.dataexplorer.controller.AggregateResponse

annotateData(HttpServletRequest, String[], String) - Method in class org.molgenis.dataexplorer.controller.AnnotatorController

Annotates an entity based on selected entity and selected annotators.

AnnotationJob - Class in org.molgenis.dataexplorer.controller

AnnotationJob(CrudRepositoryAnnotator, String, List<RepositoryAnnotator>, Repository, Progress, Authentication, TransactionTemplate) - Constructor for class org.molgenis.dataexplorer.controller.AnnotationJob

AnnotationJobFactory - Class in org.molgenis.dataexplorer.controller

Creates AnnotationJob based on its AnnotationJobExecution.

AnnotationJobFactory() - Constructor for class org.molgenis.dataexplorer.controller.AnnotationJobFactory

AnnotatorController - Class in org.molgenis.dataexplorer.controller

AnnotatorController(DataService, AnnotationService, MolgenisPermissionService, PermissionSystemService, UserAccountService, AnnotationJobFactory, ExecutorService) - Constructor for class org.molgenis.dataexplorer.controller.AnnotatorController

C

call(Progress) - Method in class org.molgenis.dataexplorer.controller.AnnotationJob

createJob(AnnotationJobExecution) - Method in class org.molgenis.dataexplorer.controller.AnnotationJobFactory

D

DataExplorerController - Class in org.molgenis.dataexplorer.controller

Controller class for the data explorer.

DataExplorerController() - Constructor for class org.molgenis.dataexplorer.controller.DataExplorerController

DataExplorerDownloadHandler - Class in org.molgenis.dataexplorer.download

DataExplorerDownloadHandler(DataService) - Constructor for class org.molgenis.dataexplorer.download.DataExplorerDownloadHandler

DataExplorerHyperlinkDirective - Class in org.molgenis.dataexplorer.freemarker

Creates a link to the dataexplorer for a dataset usage: <@dataExplorerLink dataset='celiacsprue' class='btn'>Explore data created html: Explore data

DataExplorerHyperlinkDirective(MolgenisPluginRegistry, DataService) - Constructor for class org.molgenis.dataexplorer.freemarker.DataExplorerHyperlinkDirective

DataExplorerSettings - Class in org.molgenis.dataexplorer.settings

DataExplorerSettings() - Constructor for class org.molgenis.dataexplorer.settings.DataExplorerSettings

DataRequest - Class in org.molgenis.dataexplorer.controller

DataRequest() - Constructor for class org.molgenis.dataexplorer.controller.DataRequest

DataRequest.ColNames - Enum in org.molgenis.dataexplorer.controller

DataRequest.DownloadType - Enum in org.molgenis.dataexplorer.controller

DataRequest.EntityValues - Enum in org.molgenis.dataexplorer.controller

download(String, HttpServletResponse) - Method in class org.molgenis.dataexplorer.controller.DataExplorerController

E

execute(Environment, Map, TemplateModel[], TemplateDirectiveBody) - Method in class org.molgenis.dataexplorer.freemarker.DataExplorerHyperlinkDirective

export(String, File) - Method in class org.molgenis.dataexplorer.galaxy.GalaxyDataExporter

export(String, File, String) - Method in class org.molgenis.dataexplorer.galaxy.GalaxyDataExporter

exportToGalaxy(GalaxyDataExportRequest, Model) - Method in class org.molgenis.dataexplorer.controller.DataExplorerController

G

GalaxyDataExporter - Class in org.molgenis.dataexplorer.galaxy

GalaxyDataExporter(String, String) - Constructor for class org.molgenis.dataexplorer.galaxy.GalaxyDataExporter

GalaxyDataExportException - Exception in org.molgenis.dataexplorer.galaxy

GalaxyDataExportException() - Constructor for exception org.molgenis.dataexplorer.galaxy.GalaxyDataExportException

GalaxyDataExportException(String) - Constructor for exception org.molgenis.dataexplorer.galaxy.GalaxyDataExportException

GalaxyDataExportException(String, Throwable) - Constructor for exception org.molgenis.dataexplorer.galaxy.GalaxyDataExportException

GalaxyDataExportException(Throwable) - Constructor for exception org.molgenis.dataexplorer.galaxy.GalaxyDataExportException

