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molgenis_apps-legacy-master
apps
animaldb
org
molgenis
animaldb
AnimalDBGenerate.java
AnimalDBUpdateDatabase.java
commonservice
CommonService.java
convertors
locations
ImportAteLocations.java
oldadb
LoadAnimalDB.java
prefill
PrefillAnimalDB.java
rhutdb
ConvertRhutDbToPheno.java
ulidb
ConvertUliDbToPheno.java
plugins
accessibility
AnimalDBHeader.java
AnimalDBWelcomeScreenPlugin.java
ManualPlugin.java
administration
AnimalDBReport.java
DecEntity.java
DecProject.java
DecStatus.java
DecSubproject.java
LabelGenerator.java
LabelGeneratorException.java
PrintLabelPlugin.java
ShowDecProjects.java
ShowDecSubprojects.java
VWAReport4.java
VWAReport5.java
YearlyReportModule.java
animal
AddAnimalPlugin.java
LocationPlugin.java
RemAnimalPluginMatrix.java
breeding
Breeding.java
Breedingnew.java
Litter.java
ManageLines.java
ManageLitters.java
ManageParentgroups.java
settings
BackgroundPlugin.java
GenePlugin.java
LocationInfoPlugin.java
SpeciesPlugin.java
system
AnimalDbUsers.java
CascadingDeleteAnimalsPlugin.java
ErrorCorrectionIndividualPlugin.java
ErrorCorrectionPlugin.java
LoadLegacyPlugin.java
PreFillDatabasePlugin.java
SetCustomLabelFeaturePlugin.java
viewers
AnimalDbFileViewer.java
AnimalDbFileViewerModel.java
EventViewerPluginMatrix.java
ListPluginMatrix.java
ViewFamily.java
test
AnimaldbSeleniumTest.java
arvc
org
molgenis
arvc
ArvcGenerate.java
ArvcUpdateDatabase.java
csv
UploadBatchCsvReader.java
ui
Background.java
BackgroundModel.java
ExpertSearchForm.java
Header.java
Search.java
bbmri
decorators
BiobankDecorator.java
DBIndexUpdateDecorator.java
org
molgenis
biobank
BbmriGenerate.java
BbmriUpdateDatabase.java
test
CreateAdminBiobank.java
CreateBiobank.java
CreateSimpleXlsFile.java
SearchTest.java
TestBiobankData.java
TestXlsWriter.java
UiPermissionsTest.java
VerifyNonAdminFunctionalitiesBiobank.java
testOwnInMeasurementModel.java
plugins
HtmlTree
HtmlTreePlugin.java
JqueryTree
JqueryTreePlugin.java
LuceneIndex
AdminIndexes.java
DBIndexPlugin.java
LuceneConfiguration.java
OntoCatIndexPlugin.java
OntocatQueryExpansion_lucene.java
PorterStemAnalyzer.java
TestLuceneConfFilePathClass.java
biobankers
ConceptWiki.java
contact
BbmriContactPlugin.java
header
BbmriHeader.java
help
BbmriHelpPlugin.java
listplugin
CohortsPlugin.java
CohortsPluginModel.java
mapping
GenerateN3andRDF.java
welcome
BbmriWelcomeScreenPlugin.java
bioshare
org
molgenis
bioshare
bioshareGenerate.java
bioshareUpdateDatabase.java
plugins
HarmonizationComponent
LevenshteinDistanceModel.java
LinkedInformation.java
MappingList.java
OWLFunction.java
levenshteinDistance.java
stringMatchingTest.java
tableModel.java
catalogueTreeNewVersion
catalogueTreeComponent.java
developingAlgorithm
RScriptGenerator.java
developingAlgorithm.java
testModel.java
findingProxy
RScriptGenerator.java
findingProxy.java
testModel.java
harmonization
Harmonization.java
HarmonizationModel.java
MonitorJob.java
PredictorInfo.java
StringMatchingJob.java
Terms.java
harmonizationPlugin
OntologyBuilder.java
createOntology.java
harmonizationPlugin.java
header
bioshareHeader.java
importDataWizard
bioshareImportWizard.java
welcome
bioshareWelcomeScreenPlugin.java
bioshareWelcomeScreenPluginModel.java
catalogue
org
molgenis
catalogue
OWLToPhenoMapper.java
OntologyBuilder.java
OntologyOwlLib.java
SimulateCatalogueData.java
catalogueGenerate.java
catalogueUpdateDatabase.java
test
Terms.java
TestDatatabaseSearch.java
plugins
DataTableTest.java
DataTableTestModel.java
JavascriptTests
JavascriptTestsPlugin.java
JqGridTest.java
JqGridTestModel.java
LLcatalogueSplitter
LLcatalogueSplitterPlugin.java
OpalExporter.java
OpalIndividualDataExporter.java
biobankimporter
BiobankImporter.java
TableController.java
TableField.java
catalogueTree
CatalogueTreePlugin.java
WriteExcel.java
data
ApproveUserDownloads.java
DataShaperImportExcel.java
LLDataImportExcel.java
MeasurementsDownloadForm.java
MySelectionsEditPlugin.java
OldPlacedDownloads.java
importOwlToPheno.java
emeasure
EMeasureEntityWriter.java
header
catalogueHeader.java
hl7parser
GenericDCM
HL7GenericDCM.java
HL7ObservationDCM.java
HL7OrganizerDCM.java
