A

A4_Printer - Enum Constant in Printer.PrinterType

AcademicTitle - Enum in life.qbic.datamodel.dtos.business

Possible academic titles

AcademicTitle(String) - Constructor in AcademicTitle

Private constructor to create different AcademicTitle enum items

AcademicTitleFactory - Class in life.qbic.datamodel.dtos.business

This class provides functionality for enum key retrieval

AcademicTitleFactory() - Constructor in AcademicTitleFactory

acceleratingVoltage - Property in ElectronMicroscopyParameters

Voltage is used to accelerate electrons.

acquisitionDate - Property in Image

The image acquisition date.

AcquisitionParameters - Class in life.qbic.datamodel.dtos.imaging.parameters

Description of acquisition parameters during image analysis.

AcquisitionParameters(Integer) - Constructor in AcquisitionParameters

Creates a description of acquisition parameters during image analysis.

acquisitionParameters - Property in Image

Detailed description of image acquisition parameters.

acronym - Field in Affiliation

Activator - Class in life.qbic.example

Activator() - Constructor in Activator

ADAPTER - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

addAffiliationInfo(int, String, String) - Method in Person

addChildID(int) - Method in SampleSummary

addCodes(List<ISampleBean>) - Method in SampleSummary

addFactor(Property) - Method in AOpenbisSample

addItem(ProductItem) - Method in CostEstimate

Adds a new item to the items list of the offer

addItem(ProductItem) - Method in Offer

Adds a new item to the items list of the offer

addParent(ISampleBean) - Method in TSVSampleBean

addParentID(String) - Method in TSVSampleBean

addProperty(String, Object) - Method in ExperimentModel

addProperty(String, Object) - Method in TSVSampleBean

Address - Class in life.qbic.datamodel.people

Address.Builder - Class in life.qbic.datamodel.dtos.general

Address.Builder(Affiliation, String, Integer, String) - Constructor in Address.Builder

Address() - Constructor in Address

address - Property in Contact

address - Property in Location

addressAddition - Property in Affiliation

An optional address addition.

addressAddition - Property in Affiliation.Builder

addSample(AOpenbisSample) - Method in AExperiment

Adds a single sample to the list of samples of this experiment

addSample(AOpenbisSample) - Method in ExperimentModel

addSample(ISampleBean) - Method in SampleSummary

ADMIN - Enum Constant in OpenbisSpaceUserRole

adminPrinter - Field in Printer

AExperiment - Class in life.qbic.datamodel.experiments

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

AExperiment(String, String, String) - Constructor in AExperiment

Affiliation - Class in life.qbic.datamodel.dtos.business

This class serves as a simple DTO for customer affiliations

Affiliation.Builder - Class in life.qbic.datamodel.dtos.business

Affiliation.Builder(String, String, String, String) - Constructor in Affiliation.Builder

affiliation - Property in Address

affiliation - Property in Address.Builder

Affiliation(ProjectManager.Builder) - Constructor in Affiliation

affiliation_id - Field in PersonAffiliationConnectionInfo

affiliation(Affiliation) - Method in Person.Builder

affiliation - Field in RoleAt

AffiliationCategory - Enum in life.qbic.datamodel.dtos.business

We define three major business affiliation categories here, which means that we decide between - internal: An affiliation we consider as within the University of Tübingen or University Hospital of Tübingen - external academic: An outside affiliation but an academic institution (public research institutions) - external: An outside affiliation but not academic (i.e. private sector, companies, etc)

AffiliationCategory(String) - Constructor in AffiliationCategory

Private constructor to create different AffiliationCategory enum items

AffiliationCategoryFactory - Class in life.qbic.datamodel.dtos.business

This class provides functionality for enum key retrieval

AffiliationCategoryFactory() - Constructor in AffiliationCategoryFactory

affiliationInfo - Field in Person

AffiliationLabel - Enum in life.qbic.datamodel.dtos.business

We define 2 affiliation faculty labels here, which will be associated to internal affiliations.

AffiliationLabel(String) - Constructor in AffiliationLabel

Private constructor to create different AffiliationLabel enum items

AffiliationLabelFactory - Class in life.qbic.datamodel.dtos.business

This class provides functionality for enum key retrieval

AffiliationLabelFactory() - Constructor in AffiliationLabelFactory

affiliations - Property in Person

Associated affiliations

affiliations - Property in Person.Builder

altInfo() - Method in IBarcodeBean

altInfo() - Method in NewModelBarcodeBean

amount - Property in SampleSummary

AnalysisParameters - Class in life.qbic.datamodel.dtos.imaging.parameters

DTO that describes the analysis parameter of an image

AnalysisParameters() - Constructor in AnalysisParameters

analysisParameters - Property in Image

Detailed description of image analysis parameters

ANISOTROPY - Enum Constant in Modality

AOpenbisSample - Class in life.qbic.datamodel.samples

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

AOpenbisSample(int, List<AOpenbisSample>, String, String, String, List<Property>, String) - Constructor in AOpenbisSample

Area - Class in life.qbic.datamodel.dtos.imaging.properties

DTO that describes the area of an image.

Area(Integer, Integer, ImagePlane) - Constructor in Area

DTO that describes the area of an image.

arrivalDate - Property in Location

ASIC_TEMP - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

assessFast5Content() - Method in OxfordNanoporeMeasurement

assessFastQContent() - Method in OxfordNanoporeMeasurement

assessPooledStatus() - Method in OxfordNanoporeMeasurement

assessState() - Method in OxfordNanoporeMeasurement

associatedProject - Property in Offer

The associated project identifier, if a project based on the offer exists.

associatedProject - Property in Offer.Builder

Sets an associated project

AtomicProduct - Class in life.qbic.datamodel.dtos.business.services

Describes a product type that can only have positive natural unit multipliers (N={0,1...

AtomicProduct(String, String, double, ProductUnit, ProductId) - Constructor in AtomicProduct

Basic product constructor.

AttachmentConfig - Class in life.qbic.datamodel.attachments

AttachmentConfig(int, String, String, String) - Constructor in AttachmentConfig

AttachmentInformation - Class in life.qbic.datamodel.attachments

AttachmentInformation(String, String, String, String, String, String) - Constructor in AttachmentInformation

authProviderId - Property in PortalUser

The id, that has been given by the authentication provider service, for example LDAP.

authProviderId - Field in PortalUser.Builder

B

backgroundEstimation - Field in SRMAnalysisParameters

Describes an estimate of the background color based on surrounding pixel's color.

barcode - Field in AttachmentInformation

BarcodedFolder - Class in life.qbic.datamodel.datasets.datastructure.folders.nanopore

Specialisation version of a Folder object.