GalaxyDataExportRequest - Class in org.molgenis.dataexplorer.galaxy

GalaxyDataExportRequest() - Constructor for class org.molgenis.dataexplorer.galaxy.GalaxyDataExportRequest

getAggregatesDistinctOverrides() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getAggregatesDistinctSelect() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getAttributeNames() - Method in class org.molgenis.dataexplorer.controller.DataRequest

getColNames() - Method in class org.molgenis.dataexplorer.controller.DataRequest

getDataRequest() - Method in class org.molgenis.dataexplorer.galaxy.GalaxyDataExportRequest

getDistinctAttributeName() - Method in class org.molgenis.dataexplorer.controller.AggregateRequest

getDownloadType() - Method in class org.molgenis.dataexplorer.controller.DataRequest

getEntityName() - Method in class org.molgenis.dataexplorer.controller.AggregateRequest

getEntityName() - Method in class org.molgenis.dataexplorer.controller.DataRequest

getEntityReport(String) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getEntityReports() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getEntityValues() - Method in class org.molgenis.dataexplorer.controller.DataRequest

getGalaxyApiKey() - Method in class org.molgenis.dataexplorer.galaxy.GalaxyDataExportRequest

getGalaxyExport() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getGalaxyUrl() - Method in class org.molgenis.dataexplorer.galaxy.GalaxyDataExportRequest

getGalaxyUrl() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getGenomeBrowser() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getGenomeBrowserCoordSystem() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getGenomeBrowserHighlightRegion() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getGenomeBrowserLinks() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getGenomeBrowserLocation() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getGenomeBrowserSources() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getHeaderAbbreviate() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getIcon() - Method in class org.molgenis.dataexplorer.controller.ModuleConfig

getId() - Method in class org.molgenis.dataexplorer.controller.ModuleConfig

getItemSelection() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getLabel() - Method in class org.molgenis.dataexplorer.controller.ModuleConfig

getLaunchWizard() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getMapOfAvailableAnnotators(String) - Method in class org.molgenis.dataexplorer.controller.AnnotatorController

Gets a map of all available annotators.

getMatrix() - Method in class org.molgenis.dataexplorer.controller.AggregateResponse

getModAggregates() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getModAnnotators() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getModCharts() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getModData() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getModReports() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getModule(String, String, Model) - Method in class org.molgenis.dataexplorer.controller.DataExplorerController

getModules(String) - Method in class org.molgenis.dataexplorer.controller.DataExplorerController

Returns modules configuration for this entity based on current user permissions.

getQ() - Method in class org.molgenis.dataexplorer.controller.AggregateRequest

getQuery() - Method in class org.molgenis.dataexplorer.controller.DataRequest

getSearchbox() - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

getXAxisAttributeName() - Method in class org.molgenis.dataexplorer.controller.AggregateRequest

getxLabels() - Method in class org.molgenis.dataexplorer.controller.AggregateResponse

getYAxisAttributeName() - Method in class org.molgenis.dataexplorer.controller.AggregateRequest

getyLabels() - Method in class org.molgenis.dataexplorer.controller.AggregateResponse

H

handleGalaxyDataExportException(GalaxyDataExportException) - Method in class org.molgenis.dataexplorer.controller.DataExplorerController

handleRuntimeException(RuntimeException) - Method in class org.molgenis.dataexplorer.controller.AnnotatorController

handleRuntimeException(RuntimeException) - Method in class org.molgenis.dataexplorer.controller.DataExplorerController

I

ID - Static variable in class org.molgenis.dataexplorer.controller.DataExplorerController

init(String, Model) - Method in class org.molgenis.dataexplorer.controller.DataExplorerController

Show the explorer page

InputValidationException - Exception in org.molgenis.dataexplorer.controller

InputValidationException() - Constructor for exception org.molgenis.dataexplorer.controller.InputValidationException

InputValidationException(String) - Constructor for exception org.molgenis.dataexplorer.controller.InputValidationException

InputValidationException(Throwable) - Constructor for exception org.molgenis.dataexplorer.controller.InputValidationException

InputValidationException(String, Throwable) - Constructor for exception org.molgenis.dataexplorer.controller.InputValidationException

InputValidationException(String, Throwable, boolean, boolean) - Constructor for exception org.molgenis.dataexplorer.controller.InputValidationException

M

MOD_ANNOTATORS - Static variable in class org.molgenis.dataexplorer.controller.DataExplorerController

MOD_DATA - Static variable in class org.molgenis.dataexplorer.controller.DataExplorerController

MOD_ENTITIESREPORT - Static variable in class org.molgenis.dataexplorer.controller.DataExplorerController

ModuleConfig - Class in org.molgenis.dataexplorer.controller

ModuleConfig(String, String, String) - Constructor for class org.molgenis.dataexplorer.controller.ModuleConfig