HL7ValueSetAnswerDCM.java
HL7ValueSetDCM.java
HL7Data.java
HL7LLData.java
HL7Main.java
HL7OntologyTerm.java
HL7PhenoImporter.java
PropertiesPath.java
StageLRA
HL7MeasurementLRA.java
HL7ObservationLRA.java
HL7OrganizerLRA.java
HL7StageLRA.java
HL7ValueSetAnswerLRA.java
HL7ValueSetLRA.java
XMLReader.java
predictionModel
Prediction.java
TableField.java
TableModel.java
predictionSelection
predictionSelectionPlugin.java
requestData
LifeLinesRequest.java
LifeLinesRequestModel.java
searchingForProxy
WriteExcel.java
treeViewProxyPlugin.java
testMeasurement.java
welcome
catalogueWelcomeScreenPlugin.java
catalogueWelcomeScreenPluginModel.java
chado
org
molgenis
chado
ChadoGenerate.java
ChadoUpdateDatabase.java
ui
Header.java
HeaderModel.java
chd7
org
molgenis
chd7
Chd7Generate.java
Chd7UpdateDatabase.java
csv
UploadBatchCsvReader.java
ui
Background.java
BackgroundModel.java
Header.java
HeaderModel.java
Search.java
Upload.java
col7a1
org
molgenis
col7a1
Col7a1Generate.java
Col7a1UpdateDatabase.java
csv
UploadBatchCsvReader.java
ui
Background.java
BackgroundModel.java
ExpertSearchForm.java
MutationPagerDecorator.java
Search.java
Upload.java
compute
org
molgenis
compute
ComputeContextListenerGen.java
ComputeGenerate.java
ComputeHeader.java
ComputeUpdateDatabase.java
ui
ComputeHeader.java
JobHostTester.java
PbsSubmitApplication.java
PbsSubmitApplicationModel.java
QstatPlugin.java
QstatPluginModel.java
SampleMatrix.java
SampleMatrixModel.java
compute_ui
org
molgenis
compute_ui
ComputeUiGenerate.java
ComputeUiUpdateDatabase.java
observ
ui
ApplyProtocol.java
ApplyProtocolModel.java
cvdb
org
molgenis
cvdb
CvdbGenerate.java
CvdbUpdateDatabase.java
designgg
org
molgenis
designgg
AskParametersScreen.java
CalculateDesignScreen.java
Command.java
DesignGGGenerate.java
DesignGGSeleniumTest.java
DesignParameters.java
LocalComputationResource.java
MainScreen.java
ShowResultsScreen.java
StreamGobbler.java
TestClient.java
Utils.java
euratrans
org
molgenis
euratrans
EuratransGenerate.java
EuratransResetDb.java
EuratransUpdateDatabase.java
header
MolgenisHeader.java
pilot
ConvertPilot.java
ImportPilot.java
MakeBinary.java
examples
org
molgenis
examples
ExamplesGenerate.java
ExamplesUpdateDatabase.java
ui
HelloWorldDemo.java
LookupInputsDemo.java
SimpleInputsDemo.java
TupleTableDemo.java
filemanager
org
molgenis
filemanager
FilemanagerGenerate.java
FilemangerUpdateDatabase.java
ui
LoadFromLocalPlugin.java
gcc
org
molgenis
gcc
GccGenerate.java
GccGenerateDocsOnly.java
GccJpaGenerate.java
GccUpdateDatabase.java
plugins
header
MolgenisHeader.java
gids
org
molgenis
gids
GidsGenerate.java
GidsUpdateDatabase.java
ParserForRoan.java
converters
GidsConvertor.java
phenoModelconverterandloader
CheckDOBandGender.java
Conflicts.java
DOBandGender.java
PM_Updater.java
PMconverterandloaderPlugin.java
decoratoroverriders
MeasurementDecorator.java
plugins
AddIndividual
AddIndividual.java
AddIndividualModel.java
ReferenceList.java
SelectFamily.java
EditIndividual
EditIndividual.java
EditIndividualModel.java
header
GidsHeader.java
matrix
IndividualMatrix.java
IndividualMatrixModel.java
SampleMatrix.java
SampleMatrixModel.java
gonl
org
molgenis
gonl
GonlGenerate.java
GonlUpdateDatabase.java
ui
GonlHeader.java
GonlSearch.java
GonlSearchModel.java
GonlSearchView.java
gonl_pheno
org
molgenis
gonl_pheno
DataSet.java
ImportPhenotypesGoNL.java
SampleReport.java
TupleSource.java
gscf
org
molgenis
gscf
GscfDBGenerate.java
GscfDBUpdateDatabase.java
animaldb4gscf
AnimalDBGenerate.java
AnimalDBUpdateDatabase.java
plugins
header
AnimalDb4GscfHeader.java
hemodb
org
molgenis
hemodb
HemodbGenerate.java
header
HomePage.java
MolgenisHeader.java
plugins
CalculateMeanR.java
CalculateMedianR.java
MatrixManagerHemodb.java
QuestionsModel.java
QuestionsOverview.java
ibdportal
org
molgenis
ibdportal
IBDPortalGenerate.java
IBDPortalUpdateDatabase.java
plugins
header
IBDPortalHeader.java
importer
ImportPlugin.java
Importer.java
tools
ReplaceGenoIds.java
knowledgecenter
org
molgenis
knowledgecenter
Wireframe.java
lifelinesresearchportal
decorators
MeasurementDecorator.java
org
molgenis
lifelinesresearchportal
LifelinesPortalCreateDatabase.java