BarcodedFolder(String, String, List) - Constructor in BarcodedFolder

BASE_CALLER - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

BASE_CALLER_VERSION - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

BEAMLP - Enum Constant in Filter

BEAMPOLARIZING - Enum Constant in Filter

BEAMSP - Enum Constant in Filter

beamSplitter - Field in SRMHardware

BeamSplitters are designed to efficiently reflect excitation wavelengths and pass emission wavelengths

beamSplitter - Property in SRMHardware.Builder

binning - Property in AcquisitionParameters

Binning describes the factor by which a pixel is condensed.

blinking - Field in SRMAnalysisParameters

Blinking occurs when some fluorophores switch from a bright to a dark state due to photo-induced switching.

build() - Method in Address.Builder

build() - Method in Affiliation.Builder

build() - Method in CommonPerson.Builder

build() - Method in CostEstimate.Builder

build() - Method in Customer.Builder

build() - Method in ImagingHardware.Builder

build() - Method in Offer.Builder

build() - Method in Person.Builder

build() - Method in PortalUser.Builder

build() - Method in ProductId.Builder

Constructs a product identifier based on the configuration of the builder @return

build() - Method in Project.Builder

build() - Method in ProjectManager.Builder

build() - Method in SRMHardware.Builder

Builds an immutable SRMHardware object.

C

cameraAcquisitionTime - Property in LightMicroscopyParameters

Time required to generate an image with the camera

Car - Interface in life.qbic.example

category - Property in Affiliation

An affiliation category @link{AffiliationCategory}.

category - Property in Affiliation.Builder

channel - Property in ImageSize

Channel from which the image was obtained

checksum - Property in Offer

The checksum of the offer

checksum - Property in Offer.Builder

checksum(String) - Method in SampleCodeFunctions

Computes a checksum digit for a given String.

childIDs - Property in SampleSummary

children - Field in DataFolder

chromatographyType - Field in MSProperties

city - Property in Affiliation

The affiliation city

city - Property in Affiliation.Builder

CLSM - Enum Constant in Modality

code - Field in AExperiment

code - Property in AOpenbisSample

code - Property in ExperimentBean

code - Field in NewModelBarcodeBean

code - Property in ProjectCode

code - Property in Sample

code - Property in TSVSampleBean

codedString - Field in NewModelBarcodeBean

codes - Property in SampleSummary

CollaboratorWithResponsibility - Class in life.qbic.datamodel.persons

CollaboratorWithResponsibility(int, String, String, String, String) - Constructor in CollaboratorWithResponsibility

CommonPerson - Class in life.qbic.datamodel.dtos.general

A person without a specific context.

CommonPerson.Builder - Class in life.qbic.datamodel.dtos.general

CommonPerson.Builder(String, String, String) - Constructor in CommonPerson.Builder

CommonPerson(ProjectManager.Builder) - Constructor in CommonPerson

ComparatorsTester - Class in life.qbic.datamodel.sorters

@author Gili Tzabari

ComparatorsTester() - Constructor in ComparatorsTester

Prevent construction.

compare(IBarcodeBean, IBarcodeBean) - Method in ImportantStringComparator

compare(IBarcodeBean, IBarcodeBean) - Method in SampleCodeComparator

compare(IBarcodeBean, IBarcodeBean) - Method in SampleExtIDComparator

compare(IBarcodeBean, IBarcodeBean) - Method in SampleSecondaryNameComparator

compare(IBarcodeBean, IBarcodeBean) - Method in SampleTypeComparator

compare(IBarcodeBean, IBarcodeBean) - Method in TopInfoComparator

compareAlphaNum(String, String) - Method in Helpers

humanly readable order comparator (a1 < a2 < a10)

compareSampleCodes(String, String) - Method in SampleCodeFunctions

compareTo(ProductId) - Method in ProductId

compareTo(SampleSummary) - Method in SampleSummary

CONFOCAL - Enum Constant in IlluminationMode

Constants - Class in life.qbic.datamodel

Constants() - Constructor in Constants

Contact - Class in life.qbic.datamodel.people

Contact() - Constructor in Contact

Contact - Enum Constant in PersonType

contact - Property in ProjectInfo

contactPerson - Field in Affiliation

contactPersonID - Field in Affiliation

containsAtLeastOneBarcodedFolder(DataFolder) - Method in OxfordNanoporeMeasurement

containsProperties() - Method in OpenbisExperiment

conversion - Field in SRMAnalysisParameters

The conversion factor applied for the analysis e.g 0.43 e-/ADU todo maybe rename it to conversionFactor?

copy() - Method in ISampleBean

copy() - Method in TSVSampleBean

copyMetadata(Map<String, Object>) - Method in TSVSampleBean

CostEstimate - Class in life.qbic.datamodel.accounting

A cost estimate for a project

CostEstimate.Builder - Class in life.qbic.datamodel.accounting

CostEstimate.Builder(Date, Date, Customer, ProjectManager, String, String, List<ProductItem>, double, CostEstimateId, Affiliation) - Constructor in CostEstimate.Builder

CostEstimate(ProjectManager.Builder) - Constructor in CostEstimate

CostEstimateId - Class in life.qbic.datamodel.dtos.business

A DTO to describe the cost estimate identifier

CostEstimateId(String, String, int) - Constructor in CostEstimateId

country - Property in Address

country - Property in Address.Builder

country - Property in Affiliation

The affiliation country.

country - Property in Affiliation.Builder

create(String, String) - Method in DriftCorrectionLog

create(String, String) - Method in DutyTimeLog

create(String, String) - Method in ExecutionReport

Creates the ExecutionReport object based on a report name and a relative path of it

create(String, String, List) - Method in Fast5FailFolder

Creates a new instance of a Fast5FailFolder object

create(String, String) - Method in Fast5File

create(String, String, List<Fast5File>) - Method in Fast5Folder

Creates a new instance of a Fast5Folder object

create(String, String, List<?>) - Method in Fast5PassFolder

Creates a new instance of a Fast5PassFolder object

create(String, String, List<?>) - Method in FastQFailFolder

Creates a new instance of a FastQFailFolder object.

create(String, String) - Method in FastQFile

create(String, String, List<FastQFile>) - Method in FastQFolder

Creates a new instance of a FastQFolder object

create(String, String, List<?>) - Method in FastQPassFolder

Creates a new instance of a FastQPassFolder object.

create(String, String) - Method in FastQZippedFile

create(String, String) - Method in FinalSummaryLog

create(String, String, List<?>) - Method in MeasurementFolder

Creates a new instance of a MeasurementFolder object

create(String, String) - Method in MuxScanDataLog

create(Map) - Method in OxfordNanoporeExperiment

Static factory method that creates a new instance from a Oxford Nanopore sequencer output.

create(String, String, List, Map) - Method in OxfordNanoporeMeasurement

create(String, String, List<DataFile>) - Method in PipelineInformationFolder

Creates a new instance of a PipelineInformationFolder object

create(String, String) - Method in PipelineReport

Creates the PipelineReport object based on a report name and a relative path of it

create(String, String, List<?>) - Method in ProcessFolder

Creates a new instance of a ProcessFolder object

create(String, String, List<?>) - Method in QualityControlFolder

Creates a new instance of a QualityControlFolder object

create(String, String) - Method in ReportMdLog

create(String, String) - Method in ReportPDFLog

create(String, String) - Method in RunId

Creates the RunId object based on a RunId name and a relative path of it

create(String, String) - Method in SampleIds

Creates the SampleIds object based on a report name and a relative path of it

create(String, String) - Method in SequencingSummaryLog

create(String, String) - Method in SoftwareVersions

Creates the SoftwareVersions object based on a file name and a relative path of it

create(String, String) - Method in ThroughputLog

create(String, String, List<Fast5File>) - Method in UnclassifiedFast5Folder

Creates a new instance of a UnclassifiedFastQFolder object

create(String, String, List<?>) - Method in UnclassifiedFastQFolder

Creates a new instance of a UnclassifiedFastQFolder object

createContent() - Method in OxfordNanoporeMeasurement

createCountString(int, int) - Method in SampleCodeFunctions

Creates a string with leading zeroes from a number

createFrom(Map) - Method in NfCorePipelineResult

Static factory method that creates a new nfcoreExperiment instance from the bioinformatic pipeline output.