ModulesConfigResponse - Class in org.molgenis.dataexplorer.controller

ModulesConfigResponse() - Constructor for class org.molgenis.dataexplorer.controller.ModulesConfigResponse

O

org.molgenis.dataexplorer.controller - package org.molgenis.dataexplorer.controller

org.molgenis.dataexplorer.download - package org.molgenis.dataexplorer.download

org.molgenis.dataexplorer.freemarker - package org.molgenis.dataexplorer.freemarker

org.molgenis.dataexplorer.galaxy - package org.molgenis.dataexplorer.galaxy

org.molgenis.dataexplorer.settings - package org.molgenis.dataexplorer.settings

S

scheduleAnnotatorRun(String, String[]) - Method in class org.molgenis.dataexplorer.controller.AnnotatorController

setAggregatesDistinctOverrides(Map<String, String>) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setAggregatesDistinctSelect(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setAttributeNames(List<String>) - Method in class org.molgenis.dataexplorer.controller.DataRequest

setColNames(DataRequest.ColNames) - Method in class org.molgenis.dataexplorer.controller.DataRequest

setDataRequest(DataRequest) - Method in class org.molgenis.dataexplorer.galaxy.GalaxyDataExportRequest

setDistinctAttributeName(String) - Method in class org.molgenis.dataexplorer.controller.AggregateRequest

setDownloadType(DataRequest.DownloadType) - Method in class org.molgenis.dataexplorer.controller.DataRequest

setEntityName(String) - Method in class org.molgenis.dataexplorer.controller.AggregateRequest

setEntityName(String) - Method in class org.molgenis.dataexplorer.controller.DataRequest

setEntityReports(String) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setEntityValues(DataRequest.EntityValues) - Method in class org.molgenis.dataexplorer.controller.DataRequest

setGalaxyApiKey(String) - Method in class org.molgenis.dataexplorer.galaxy.GalaxyDataExportRequest

setGalaxyExport(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setGalaxyUrl(String) - Method in class org.molgenis.dataexplorer.galaxy.GalaxyDataExportRequest

setGalaxyUrl(URI) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setGenomeBrowser(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setGenomeBrowserCoordSystem(String) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setGenomeBrowserHighlightRegion(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setGenomeBrowserLinks(String) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setGenomeBrowserLocation(String) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setGenomeBrowserSources(String) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setHeaderAbbreviate(int) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setItemSelection(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setLaunchWizard(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setModAggregates(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setModAnnotators(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setModCharts(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setModData(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setModReports(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setQ(List<QueryRule>) - Method in class org.molgenis.dataexplorer.controller.AggregateRequest

setQuery(QueryImpl) - Method in class org.molgenis.dataexplorer.controller.DataRequest

setSearchbox(boolean) - Method in class org.molgenis.dataexplorer.settings.DataExplorerSettings

setXAxisAttributeName(String) - Method in class org.molgenis.dataexplorer.controller.AggregateRequest

setYAxisAttributeName(String) - Method in class org.molgenis.dataexplorer.controller.AggregateRequest

showCopy(String) - Method in class org.molgenis.dataexplorer.controller.DataExplorerController

U

URI - Static variable in class org.molgenis.dataexplorer.controller.AnnotatorController

URI - Static variable in class org.molgenis.dataexplorer.controller.DataExplorerController

V

valueOf(String) - Static method in enum org.molgenis.dataexplorer.controller.DataRequest.ColNames

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

valueOf(String) - Static method in enum org.molgenis.dataexplorer.controller.DataRequest.DownloadType

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

valueOf(String) - Static method in enum org.molgenis.dataexplorer.controller.DataRequest.EntityValues

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

values() - Static method in enum org.molgenis.dataexplorer.controller.DataRequest.ColNames

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

values() - Static method in enum org.molgenis.dataexplorer.controller.DataRequest.DownloadType

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

values() - Static method in enum org.molgenis.dataexplorer.controller.DataRequest.EntityValues

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

viewEntityDetails(String, String, Model) - Method in class org.molgenis.dataexplorer.controller.DataExplorerController

Builds a model containing one entity and returns the entityReport ftl view

W

writeToCsv(DataRequest, OutputStream, char) - Method in class org.molgenis.dataexplorer.download.DataExplorerDownloadHandler

writeToCsv(DataRequest, OutputStream, char, boolean) - Method in class org.molgenis.dataexplorer.download.DataExplorerDownloadHandler

writeToExcel(DataRequest, OutputStream) - Method in class org.molgenis.dataexplorer.download.DataExplorerDownloadHandler

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