LifelinesResearchPortalGenerate.java
LifelinesResearchPortalUpdateDatabase.java
backend
PhenoMatrixViewBackend.java
controllers
MatrixController.java
importer
mainImporter.java
legacy
ImportMapper.java
XWBLLUpdateDatabaseJPA.java
models
MatrixModel.java
PhenoMatrix.java
plugins
catalogue
GenericDCM
HL7GenericDCM.java
HL7ObservationDCM.java
HL7OrganizerDCM.java
HL7ValueSetAnswerDCM.java
HL7ValueSetDCM.java
StageLRA
HL7MeasurementLRA.java
HL7ObservationLRA.java
HL7OrganizerLRA.java
HL7StageLRA.java
HL7ValueSetAnswerLRA.java
HL7ValueSetLRA.java
header
MolgenisHeader.java
hl7parser
HL7Data.java
HL7LLData.java
HL7Main.java
HL7OntologyTerm.java
HL7PhenoImporter.java
PropertiesPath.java
XMLReader.java
homepage
LifeLines.java
loader
ImportMapper.java
LifeLinesLoaderPlugin.java
ThreadReaders
CSVFileSpliter.java
listeners
ImportTupleLoader.java
LifeLinesMedicatieListener.java
LifeLinesStandardListener.java
VWCategoryLoader.java
VwDictLoader.java
loaders
EAVToView.java
FillEAVFromTables.java
LoaderUtils.java
MyMonitorThread.java
OracleToLifelinesPheno.java
OracleToPheno.java
Test.java
plinkdownload
PlinkDownload.java
phenotypeViewer
PhenotypeViewer.java
lifelinesresearchportalimporter
org
molgenis
lifelines
ListUtils.java
OracleImporter.java
listeners
CategoryLoader.java
DictLoader.java
utils
EAVToView.java
LoaderUtils.java
MyMonitorThread.java
maze
plugins
mazeexperiment
ConvertRawToBinaryData.java
GoogleBarChart.java
plotActogram.java
rawdataconverter.java
rawdataimporter.java
myo5b
org
molgenis
myo5b
Myo5bGenerate.java
Myo5bUpdateDatabase.java
csv
UploadBatchCsvReader.java
ui
AllPublications.java
Background.java
BackgroundModel.java
ExpertSearchForm.java
Header.java
Search.java
ngs
org
molgenis
ngs
NGSGenerate.java
NGSUpdateDatabase.java
decorators
FlowcellDecorator.java
LibraryLaneDecorator.java
load
WorksheetLoader.java
plugins
batch
BatchOverview.java
project
CreateNewProject.java
ProjectOverview.java
ui
AnalysisWorksheet.java
ImportCompute.java
ImportWorksheet.java
NgsHeader.java
tableview
TableModel.java
TableModelNgsAnalysisWorksheet.java
TableModelProtocolApp.java
TableViewColumn.java
TableViewService.java
test
TableModelPaTest.java
omicsconnect
org
molgenis
omicsconnect
OmicsConnectGenerate.java
OmicsConnectUpdateDatabase.java
minigui
CleanHome.java
OmicsConnectGenerateMiniGUI.java
plugins
browser
GenomeBrowserPlugin.java
eutils
Efetch.java
experiment
ExpTable.java
ExpTableModel.java
header
Header.java
ontocat
Annotator.java
OntoCat.java
OntoCatModel.java
OntoCatTest.java
pubmed
GetData.java
PubMedLookup.java
PubMedLookupModel.java
services
DownloadFile.java
PerformUpload.java
UploadFile.java
ViewFile.java
test
GenerateExampleData.java
patho
org
molgenis
patho
ConvertVcfToPheno.java
PathoGenerate.java
PathoUpdateDatabase.java
csv
UploadBatchCsvReader.java
decoratoroverriders
NameableDecorator.java
ui
PathoHeader.java
PathoSearch.java
PathoSearchModel.java
PathoSearchView.java
phenoflow
converters
dbgap
DbGapService.java
DbGapToPheno.java
jaxb
Study.java
data_dict
Data_Dict.java
Value.java
Variable.java
var_report
CaseControl.java
Sex.java
Stat.java
SubjectProfile.java
Summary.java
Var_Report.java
VariableSummary.java
magetab
ConvertMageTabToPheno.java
mpd
ConvertMpdToPheno.java
opal
ConvertOpalExcelToPheno.java
loaders
LoadAllEBIData.java
LoadDbGapDownloads.java
LoadMpdFromConvertor.java
org
molgenis
phenoflow
PhenoflowGenerate.java
PhenoflowUpdateDatabase.java
ui
EbiStyleLoader.java
EbiStyleLoaderModel.java
sandbox
org
molgenis
framework
ui
html
CustomHtml.java
sandbox
SandboxGenerate.java
SandboxUpdateDatabase.java
plugins
FreemarkerTaglibExamples.java
FreemarkerTaglibExamplesModel.java
Test.java
TestModel.java
TestThree.java
TestThreeModel.java
ui
AnotherMatrix.java
AnotherMatrixModel.java
AnotherMatrixView.java
BootstrapTest.java
FreemarkerEditor.java
FreemarkerEditorModel.java
FreemarkerWidgets.java
HtmlEditor.java
HtmlEditorModel.java
InputsTest.java
InputsTestModel.java
InvestigationPager.java
LayoutTests.java
LayoutTestsModel.java
PagerHtmlInput.java
TestListView.java
scrum
org
molgenis
scrum
ScrumGenerate.java
ScrumUpdateDatabase.java
decorators