cumulativeElectronDose - Property in ElectronMicroscopyParameters

The accumulated amount of electrons that are applied to an area of the sample

currency - Property in Product

Describes the currency under which the product is charged

currentLocation - Property in Sample

Customer - Class in life.qbic.datamodel.dtos.business

This class serves as a simple DTO for customer data

Customer.Builder - Class in life.qbic.datamodel.dtos.business

Customer.Builder(String, String, String) - Constructor in Customer.Builder

customer - Property in CostEstimate

The customer for which the estimate is created

customer - Property in CostEstimate.Builder

Customer(ProjectManager.Builder) - Constructor in Customer

customer - Property in Offer

The customer for which this offer was created

customer - Property in Offer.Builder

customer - Property in ProjectApplication

The associated customer

cutOff - Field in SRMAnalysisParameters

It describes the limiting spatial frequency of the microscope Based on this value the smallest object resolvable by the microscope can be determined

D

DATA_AT_QBIC - Enum Constant in Status

@deprecated this is deprecated since 2.4.0 please use DATA_AVAILABLE instead

DATA_AVAILABLE - Enum Constant in Status

DATA_STORAGE - Enum Constant in ProductCategory

DATA_STORAGE - Enum Constant in ProductType

DataFile - Class in life.qbic.datamodel.datasets.datastructure.files

A DataFile object represents a file with a name, a path and a fileType

DataFile(String, String, String) - Constructor in DataFile

DataFolder - Class in life.qbic.datamodel.datasets.datastructure.folders

DataFolder(String, String, List) - Constructor in DataFolder

DataStorage - Class in life.qbic.datamodel.dtos.business.services

Describes a product for data storage services.

DataStorage(String, String, double, ProductUnit, long) - Constructor in DataStorage

Basic product constructor.

date - Property in ExperimentBean

description - Property in Product

Provides a more detailed description of the product

description - Property in ProjectInfo

Detector - Class in life.qbic.datamodel.dtos.imaging.properties

DTO class for detectors in the imaging context.

Detector(String) - Constructor in Detector

DTO class for detectors in the imaging context.

detector - Field in ImagingHardware

The detector used in the instrument

detector - Property in ImagingHardware.Builder

DETECTOR - Enum Constant in Size

determineMethod(Class) - Method in OxfordNanoporeExperiment

device - Field in MSProperties

DEVICE_TYPE - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

Dimensionality - Enum in life.qbic.datamodel.dtos.imaging.properties

A DTO to describe the dimensionality of an image

Dimensionality(String) - Constructor in Dimensionality

A DTO to describe the dimensionality of an image

dimensionality - Field in SRMAnalysisParameters

Describes the dimensionality of an image

DOCTOR - Enum Constant in AcademicTitle

driftCorrection - Field in SRMAnalysisParameters

During sample collection, in the process of analysing the sample, it can drift.

DriftCorrectionLog - Class in life.qbic.datamodel.datasets.datastructure.files.nanopore

A specialisation of a DataFile, represents an Oxford Nanopore Drift Correction file

DriftCorrectionLog(String, String) - Constructor in DriftCorrectionLog

DSTOR - Enum Constant in Modality

DutyTimeLog - Class in life.qbic.datamodel.datasets.datastructure.files.nanopore

A specialisation of a DataFile, represents an Oxford Nanopore duty time log file

DutyTimeLog(String, String) - Constructor in DutyTimeLog

E

ElectronMicroscopyParameters - Class in life.qbic.datamodel.dtos.imaging.parameters.electronmicroscopy

Describes the properties of electron microscopy

ElectronMicroscopyParameters(Integer, Integer, Float, Float) - Constructor in ElectronMicroscopyParameters

Creates a description of the properties of electron microscopy

email - Property in Contact

email - Field in Person

emailAddress - Property in Person

The person's email address

emailAddress - Property in Person.Builder

EMISSION510LP - Enum Constant in Filter

EMISSION550BP - Enum Constant in Filter

EMISSION580LP - Enum Constant in Filter

EMISSION600BP - Enum Constant in Filter

emissionFilter - Field in SRMHardware

It filters out the entire excitation range of the fluorophore under inspection

emissionFilter - Property in SRMHardware.Builder

emissionFilterChannels - Field in SRMHardware

Different channels can have different filters, this variable collects all filter applied for different channels

emissionFilterChannels - Property in SRMHardware.Builder

emissionPerChannel - Property in LightMicroscopyParameters

Wavelength of emission light per channel.

EmissionRange - Class in life.qbic.datamodel.dtos.imaging.properties

Class storing the emissions from a light source as a range of wave lengths

EmissionRange(int, int) - Constructor in EmissionRange

Class storing the emissions from a light source as a range of wave lengths

endWavelength - Property in EmissionRange

Its the biggest wavelength within the emission range e.g 530 nm

EntityExperiment - Class in life.qbic.datamodel.experiments

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

EntityExperiment(String, String, String) - Constructor in EntityExperiment

EnumFactory - Class in life.qbic.datamodel.dtos

This class provides functionality for enum key retrieval

EnumFactory() - Constructor in EnumFactory

equals(Object) - Method in Address

equals(Object) - Method in DataFile

equals(Object) - Method in DataFolder

equals(Object) - Method in LigandPrepRun

equals(Object) - Method in Location

equals(Object) - Method in MSProperties

equals(Object) - Method in MSRunCollection

equals(Object) - Method in Person

equals(Object) - Method in ProjectCode

equals(Object) - Method in ProjectSpace

equals(Object) - Method in RoleAt

equals(Object) - Method in SampleSummary

equals(Object) - Method in TSVSampleBean

escapeSpecials(String) - Method in OpenbisExperiment

Example - Class in life.qbic.example

Example() - Constructor in Example

excitationBeamSplitter - Field in SRMHardware

A beam splitter is an optical device that splits a beam of light in two.

excitationBeamSplitter - Property in SRMHardware.Builder

excitationPerChannel - Field in LightMicroscopyParameters

It is light that excites fluorochromes.

ExecutionReport - Class in life.qbic.datamodel.datasets.datastructure.files.nfcore

A specialisation of a DataFile, represents a nf-core Pipeline execution report file

ExecutionReport(String, String) - Constructor in ExecutionReport

executionReport - Property in PipelineInformationFolder

experiment - Field in AOpenbisSample

experiment - Property in ISampleBean

experiment - Property in TSVSampleBean

experiment_type - Property in ExperimentBean

experimentalDesign - Property in Offer

The experimental design of a project

experimentalDesign - Property in Offer.Builder

experimentalDesign - Property in ProjectApplication

A description about the experimental design

experimentalPSF - Field in SRMAnalysisParameters

PSF stands for point spread function and describes the three-dimensional diffraction pattern of light emitted from an infinitely small point source.

ExperimentBean - Class in life.qbic.datamodel.experiments

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

ExperimentBean(String, String, String, String, boolean) - Constructor in ExperimentBean

Creates a new ExperimentBean

experimentCode - Field in OpenbisExperiment

ExperimentCodeFunctions - Class in life.qbic.datamodel.identifiers

ExperimentCodeFunctions() - Constructor in ExperimentCodeFunctions

ExperimentFolder - Interface in life.qbic.datamodel.datasets

ExperimentModel - Class in life.qbic.datamodel.experiments

ExperimentModel(ExperimentModel) - Constructor in ExperimentModel

ExperimentType - Enum in life.qbic.datamodel.experiments

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

expirationDate - Property in CostEstimate

The date on which the cost estimate expires

expirationDate - Property in CostEstimate.Builder

expirationDate - Property in Offer

The date on which the offer expires

expirationDate - Property in Offer.Builder

EXTERNAL_ACADEMIC - Enum Constant in AffiliationCategory

EXTERNAL - Enum Constant in AffiliationCategory

extID - Field in NewModelBarcodeBean

ExtractionExperiment - Class in life.qbic.datamodel.experiments

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

ExtractionExperiment(String, String, String) - Constructor in ExtractionExperiment

extractLibraryKit(String) - Method in OxfordNanoporeMeasurement

F

factors - Property in AOpenbisSample

factorValue - Field in SampleSummary

faculty - Field in Affiliation

FAILED_QC - Enum Constant in Status

Fast5FailFolder - Class in life.qbic.datamodel.datasets.datastructure.folders.nanopore

A special case of a DataFolder, its name contains always fast5_fail.

Fast5FailFolder(String, String, List) - Constructor in Fast5FailFolder

Fast5File - Class in life.qbic.datamodel.datasets.datastructure.files.nanopore

A specialisation of a DataFile, represents an Oxford Nanopore fast5 file

Fast5File(String, String) - Constructor in Fast5File

Fast5Folder - Class in life.qbic.datamodel.datasets.datastructure.folders.nanopore

A class that is a special case of a BarcodedFolder.

Fast5Folder(String, String, List<Fast5File>) - Constructor in Fast5Folder

Fast5PassFolder - Class in life.qbic.datamodel.datasets.datastructure.folders.nanopore

A special case of a DataFolder, its name is always fast5_pass.

Fast5PassFolder(String, String, List<?>) - Constructor in Fast5PassFolder

FastQFailFolder - Class in life.qbic.datamodel.datasets.datastructure.folders.nanopore

A special case of a DataFolder.

FastQFailFolder(String, String, List<?>) - Constructor in FastQFailFolder

FastQFile - Class in life.qbic.datamodel.datasets.datastructure.files.nanopore

FastQFile(String, String) - Constructor in FastQFile

FastQFolder - Class in life.qbic.datamodel.datasets.datastructure.folders.nanopore

A class that is a special case of a BarcodedFolder.

FastQFolder(String, String, List<FastQFile>) - Constructor in FastQFolder

FastQPassFolder - Class in life.qbic.datamodel.datasets.datastructure.folders.nanopore

A special case of a DataFolder.

FastQPassFolder(String, String, List<?>) - Constructor in FastQPassFolder

FastQZippedFile - Class in life.qbic.datamodel.datasets.datastructure.files.nanopore

FastQZippedFile(String, String) - Constructor in FastQZippedFile

fetchParentIDs() - Method in IBarcodeBean

fetchParentIDs() - Method in NewModelBarcodeBean

FILE_TYPE - Field in DriftCorrectionLog

FILE_TYPE - Field in DutyTimeLog

FILE_TYPE - Field in ExecutionReport

FILE_TYPE - Field in Fast5File

FILE_TYPE - Field in FastQFile

FILE_TYPE - Field in FastQZippedFile

FILE_TYPE - Field in FinalSummaryLog

FILE_TYPE - Field in MuxScanDataLog

FILE_TYPE - Field in PipelineReport

FILE_TYPE - Field in ReportMdLog

FILE_TYPE - Field in ReportPDFLog

FILE_TYPE - Field in RunId

FILE_TYPE - Field in SampleIds

FILE_TYPE - Field in SequencingSummaryLog

FILE_TYPE - Field in SoftwareVersions

FILE_TYPE - Field in ThroughputLog

fileType - Field in DataFile

The file type

fillInFactors(Map<String, String>) - Method in AOpenbisSample

Parses XML properties to the right format

Filter - Enum in life.qbic.datamodel.dtos.imaging.properties

Enumeration of different image filters.

Filter(String) - Constructor in Filter

Enumeration of different image filters.

filterSize - Field in SRMAnalysisParameters

Size of the filter in pixels

FinalSummaryLog - Class in life.qbic.datamodel.datasets.datastructure.files.nanopore

A specialisation of a DataFile, represents an Oxford Nanopore duty time log file

FinalSummaryLog(String, String) - Constructor in FinalSummaryLog

findAllQbicSampleCodes(String) - Method in SampleCodeFunctions

Finds all QBiC sample codes in a String object.

firstDimensionValue - Property in Area

Describes the value in µm of the first dimension of the area, e.g. 40 µm

firstInfo() - Method in IBarcodeBean

firstInfo() - Method in NewModelBarcodeBean

firstName - Field in Person

firstName - Property in Person.Builder

FLCS - Enum Constant in Modality

FLIM - Enum Constant in Modality

FLOWCELL_ID - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

FLOWCELL_POSITION - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

FLOWCELL_TYPE - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

folders - Field in OxfordNanoporeMeasurement

formatSpaceName(String) - Method in ProjectSpace

forwardDate - Field in Location

FQDN_FILES - Field in NfCorePipelineResult

FQDN_FILES - Field in OxfordNanoporeExperiment

FQDN_FOLDERS - Field in NfCorePipelineResult

FQDN_FOLDERS - Field in OxfordNanoporeExperiment

fromString(String) - Method in Printer.PrinterType

fullName - Property in Contact

G

Garage - Class in life.qbic.example

Garage() - Constructor in Garage

getAcronym() - Method in Affiliation

getAdapter() - Method in OxfordNanoporeMeasurement

Provides access to the adapter type used in the measurement.

getAddress() - Method in Contact

Get address

getAddress() - Method in Location

Get address

getAddressString() - Method in Affiliation

getAffiliation() - Method in Address

Get affiliation

getAffiliation_id() - Method in PersonAffiliationConnectionInfo

getAffiliation() - Method in RoleAt

getAffiliationInfos() - Method in Person

getAffiliations() - Method in Person

getAmount() - Method in SampleSummary

getArrivalDate() - Method in Location

Get arrival_date

getAsicTemp() - Method in OxfordNanoporeMeasurement

Provides access to the asic temperature.