TaskDecorator.java
plugins
BurndownChart.java
ScrumHeader.java
UpdateDatabase.java
Whiteboard.java
tifn
org
molgenis
tifn
TifnGenerate.java
header
TifnHeader.java
wormqtl
org
molgenis
plantqtl
PlantqtlGenerate.java
header
HomePage.java
MolgenisHeader.java
help
Help.java
HelpModel.java
wormqtl
WormqtlGenerate.java
etc
parseGOdata.java
exptable
ExpTable.java
ExpTableModel.java
header
HomePage.java
MolgenisHeader.java
help
Help.java
HelpModel.java
xqtl
org
molgenis
xqtl
XqtlGenerate.java
minigui
CleanHome.java
XqtlGenerateMiniGUI.java
modules
auth
org
molgenis
auth
AuthtestGenerate.java
AuthtestUpdateDatabase.java
DatabaseLogin.java
OpenIdLogin.java
service
MolgenisCaptchaService.java
MolgenisUserException.java
MolgenisUserService.java
permissionmanagement
PermissionManagementModel.java
PermissionManagementPlugin.java
PermissionManagementService.java
persontouser
PersonToUser.java
PersonToUserModel.java
tokenmanager
TokenManager.java
TokenManagerModel.java
ui
SimpleUserLogin.java
SimpleUserLoginModel.java
UserLogin.java
UserLoginModel.java
form
DatabaseAuthenticationForm.java
ForgotForm.java
OpenIdAuthenticationForm.java
RegistrationForm.java
UserAreaForm.java
util
PasswordHasher.java
vo
MolgenisUserSearchCriteriaVO.java
plugin
topmenu
LoginScreen.java
batch
org
molgenis
batch
BatchGenerate.java
BatchUpdateDatabase.java
service
BatchService.java
ui
AnimalDBHeader.java
form
BatchEntitySelectForm.java
BatchSelectForm.java
plugins
batch
Batch.java
BatchContainer.java
BatchPlugin.java
BatchPluginModel.java
BatchService.java
BatchViewPlugin.java
BatchViewPluginModel.java
BatchViewUi.java
compute
org
molgenis
compute
commandline
ComputeBundle.java
ComputeBundleFromDirectory.java
ComputeCmdOptions.java
ComputeCommandLine.java
ExportImportToTemplates.java
FreemarkerHelper.java
ParameterWeaverCommandLine.java
StartCommandLineGeneration.java
WorkflowGeneratorCommandLine.java
Worksheet.java
WorksheetHelper.java
options
OptionData.java
OptionSet.java
Options.java
grid
GridStarter.java
host
AbstractComputeHost.java
ComputeHost.java
Glite.java
Job.java
Pbs.java
test
GliteTest.java
PbsTest.java
monitor
ClusterLoggingReaderGridGain.java
ClusterLoggingReaderSsh.java
ComputeAppPaths.java
DatabaseUpdater.java
DatabaseUpdaterCluster.java
DatabaseUpdaterGrid.java
DatabaseUpdaterGridGain.java
DatabaseUpdaterSsh.java
GridMonitor.java
LoggingReader.java
LoggingReaderSsh.java
RemoteFileReader.java
RemoteFileToStringReader.java
pipelinemodel
ClusterScript.java
FileToSaveRemotely.java
GridScript.java
Pipeline.java
Script.java
Step.java
queue
ComputeApplicationManager.java
ComputeBackend.java
SubmissionStrategy.java
remoteexecutor
RemoteGridGainStarter.java
RemoteResult.java
RemoteScriptSubmitter.java
resourcemanager
NodeManager.java
ResourceManager.java
TestResourceManager.java
scriptserver
ClusterPipelineThreadGridGain.java
ClusterPipelineThreadSsh.java
GridPipelineThreadSsh.java
MCF.java
MCFServerGridGain.java
MCFServerSsh.java
PipelineExecutor.java
PipelineThread.java
PipelineThreadSsh.java
ssh
SshData.java
sysexecutor
AsyncStreamReader.java
EnvironmentVar.java
ILogDevice.java
SysCommandExecutor.java
ui
ConsolePlugin.java
HelloGridWorld.java
HelloGridWorldView.java
JobHostTester.java
RunWorkflow.java
RunWorkflowModel.java
RunWorkflowView.java
StartNgs.java
StartNgsView.java
TestR.java
TestRView.java
WorkflowParametersWeaver.java
WorksheetBatchCommand.java
workflowgenerator
ParameterWeaver.java
WorkflowGeneratorDB.java
convertors
galaxy
Action.java
Code.java
Column.java
Command.java
Data.java
Display.java
Filter.java
Input.java
Option.java
Output.java
Outputs.java
Param.java
ParamConditional.java
ParamOptions.java
ParamRepeat.java
RequestParamTranslation.java
Section.java
Test.java
TestOutput.java
TestParam.java
Tool.java
ToolFile.java
ToolParser.java
Toolbox.java
Validator.java
When.java
compute3
org
molgenis
commandline
CommandLineGenerator.java
options
OptionData.java
OptionSet.java
Options.java
generator
Compute3JobGenerator.java
FoldingMaker.java
FoldingParser.java
FoldingUniqueContainer.java
GenericJobGenerator.java
GridTransferContainer.java
JobGenerator.java
ModelLoader.java