getBarcode() - Method in AttachmentInformation

getBarcodeRange(List<String>) - Method in SampleCodeFunctions

Returns a String denoting the range of a list of barcodes as used in QBiC

getBaseCaller() - Method in OxfordNanoporeMeasurement

Provides access to the base caller.

getBaseCallerVersion() - Method in OxfordNanoporeMeasurement

Provides access to the base caller version.

getChildIDs() - Method in SampleSummary

getChildren() - Method in DataFolder

Returns the children of the folder.

getChromatographyType() - Method in MSProperties

getCity() - Method in Affiliation

getCode() - Method in AOpenbisSample

getCode() - Method in ExperimentBean

getCode() - Method in IBarcodeBean

getCode() - Method in ISampleBean

getCode() - Method in NewModelBarcodeBean

getCode() - Method in Sample

Get code

getCode() - Method in TSVSampleBean

getCodedString() - Method in IBarcodeBean

getCodedString() - Method in NewModelBarcodeBean

getCodes() - Method in SampleSummary

getContact() - Method in ProjectInfo

getContactPerson() - Method in Affiliation

getContactPersonID() - Method in Affiliation

getCountry() - Method in Address

Get country

getCountry() - Method in Affiliation

getCurrentLocation() - Method in Sample

Get currentLocation

getDate() - Method in ExperimentBean

getDescription() - Method in ProjectInfo

getDetector() - Method in ImagingHardware

Returns the detector described in the hardware

getDevice() - Method in MSProperties

getDeviceType() - Method in OxfordNanoporeMeasurement

Provides access to the device type.

getEmail() - Method in Contact

Get email

getEMail() - Method in Person

getExecutionReport() - Method in PipelineInformationFolder

Provides access to the information stored in the sampleIds file

getExperiment() - Method in ISampleBean

getExperiment() - Method in TSVSampleBean

getExperiment_type() - Method in ExperimentBean

getExperimentCode() - Method in OpenbisExperiment

getExperimentID() - Method in CollaboratorWithResponsibility

getExperimentIdentifier(String, String, int) - Method in ExperimentCodeFunctions

getExtID() - Method in IBarcodeBean

getExtID() - Method in NewModelBarcodeBean

getFactorLabels() - Method in AOpenbisSample

getFactors() - Method in AOpenbisSample

getFactorStrings() - Method in AOpenbisSample

getFactorStringsWithoutLabel() - Method in AOpenbisSample

getFactorValue() - Method in SampleSummary

getFaculty() - Method in Affiliation

getFileName() - Method in AttachmentInformation

getFileType() - Method in DataFile

getFirstName() - Method in Person

getFlowcellId() - Method in OxfordNanoporeMeasurement

Provides access to the flow cell id.

getFlowCellPosition() - Method in OxfordNanoporeMeasurement

Provides access to the flow cell position.

getFlowCellType() - Method in OxfordNanoporeMeasurement

Provides access to the flow cell type.

getFolder() - Method in AttachmentInformation

Returns the file name as it should be sent to the dropbox handler, including barcode, user name and optional secondary name.

getForString(String) - Method in AcademicTitleFactory

{@InheritDoc}

getForString(String) - Method in AffiliationCategoryFactory

{@InheritDoc}

getForString(String) - Method in AffiliationLabelFactory

{@InheritDoc}

getForString(String) - Method in EnumFactory

This method returns the enum with the provided String value.

getForString(String) - Method in ProductCategoryFactory

This method returns the enum with the provided String value.

getForString(String) - Method in ProductUnitFactory

{@InheritDoc}

getForwardDate() - Method in Location

Get forward_date

getFullName() - Method in Contact

Get fullName

getGroupName() - Method in Affiliation

getHeadID() - Method in Affiliation

getHeadName() - Method in Affiliation

getHostname() - Method in Printer

getID() - Method in AExperiment

getID() - Method in Affiliation

getID() - Method in ExperimentBean

getID() - Method in ExperimentModel

getId() - Method in SampleSummary

getIdentifier() - Method in ProductId

Returns the identifying running number

getIdentifier() - Method in TomatoId

Assembles the identifier from the class attributes.

getInfo() - Method in AttachmentInformation

getInfoExperimentID(String, String) - Method in ExperimentCodeFunctions

returns -1 if code doesn't fit standard or integer can't be parsed

getInstance() - Method in ImportantStringComparator

getInstance() - Method in SampleCodeComparator

getInstance() - Method in SampleExtIDComparator

getInstance() - Method in SampleSecondaryNameComparator

getInstance() - Method in SampleTypeComparator

getInstance() - Method in TopInfoComparator

getInstitute() - Method in Affiliation

getInstituteID() - Method in Person

getInvestigator() - Method in ProjectInfo

getItems() - Method in CostEstimate

Returns an unmodifiable list from the given items @return

getItems() - Method in Offer

Returns an unmodifiable list from the given items @return

getLastName() - Method in Person

getLcmsDescription() - Method in MSProperties

getLcmsMethod() - Method in MSProperties

getLeaf() - Method in SampleSummary

getLibraryPreparationKit() - Method in OxfordNanoporeMeasurement

Provides access to the library kit used.

getLocation() - Method in Printer

getLogFileCollection() - Method in OxfordNanoporeMeasurement

getLogFiles() - Method in OxfordNanoporeMeasurement

This method returns a list of all log files from the Oxford Nanopore measurement.

getMachineHost() - Method in OxfordNanoporeMeasurement

Provides access to the machine host name.

getManager() - Method in ProjectInfo

getMaxSize() - Method in AttachmentConfig

getMeasuredPercent() - Method in SampleSummary

getMeasurements() - Method in OxfordNanoporeExperiment

Provides a list of measurements contained within the experiment folder.

getMetadata() - Method in ISampleBean

getMetadata() - Method in OpenbisExperiment

getMetadata() - Method in TSVSampleBean

getName() - Method in AttachmentInformation

getName() - Method in DataFile

getName() - Method in DataFolder

Returns the name of the folder @return

getName() - Method in Location

Get name

getName() - Method in Printer

getName() - Method in SampleSummary

getObjective() - Method in ImagingHardware

Returns the objective described in the hardware

getOneAffiliationWithRole() - Method in Person

returns a random affiliation with its role for this user

getOpenbisCode() - Method in CollaboratorWithResponsibility

getOpenbisIdentifier() - Method in CollaboratorWithResponsibility

getOpenbisType() - Method in CollaboratorWithResponsibility

getOrganization() - Method in Affiliation

getParent() - Method in AOpenbisSample

getParentIDs() - Method in ISampleBean

getParentIDs() - Method in TSVSampleBean

getParents() - Method in AOpenbisSample

getPass() - Method in AttachmentConfig

getpastLocations() - Method in Sample

Get pastLocations

getPercentageStep(int) - Method in SampleCodeFunctions

getPerson() - Method in CollaboratorWithResponsibility

getPerson_id() - Method in PersonAffiliationConnectionInfo

getPersonID() - Method in OpenbisExperiment

getPhone() - Method in Person

getPipelineInformation() - Method in NfCorePipelineResult

Provides access to the information stored in the pipeline information folder

getPipelineReport() - Method in PipelineInformationFolder

Provides access to the information stored in the runId file

getProcessFolders() - Method in NfCorePipelineResult

Provides access to the information stored in the process folders

getProject() - Method in ISampleBean

getProject() - Method in TSVSampleBean

getProjectCode() - Method in ProjectInfo

getProjectConservedPart() - Method in TomatoId

Returns the project conserved part of the identifier

getProjectID() - Method in ProjectInfo

getProjectPrefix(String) - Method in SampleCodeFunctions

Returns the 5 character project prefix used for samples in openBIS.