gridhandler
CommandLineGridHandler.java
CommandLineImputationGridHandler.java
GridHandler.java
model
ComputeDag.java
compute4
org
molgenis
compute
commandline
ArgumentParser.java
ComputeBundle.java
ComputeBundleFromDirectory.java
ComputeBundleValidator.java
ComputeCommandLine.java
FreemarkerHelper.java
Worksheet.java
WorksheetHelper.java
options
OptionData.java
OptionSet.java
Options.java
host
AbstractComputeHost.java
ComputeHost.java
Glite.java
Job.java
Pbs.java
test
GliteTest.java
PbsTest.java
test
GenerateDemoTasks.java
NGSDemo.java
PilotDemo.java
RunDemoTasksCluster.java
RunPilotsOnBackEnd.java
RunPilotsOnLocalhost.java
executor
ComputeExecutor.java
ComputeExecutorPilotDB.java
ExecutionHost.java
generator
ComputeGenerator.java
ComputeGeneratorDB.java
ComputeGeneratorDBWorksheet.java
ComputeGeneratorFile.java
FakeFoldingMaster.java
FoldingMaster.java
RealFoldingMaster.java
pilot
PilotService.java
reader
WorkflowReader.java
WorkflowReaderDBJDBC.java
WorkflowReaderDBJPA.java
WorkflowReaderFile.java
sysexecutor
AsyncStreamReader.java
EnvironmentVar.java
ILogDevice.java
SysCommandExecutor.java
temp
Target.java
util
AddComputeHost.java
ImportWorksheetOptions.java
ParseTestResults.java
PrepareTest.java
TemplateWeaver.java
WorkflowImporterJDBC.java
WorkflowImporterJPA.java
WorkflowImporterPilotDemo.java
WorksheetImporter.java
datamodel
external
ExtractCaTissueModel.java
ExtractCbmModel.java
ExtractPsiModel.java
ModelToExcel.java
datatable
org
molgenis
datatable
model
AnimalDBTable.java
JoinQueryCreator.java
ProtocolTable.java
QueryCreator.java
QueryTable.java
plugin
JQGridPluginAnimal.java
JQGridPluginEntity.java
JQGridPluginMemory.java
JQGridPluginProtocol.java
JQGridPluginProtocolFilterable.java
JQGridPluginTestProtocol.java
services
downloadpheno.java
test
CreateProtocolData.java
TestEntityTable.java
TestJoinQueryTable.java
TestProtocolTable.java
TestQueryTable.java
util
JQueryUtil.java
MolgenisUpdateDatabase.java
decorators
auth
decorators
AuthorizableDecorator.java
MolgenisUserDecorator.java
core
decorators
MolgenisFileDecorator.java
MolgenisFileHandler.java
NameConvention.java
NameableDecorator.java
data
decorators
DataDecorator.java
pheno
decorators
MeasurementDecorator.java
download
org
molgenis
download
DownloadExample.java
ui
Download.java
DownloadModel.java
dsleditor
org
molgenis
dsleditor
DSLEditor.java
DSLEditorModel.java
HandleRequest_Add.java
HandleRequest_Edit.java
HandleRequest_Remove.java
HandleRequest_Save.java
Helper.java
feedback
org
molgenis
feedback
FeedbackForm.java
file
filehandling
generic
ExampleUsage.java
PerformUpload.java
storage
Report.java
StorageHandler.java
services
downloadfile.java
uploadfile.java
viewfile.java
import
plugins
archiver
Archiver.java
ArchiverModel.java
genericwizard
GenericWizard.java
GenericWizardModel.java
load
org
molgenis
load
cmdline
LoadFromDirectory.java
ui
LoadFromDirectory.java
LoadFromDirectoryModel.java
LoadFromDirectoryView.java
matrix
org
molgenis
matrix
BinaryMatrix.java
CsvMemoryMatrix.java
DoubleCsvMemoryMatrix.java
DoubleMatrix.java
DoubleMemoryMatrix.java
EditableMatrix.java
EntityMatrix.java
FilterableMatrix.java
Matrix.java
MatrixException.java
MemoryMatrix.java
PhenoMemoryMatrix.java
SortableMatrix.java
StringCsvMemoryMatrix.java
StringMatrix.java
StringMemoryMatrix.java
TableModel.java
TargetFeatureMatrix.java
TargetFeatureMemoryMatrix.java
TupleMatrix.java
Utils
MatrixExporters.java
component
AbstractObservationElementMatrix.java
Column.java
MatrixViewer.java
SliceablePhenoMatrix.java
SliceablePhenoMatrixMV.java
general
MatrixColHeaderFilter.java
MatrixColValueFilter.java
MatrixQueryRule.java
MatrixRowHeaderFilter.java
MatrixRowValueFilter.java
interfaces
BasicMatrix.java
DatabaseMatrix.java
SliceableMatrix.java
legacy
AbstractSliceableMatrix.java
Helper.java
MatrixRenderer.java
MatrixRendererHelper.java
MatrixRenderer_old.java
Mover.java
ObservationElementMatrixViewer.java
ObservationElementMatrixViewerMV.java
ObservedValueMatrix.java
PhenoMatrix.java
PhenoMatrixOld.java
RenderDescriptor.java
RenderableMatrix.java
RenderableMatrixImpl.java
RendererModel.java
SomeColType.java
SomeRowType.java
SomeValueType.java
SourceMatrix.java
TestImpl.java
TestMatrixComponent.java
TestObservedValueMatrix.java
Validate.java
plugin
MatrixPlugin.java
sqlbackend
Backend.java
BackendUtils.java
EAVBackend.java
EAVRelationalBackend.java
EAVViewBackend.java
test
TestSliceablePhenoMatrix.java
convertors
DoubleConvertor.java
StringConvertor.java
ValueConvertor.java
example
MatrixViewExample1.java
MatrixViewExample1Model.java
StringMatrixViewExample.java
StringMatrixViewExampleModel.java
package-info.java
test
MemoryMatrixFactory.java
TestMatrixParams.java
TestMemoryMatrix.java
TestPhenoMatrix.java
VerifyCsv.java
ui
MatrixViewer.java
PhenoMatrixView.java
StringMatrixView.java
manager
Browser.java
BrowserModel.java
MatrixManager.java
MatrixManagerModel.java
OverlibText.java
RequestHandler.java
upload
UploadSampleReport.java
UploadSampleReportModel.java
minigui
org
molgenis
minigui
MiniGUI.java
MiniGUIModel.java
mutation
org
molgenis
chd7
csv
UploadBatchCsvReader.java
ui
Background.java
BackgroundModel.java
Header.java
HeaderModel.java
Search.java
Upload.java
col7a1
csv
UploadBatchCsvReader.java
ui
Background.java
BackgroundModel.java
Header.java
HeaderModel.java
Search.java
Upload.java
core
service
PublicationService.java
ui
AllPublications.java
AllPublicationsModel.java
vo
PublicationVO.java
cvdb
ui
CvdbHeader.java
feedback
ui
Chd7Contact.java
Col7a1Contact.java
Contact.java
ContactForm.java
ContactModel.java
mutation
excel
UploadBatchExcelReader.java
service
ExonService.java
ExportService.java
FastaService.java
GffService.java
MutationService.java
PatientService.java
SearchService.java
UploadService.java
ui
LimitOffsetPager.java
export
Export.java
ExportModel.java
html
ExonIntronPanel.java
GenePanel.java
ProteinDomainPanel.java
SequencePanel.java
mymutation
MyMutation.java
MyMutationModel.java
search
SearchModel.java
SearchPlugin.java
form
BackToSimpleSearchForm.java
DisplayOptionsForm.java
ExpertSearchForm.java
ListAllMutationsForm.java
ListAllPatientsForm.java
ShowMutationForm.java
SimpleSearchForm.java
ToExpertSearchForm.java
ToSimpleSearchForm.java
upload
Upload.java
form
MutationForm.java
PatientForm.java
util
MutationComparator.java
PatientComparator.java
PatientSummaryVOComparator.java
SequenceUtils.java
StringUtils.java
vo
BackgroundSummaryVO.java
ExonSearchCriteriaVO.java
ExonSummaryVO.java
ExonVO.java
GeneVO.java
MBrowseVO.java
MutationSearchCriteriaVO.java
MutationSummaryVO.java
MutationUploadVO.java
MyCOL7A1VO.java
ObservedValueVO.java
PatientSearchCriteriaVO.java
PatientSummaryVO.java
PhenotypeDetailsVO.java
PhenotypeSearchCriteriaVO.java
ProteinDomainSummaryVO.java
ProteinDomainVO.java
QueryParametersVO.java
SearchPluginVO.java
web
FastaServlet.java
GffServlet.java
protocol
service
WorkflowService.java
news
org
molgenis
news
service
NewsService.java
ui
News.java
NewsModel.java
plugins
news
News.java
NewsModel.java
NewsService.java
omx
org
molgenis
omx
decorators
IdentifiableDecorator.java
MolgenisFileDecorator.java
MolgenisFileHandler.java
NameConvention.java
services
Report.java
StorageHandler.java
omx-dataviewer
org
molgenis
omx
dataset
DataSetTable.java
DataSetViewerPlugin.java
view
DataSetChooser.java
omx-hl7parser
org
molgenis
omx
hl7
HL7Data.java
HL7LLData.java
HL7Main.java
HL7OmicsConnectImporter.java
HL7OntologyTerm.java
PropertiesPath.java
XMLReader.java
generic
HL7GenericDCM.java
HL7ObservationDCM.java
HL7OrganizerDCM.java
HL7ValueSetAnswerDCM.java
HL7ValueSetDCM.java
lra
HL7MeasurementLRA.java
HL7ObservationLRA.java
HL7OrganizerLRA.java
HL7StageLRA.java
HL7ValueSetAnswerLRA.java
HL7ValueSetLRA.java
omx-importer
org
molgenis
omx
dataset
DataSetImporter.java
plugins
ImportFileWizardPage.java
ImportResultsWizardPage.java
ImportWizard.java
ImportWizardController.java
UploadWizardPage.java
ValidationResultWizardPage.java
WizardModel.java
WizardPage.java
omx-protocolviewer
org
molgenis
omx
EMeasureFeatureWriter.java
plugins
ProtocolViewer.java
ProtocolViewerController.java
pheno
convertors
CopyOfGenericConvertor.java
GenericConvertor.java
loaders
ConverterLifeLinesPheno.java
LoadLifeLinesData.java
XgapLoadPanelTypes.java
org
molgenis
pheno
PhenoGenerate.java