getProperties() - Method in ExperimentModel

getPropertiesString() - Method in OpenbisExperiment

getPropertyMap() - Method in MSProperties

getQ_ADDITIONAL_NOTES() - Method in AOpenbisSample

getQ_ADDITIONAL_NOTES() - Method in OpenbisExperiment

getQ_EXTERNALDB_ID() - Method in AOpenbisSample

getQ_SECONDARY_NAME() - Method in AOpenbisSample

getQ_SECONDARY_NAME() - Method in OpenbisExperiment

getQualityControlFolder() - Method in NfCorePipelineResult

Provides access to the information stored in the quality Control folder

getRandomPart() - Method in TomatoId

Returns the random part of the identifier

getRawDataPerSample(ExperimentFolder) - Method in OxfordNanoporeMeasurement

This method aggregates all fast5 files and fastq files of an Oxford Nanopore measurement by sample code.

getRelativePath() - Method in DataFile

getRelativePath() - Method in DataFolder

Returns the relative path of the folder @return

getRelativePath() - Method in OxfordNanoporeMeasurement

This method is used to return the relative path of a Oxford Nanopore measurement.

getResponsibleEmail() - Method in Location

Get responsibleEmail

getResponsiblePerson() - Method in Location

Get responsiblePerson

getRole() - Method in CollaboratorWithResponsibility

getRole() - Method in PersonAffiliationConnectionInfo

getRole() - Method in RoleAt

getRunId() - Method in NfCorePipelineResult

Provides access to the information stored in the runId file

getSampleCode() - Method in BarcodedFolder

Returns the sample id of the barcoded folder @return

getSampleCode() - Method in ExperimentFolder

Returns the QBiC sample Id that is associated with this Experiment.

getSampleCode() - Method in OxfordNanoporeExperiment

getSampleIds() - Method in NfCorePipelineResult

Provides access to the information stored in the sampleIds file

getSamples() - Method in AExperiment

getSamples() - Method in ExperimentBean

getSamples() - Method in ExperimentModel

getSamples() - Method in SampleSummary

getSampleType() - Method in SampleSummary

getSchemaAsStream() - Method in ImageMetadata

Returns the json imaging schema based on the path defined in ImageMetadata

getSchemaAsStream() - Method in OxfordNanoporeInstrumentOutput

getSchemaAsStream() - Method in PipelineOutput

getSecondaryName() - Method in IBarcodeBean

getSecondaryName() - Method in ISampleBean

getSecondaryName() - Method in NewModelBarcodeBean

getSecondaryName() - Method in ProjectInfo

getSecondaryName() - Method in TSVSampleBean

getSoftwareVersions() - Method in PipelineInformationFolder

Provides access to the information stored in the process folders

getSource() - Method in SampleSummary

getSpace() - Method in AOpenbisSample

getSpace() - Method in ISampleBean

getSpace() - Method in ProjectInfo

getSpace() - Method in TSVSampleBean

getStartDate() - Method in OxfordNanoporeMeasurement

Provides access to the experiment start date.

getStatus() - Method in Location

Get sample status

getStreet() - Method in Address

Get street

getStreet() - Method in Affiliation

getTempID() - Method in AOpenbisSample

getTempParentIDs() - Method in AOpenbisSample

getText() - Method in Printer.PrinterType

getTitle() - Method in Person

getTmpID() - Method in ExperimentModel

getType() - Method in AttachmentInformation

getType() - Method in IBarcodeBean

getType() - Method in ISampleBean

getType() - Method in NewModelBarcodeBean

getType() - Method in OpenbisExperiment

getType() - Method in Printer

getType() - Method in ProductId

Returns the type of the identifier @return

getType() - Method in TomatoId

Returns the type of the identifier @return

getType() - Method in TSVSampleBean

getUnclassifiedData() - Method in OxfordNanoporeMeasurement

This method aggregates only *unclassified* fast5 files and fastq files of an Oxford Nanopore measurement.

getUniqueId() - Method in ProductId

Returns the identifying running number

getUnknownMetadataValuesForVocabulary(String, List<String>) - Method in ISampleBean

Given a vocabulary of terms for a propertyName, find if property value(s) of this sample do fit the vocabulary and return all the unknown values in a list

getUnknownMetadataValuesForVocabulary(String, List<String>) - Method in TSVSampleBean

getUri() - Method in AttachmentConfig

getUser() - Method in AttachmentConfig

getUser() - Method in AttachmentInformation

getUserGroup() - Method in Printer

getUsername() - Method in Person

getValue() - Method in AcademicTitle

Returns to the enum item value @return

getValue() - Method in AffiliationCategory

Returns to the enum item value @return

getValue() - Method in AffiliationLabel

Returns to the enum item value @return

getValue() - Method in Dimensionality

The String representation of the dimensionality item.

getValue() - Method in Filter

The string representation of the filter item.

getValue() - Method in IlluminationMode

The string representation of the illumination mode item.

getValue() - Method in ImagePlane

The string representation of the image plane item.

getValue() - Method in Modality

The string representation of the modality item.

getValue() - Method in ProductCategory

Returns the value associated to the given enum This is NOT the same as toString

getValue() - Method in ProductType

Returns to the enum item value @return

getValue() - Method in ProductUnit

Returns to the enum item value @return

getValue() - Method in ScanMode

The string representation of the image plane item.

getValue() - Method in Size

The string representation of the illumination mode item.

getValueMap() - Method in AOpenbisSample

Returns a map of all metadata fields and values of this sample

getValueMap() - Method in OpenbisBiologicalEntity

getValueMap() - Method in OpenbisBiologicalSample

getValueMap() - Method in OpenbisMHCExtractSample

getValueMap() - Method in OpenbisMSSample

getValueMap() - Method in OpenbisTestSample

getVersion() - Method in TomatoId

Returns the version of the identifier @return

getWebpage() - Method in Affiliation

getZipCode() - Method in Address

Get zipCode

getZipCode() - Method in Affiliation

groupName - Field in Affiliation

H

hardware - Property in Instrument

A more detailed description of the hardware setup.