PhenoUpdateDatabase.java
dto
FeatureDTO.java
ObservationElementDTO.java
ObservedValueDTO.java
ProtocolApplicationDTO.java
ProtocolDTO.java
service
PhenoService.java
PhenoServiceException.java
ui
ObservationElementViewer.java
ObservationElementViewerModel.java
form
ApplyProtocolForm.java
ObservationTargetForm.java
SelectProtocolForm.java
plugins
header
PhenoHeader.java
richwizard
Helper.java
RichWizard.java
RichWizardModel.java
view
AllObservations.java
protocol
org
molgenis
protocol
ApplyProtocolPlugin.java
ApplyProtocolPluginModel.java
ApplyProtocolService.java
ApplyProtocolUI.java
search
plugin
search
SimpleWholeDatabaseSearch.java
SimpleWholeDatabaseSearchModel.java
settings
MolgenisExtractModel.java
plugins
emptydb
EmptyDbPlugin.java
emptyDatabase.java
system
settings
Settings.java
variant
org
molgenis
core
dto
PublicationDTO.java
service
PublicationService.java
PublicationServiceException.java
ui
AllPublications.java
AllPublicationsModel.java
feedback
ui
Chd7Contact.java
Col7a1Contact.java
Contact.java
ContactForm.java
ContactModel.java
mutation
ServiceLocator.java
dto
CafeVariomeDTO.java
ExonDTO.java
ExonSearchCriteriaDTO.java
GeneDTO.java
LovdDTO.java
MutationSearchCriteriaDTO.java
MutationSummaryDTO.java
MutationUploadDTO.java
PatientSearchCriteriaDTO.java
PatientSummaryDTO.java
PatientUploadDTO.java
ProteinDomainDTO.java
QueryParametersDTO.java
VariantDTO.java
excel
UploadBatchExcelReader.java
service
CafeVariomeService.java
CafeVariomeServiceException.java
CmsService.java
CmsServiceException.java
ExportService.java
FastaService.java
GffService.java
LovdService.java
LovdServiceException.java
MolgenisVariantService.java
SearchService.java
SearchServiceException.java
StatisticsService.java
StatisticsServiceException.java
UploadService.java
UploadServiceException.java
ui
HtmlFormWrapper.java
LimitOffsetPager.java
export
Export.java
ExportModel.java
header
Header.java
HeaderModel.java
html
DisplaytagTableDecorator.java
ExonIntronPanel.java
GenePanel.java
GenomePanel.java
MBrowse.java
ProteinDomainPanel.java
SequencePanel.java
mymutation
MyMutation.java
MyMutationModel.java
search
SearchModel.java
SearchPlugin.java
form
BackToSimpleSearchForm.java
DisplayOptionsForm.java
ExpertSearchForm.java
ListAllMutationsForm.java
ListAllPatientsForm.java
ShowMutationForm.java
SimpleSearchForm.java
ToExpertSearchForm.java
ToSimpleSearchForm.java
upload
Upload.java
UploadModel.java
form
BatchForm.java
MutationForm.java
PatientForm.java
util
AlternateIdComparator.java
SequenceUtils.java
StringUtils.java
web
AtomFeed.java
CafeVariomeServlet.java
FastaServlet.java
GffServlet.java
LovdServlet.java
MutationFrontController.java
webserver
boot
Helper.java
RunStandalone.java
generic
CommandExecutor.java
FileUtils.java
JavaCompiler.java
OpenBrowser.java
Utils.java
ircbot
IRCClient.java
IRCClientData.java
IRCHandler.java
IRCJobStruct.java
xgap
convertors
ChopFile.java
gerard
GerardParser.java
hapmap
HapMapParser.java
pedmap
PedMapParser.java
matrix
AbstractDataMatrixInstance.java
AbstractDataMatrixQueries.java
DataMatrixInstance.java
datatable
BinaryTupleTable.java
BinaryTupleTableTest.java
JQGridPluginPedMap.java
JQGridPlugin_xQTL.java
PedMapTupleTable.java
TestPedMapTable_XqtlTestNG.java
general
BinToCsv.java
CsvToBin.java
DataMatrixHandler.java
Importer.java
MatrixReadException.java
PreProcessMatrix.java
TestPreProcessMatrix.java
VerifyCsv.java
VerifyCsvException.java
implementations
binary
BinaryDataMatrixInstance.java
BinaryDataMatrixInstance_NEW.java
BinaryDataMatrixWriter.java
etc
ElementLengthException.java
TryOut.java
csv
CSVDataMatrixInstance.java
CSVDataMatrixWriter.java
database
DatabaseDataMatrixInstance.java
DatabaseDataMatrixWriter.java
memory
MemoryDataMatrixInstance.java
test
converters
BinToCsvTest.java
CsvToBinTest.java
MatrixToListTest.java
implementations
binary
TestBinMatrix.java
TestBinMatrix2.java
TestBinSubMatrix.java
csv
TestFileMatrix.java
database
TestDatabaseMatrix.java
general
Helper.java
Params.java
TestingMethods.java
Verifiers.java
memory
TestMemoryMatrix.java
org
molgenis
xgap
decoratoroverriders
DataDecorator.java
MeasurementDecorator.java
MolgenisFileDecorator.java
NameableDecorator.java
other
xgap_vanilla
XgapGenerate.java
XgapUpdateDatabase.java
xqtl_gids
XqtlGidsGenerate.java
xqtl_icc
XqtlIccGenerate.java
xqtl_tifn
XqtlTifnGenerate.java
xqtlworkbench_euratrans
XqtlEuratransGenerate.java
XqtlEuratransUpdateDatabase.java
xqtlworkbench_vanilla
XqtlWorkbenchGenerate.java
XqtlWorkbenchUpdateDatabase.java
test
Archiver_XqtlTestNG.java
DatabaseSearch_XqtlTestNG.java
Matrix_XqtlTestNG.java
Stress_XqtlTestNG_IGNORED.java
TestGeneric.java
XgapTestGenerate.java
XgapUpdateTestDatabase.java
XqtlSeleniumTest.java
xqtlworkbench
ResetXgapDb.java
header
MolgenisHeader.java
plugins
archiveexportimport
ArchiveExportImportPlugin.java
CsvWriterNoExportDataElement.java
ExcelWriterNoExportDataElement.java
XgapCommonImport.java
XgapCsvExport.java
XgapCsvImport.java
XgapExcelExport.java
XgapExcelImport.java
XgapMatrixExport.java
autohidelogin
AutoHideLogin.java
AutoHideLoginModel.java
botresource
BotResource.java
cluster
ClusterPlugin.java
ClusterPluginModel.java
addnewtoolshelp.java
demo
ClusterDemo.java
dependencymanager
DependencyManager.java
DependencyManagerModel.java
homepage
Gids.java
Icc.java
LifeLines.java
Tifn.java
xqtleuratransheader
MolgenisHeader.java
xqtlgidsheader
MolgenisHeader.java
xqtliccheader
MolgenisHeader.java
xqtltifnheader
MolgenisHeader.java
xwbllheader
MolgenisHeader.java
helper
Command.java
HelperFunctions.java
LoginSettings.java
Tester.java
implementations
BotNetworkComputationResource.java
ClusterComputationResource.java
DatabaseJobManager.java
LocalComputationResource.java
StreamGobbler.java
TestLocalExecution.java
interfaces
ComputationResource.java
Job.java
JobManager.java
ssh
BasicClient.java
datasetexplorer
DatasetExplorer.java
DatasetExplorerModel.java
genenetwork
GeneNetwork.java
GeneNetworkModel.java
genomebrowser
GenomeBrowser.java
GenomeBrowserModel.java
help
duplicates
DuplicatesPlugin.java
naming
NamingPlugin.java
investigationoverview
InvestigationOverviewModel.java
InvestigationOverviewPlugin.java
kegg
KEGGGene.java
PathwayPlugin.java
keggplugin
KeggToolsPlugin.java
matrix
admin
MatrixAdmin.java
MatrixAdminModel.java
inspector
MatrixInspector.java
MatrixInspectorModel.java
WarningsAndErrors.java
manager
Browser.java
BrowserModel.java
CreateBrowserInstance.java
MatrixManager.java
MatrixManagerModel.java
OverlibText.java
RequestHandler.java
molgenisfile
MolgenisFileManager.java
MolgenisFileManagerModel.java
plink
PlinkFileManager.java
PlinkFileManagerModel.java
qtlfinder
QTLInfo.java
QTLMultiPlotResult.java
QtlFinder.java
QtlFinderModel.java
QtlPlotDataPoint.java
Result.java
qtlfinder2
PlotHelper.java
QtlFinder2.java
QtlFinderModel2.java
linkback
LinkBack.java
LinkBackModel.java
reportbuilder
MatrixLocation.java
Report.java
ReportBuilder.java
ReportBuilderModel.java
Statistics.java
ronline
ROnline.java
ROnlineModel.java
RProcess.java
rplot
HeatmapScriptInstance.java
MakeRPlot.java
PlotParameters.java
RplotPlugin.java
RplotPluginModel.java
ScriptInstance.java
snpannotator
RsList.java
SnpAnnotator.java
machielAnnotator.java
system
appcustomizer
AppCustomizer.java
database
Settings.java
xgapwizard
DataInfo.java
MatrixWizard.java
MatrixWizardModel.java
QTLDataSetWizard.java
QTLDataSetWizardModel.java
regressiontest
cluster
AddClusterMetaModel.java
AddExampleData.java
DataLoader.java
csv
DirectoryCompare.java
excel
TestExcelExport.java
TestExcelImport.java
misc
TestNameConvention.java
molgenisfile
upload
UploadTest.java
processes
RProcessTest.java
util
Util.java
services
AutoHideLoginService.java
XqtlRApiService.java
downloadmatrixascsv.java
downloadmatrixasexcel.java
downloadmatrixasrobject.java
getlogs.java
getmatrixinfo.java
showjavadirs.java
taskreporter.java
xgap
importexport
CreateZIP.java
DataElementImportByFile.java
publicdata
xqtl
XqtlExampleData.java
test
modules
omx-dataviewer
org
molgenis
omx
dataset
DataSetViewerPluginTest.java
omx-importer
org
molgenis
omx
dataset
DataSetTableTest.java
omx-protocolviewer
org
molgenis
omx
EMeasureFeatureWriterTest.java
plugins
ProtocolViewerControllerTest.java
package matrix.test.implementations.general; public class Verifiers { }