hashCode() - Method in DataFile

hashCode() - Method in DataFolder

hashCode() - Method in LigandPrepRun

hashCode() - Method in MSProperties

hashCode() - Method in MSRunCollection

hashCode() - Method in SampleSummary

hashCode() - Method in TSVSampleBean

hasParents() - Method in IBarcodeBean

hasParents() - Method in ISampleBean

hasParents() - Method in NewModelBarcodeBean

hasParents() - Method in TSVSampleBean

headID - Field in Affiliation

headName - Field in Affiliation

Helpers - Class in life.qbic.datamodel.sorters

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

Helpers() - Constructor in Helpers

hostname - Field in Printer

I

IBarcodeBean - Interface in life.qbic.datamodel.printing

Interface for openBIS sample models.

id - Field in Affiliation

id - Field in CollaboratorWithResponsibility

ID - Field in ExperimentBean

iD - Property in ExperimentModel

id - Property in SampleSummary

identifier - Property in CostEstimate

An identifier which makes the CostEstimate distinguishable from other CostEstimates

identifier - Property in CostEstimate.Builder

identifier - Field in ExperimentModel

identifier - Property in Offer

The identifier for the offer which makes it distinguishable from other offers

identifier - Property in Offer.Builder

IlluminationMode - Enum in life.qbic.datamodel.dtos.imaging.properties

A DTO to describe the illumination mode in context of imaging

IlluminationMode(String) - Constructor in IlluminationMode

A DTO to describe the illumination mode in context of imaging

illuminationMode - Field in SRMHardware

A microscope can have different illumination modes.

illuminationMode - Property in SRMHardware.Builder

Image - Class in life.qbic.datamodel.dtos.imaging

This DTO class describes the image resulting from imaging experiments

Image(Date, AcquisitionParameters, AnalysisParameters, Instrument, Integer, Modality, ImageSize, PixelSize, Float) - Constructor in Image

This DTO class describes the image resulting from imaging experiments

imageId - Property in Image

The image identifier in OMERO.

ImageMetadata - Class in life.qbic.datamodel.datasets.imaging

Represents the schema for the imaging metadata model.

ImageMetadata() - Constructor in ImageMetadata

ImagePlane - Enum in life.qbic.datamodel.dtos.imaging.properties

Enumeration of different image planes.

ImagePlane(String) - Constructor in ImagePlane

Enumeration of different image planes.

ImageSize - Class in life.qbic.datamodel.dtos.imaging.properties

A DTO to describe the size of images obtained from imaging experiments

imageSize - Property in Image

Information about the image size.

ImageSize(Integer, Integer, Integer, Integer, Integer) - Constructor in ImageSize

@param timePoint {@see ImageSize#timePoint}

ImagingHardware - Class in life.qbic.datamodel.dtos.imaging.parameters

Describes hardware properties for an instrument in the imaging context

ImagingHardware.Builder - Class in life.qbic.datamodel.dtos.imaging.parameters

ImagingHardware.Builder(String, Detector) - Constructor in ImagingHardware.Builder

ImagingHardware(Builder<?>) - Constructor in ImagingHardware

ImportantStringComparator - Class in life.qbic.datamodel.sorters

Compares IBarcodeBeans by sample ID

ImportantStringComparator() - Constructor in ImportantStringComparator

incrementSampleCode(String) - Method in SampleCodeFunctions

Increments to the next sample string in the order, meaning the project code stays the same and the 3 letter number is incremented, except if it's 999, then the following letter is incremented and the number starts with 001 again.

incrementUppercase(char) - Method in SampleCodeFunctions

Increments the value of an upper case char.

info1 - Field in NewModelBarcodeBean

info2 - Field in NewModelBarcodeBean

instance - Field in ImportantStringComparator

instance - Field in SampleCodeComparator

instance - Field in SampleExtIDComparator

instance - Field in SampleSecondaryNameComparator

instance - Field in SampleTypeComparator

instance - Field in TopInfoComparator

institute - Field in Affiliation

instituteID - Field in Person

Instrument - Class in life.qbic.datamodel.dtos.imaging

DTO that describes an instrument in the imaging context

instrument - Property in Image

A detailed instrument description that was used to create the image.

Instrument(String, String, String, Location, String, ImagingHardware) - Constructor in Instrument

DTO that describes an instrument in the imaging context

INTERNAL - Enum Constant in AffiliationCategory

Investigator - Enum Constant in PersonType

investigator - Property in ProjectInfo

isAdminPrinter() - Method in Printer

ISampleBean - Interface in life.qbic.datamodel.samples

isInteger(String) - Method in SampleCodeFunctions

Checks if a String can be parsed to an Integer

isMeasurementOfBarcode(String, String) - Method in SampleCodeFunctions

ISO_8601_DATETIME_FORMAT - Field in Constants

isPilot() - Method in ExperimentBean

isPilot - Field in ProjectInfo

isQbicBarcode(String) - Method in SampleCodeFunctions

Checks if a String fits the QBiC barcode pattern and has a correct checksum

isQbicEntityCode(String) - Method in SampleCodeFunctions

Checks if a String fits the QBiC entity code pattern, as used for the species level

items - Property in CostEstimate

A list of items which for which the customer will be charged

items - Property in CostEstimate.Builder

items - Property in Offer

A list of items for which the customer will be charged

items - Property in Offer.Builder

itemsWithoutOverhead - Property in Offer

A list of Items for which an overhead cost is not applicable

itemsWithoutOverhead - Property in Offer.Builder

itemsWithoutOverheadNet - Property in Offer.Builder

itemsWithoutOverheadNetPrice - Property in Offer

The net price of all items for which an overhead cost is not applicable, without overhead and taxes

itemsWithOverhead - Property in Offer

A list of items for which an overhead cost is applicable

itemsWithOverhead - Property in Offer.Builder

itemsWithOverheadNet - Property in Offer.Builder

itemsWithOverheadNetPrice - Property in Offer

The net price of all items for which an overhead cost is applicable, without overhead and taxes

J

K

L

label - Property in Affiliation

An affiliation label @link{AffiliationLabel}.

label - Property in Affiliation.Builder

Label_Printer - Enum Constant in Printer.PrinterType

laserLineFilter - Field in SRMHardware

Describes the filter that has been applied to the laser lines.

laserLineFilter - Property in SRMHardware.Builder

laserLinesCw - Field in SRMHardware

Cw stands for cool white and describes the brightness of the light / laser beam

laserLinesCw - Property in SRMHardware.Builder

laserLinesPulsed - Field in SRMHardware

Describes the wavelength of pulsed laser lines e.g. 488 nm

laserLinesPulsed - Property in SRMHardware.Builder

laserPowerBeamSplitter - Property in LightMicroscopyParameters

Amount of power of the laser beam split at the beam splitter.

laserPowerTIRFLens - Property in LightMicroscopyParameters

Total Internal Reflection Fluorescence (TIRF) Amount of power of the laser beam at the TIRF lens.

laserRepetitionRate - Field in SRMHardware

Describes the number of pulses per second(frequency) of a laser employed in pulse mode.

laserRepetitionRate - Property in SRMHardware.Builder

lastName - Field in Person

lastName - Property in Person.Builder

lcmsDescription - Field in MSProperties

lcmsMethod - Field in MSProperties

leaf - Field in SampleSummary

LIBRARY_PREP_FINISHED - Enum Constant in Status

LIBRARY_PREP_KIT_SCHEMA - Field in OxfordNanoporeMeasurement

LIBRARY_PREPARATION_KIT - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

ligandPrep - Field in MSRunCollection

LigandPrepRun - Class in life.qbic.datamodel.ms

LigandPrepRun(String, String, String, String) - Constructor in LigandPrepRun

LightMicroscopyParameters - Class in life.qbic.datamodel.dtos.imaging.parameters.lightmicroscopy

Description of light microscope parameters during image analysis.

LightMicroscopyParameters(Integer, List<Integer>, List<EmissionRange>, Float, Float, Float, Position, Integer, Position, ScanMode, Integer, Area) - Constructor in LightMicroscopyParameters

Creates a description of light microscope parameters during image analysis.

linkedOffer - Property in Project

The associated offer

linkedOffer - Property in ProjectApplication

The associated offer

linkedOfferId - Field in Project.Builder

Location - Class in life.qbic.datamodel.samples

location - Property in Instrument

The location of the instrument.

Location() - Constructor in Location

location - Field in Printer

logFilesCollection - Field in OxfordNanoporeMeasurement

logger - Field in ExperimentCodeFunctions

logger - Field in OpenbisExperiment

logger - Field in SampleCodeComparator

logger - Field in SampleCodeFunctions

logger - Field in TSVSampleBean

M

MACHINE_HOST - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

Manager - Enum Constant in PersonType

manager - Property in ProjectInfo

manufacturer - Property in Instrument

The manufacturer of the instrument.

mapToChar(int) - Method in SampleCodeFunctions

Maps an integer to a char representation.

max(String, String) - Method in SampleCodeFunctions

Checks which of two Strings can be parsed to a larger Integer and returns it.

maxJumpDistance - Field in SRMAnalysisParameters

Describes the maximal distance that a molecule can "jump" within two frames in order to be traced In context of SMT - Single Molecule Tracking

maxSize - Field in AttachmentConfig

measuredPercent - Property in SampleSummary

MeasurementFolder - Class in life.qbic.datamodel.datasets.datastructure.folders.nanopore

A special case of a DataFolder.

MeasurementFolder(String, String, List) - Constructor in MeasurementFolder

measurementFolder - Field in OxfordNanoporeMeasurement

measurements - Field in OxfordNanoporeExperiment

METABOLOMIC - Enum Constant in ProductCategory

METABOLOMIC - Enum Constant in ProductType

MetabolomicAnalysis - Class in life.qbic.datamodel.dtos.business.services

Describes a product for metabolomics services.

MetabolomicAnalysis(String, String, double, ProductUnit, long) - Constructor in MetabolomicAnalysis

Basic product constructor.

metadata - Property in OpenbisExperiment

metadata - Field in OxfordNanoporeMeasurement

METADATA_REGISTERED - Enum Constant in Status

metadata - Property in TSVSampleBean

MFT - Enum Constant in AffiliationLabel

MNF - Enum Constant in AffiliationLabel

Modality - Enum in life.qbic.datamodel.dtos.imaging.properties

Enumeration of different microscopy and spectroscopy modalities.

modality - Property in Image

The image modality.

Modality(String) - Constructor in Modality

Enumeration of different microscopy and spectroscopy modalities.

model - Property in Instrument

The model type of the instrument.

modificationDate - Property in CostEstimate

The date on which the cost estimate was created

modificationDate - Property in CostEstimate.Builder

modificationDate - Property in Offer

Date on which the offer was lastly modified

modificationDate - Property in Offer.Builder

MSProperties - Class in life.qbic.datamodel.ms

MSProperties(String, String, String, String) - Constructor in MSProperties

MSRunCollection - Class in life.qbic.datamodel.ms

MSRunCollection(LigandPrepRun, String) - Constructor in MSRunCollection

MuxScanDataLog - Class in life.qbic.datamodel.datasets.datastructure.files.nanopore

A specialisation of a DataFile, represents an Oxford Nanopore Mux scan data log file

MuxScanDataLog(String, String) - Constructor in MuxScanDataLog

N

name - Field in AttachmentInformation

name - Field in DataFile

The file name

name - Field in DataFolder

name - Property in Location

name - Field in Printer

name - Field in Printer.PrinterType

name - Property in ProjectSpace

The project space name

name - Property in SampleSummary

NAME_SCHEMA - Field in DriftCorrectionLog

NAME_SCHEMA - Field in DutyTimeLog

NAME_SCHEMA - Field in ExecutionReport

NAME_SCHEMA - Field in Fast5FailFolder

NAME_SCHEMA - Field in Fast5File

NAME_SCHEMA - Field in Fast5PassFolder

NAME_SCHEMA - Field in FastQFailFolder

NAME_SCHEMA - Field in FastQFile

NAME_SCHEMA - Field in FastQPassFolder

NAME_SCHEMA - Field in FastQZippedFile

NAME_SCHEMA - Field in FinalSummaryLog

NAME_SCHEMA - Field in MeasurementFolder

The name schema of a Oxford Nanopore measurement (run).

NAME_SCHEMA - Field in MuxScanDataLog

NAME_SCHEMA - Field in PipelineInformationFolder

NAME_SCHEMA - Field in PipelineReport

NAME_SCHEMA - Field in QualityControlFolder

NAME_SCHEMA - Field in ReportMdLog

NAME_SCHEMA - Field in ReportPDFLog

NAME_SCHEMA - Field in RunId

NAME_SCHEMA - Field in SampleIds

NAME_SCHEMA - Field in SequencingSummaryLog

NAME_SCHEMA - Field in SoftwareVersions

NAME_SCHEMA - Field in ThroughputLog

NAME_SCHEMA - Field in UnclassifiedFast5Folder

NAME_SCHEMA - Field in UnclassifiedFastQFolder

name - Field in ServiceUser

nanoporeFileTypes - Field in OxfordNanoporeExperiment

nanoporeFolderTypes - Field in OxfordNanoporeExperiment

ncbiOrganism - Field in OpenbisBiologicalEntity

netPrice - Property in Offer

The net price of all items without taxes and overhead

netPrice - Property in Offer.Builder

NewModelBarcodeBean - Class in life.qbic.datamodel.printing

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

NewModelBarcodeBean(String, String, String, String, String, List<String>, String, String) - Constructor in NewModelBarcodeBean

nfCoreFileTypes - Field in NfCorePipelineResult

nfCoreFolderTypes - Field in NfCorePipelineResult

NfCorePipelineResult - Class in life.qbic.datamodel.datasets

Class that holds information about a the output of a nf-core pipeline

NfCorePipelineResult(PipelineInformationFolder, QualityControlFolder, List<DataFolder>, RunId, SampleIds) - Constructor in NfCorePipelineResult

NON - Enum Constant in Size

NONE - Enum Constant in AcademicTitle

numOfSamples - Field in ExperimentBean

O

objective - Field in ImagingHardware

The objective used in the instrument

objective - Property in ImagingHardware.Builder

OBSERVER - Enum Constant in OpenbisSpaceUserRole

Offer - Class in life.qbic.datamodel.accounting

An offer for a project

Offer.Builder - Class in life.qbic.datamodel.dtos.business

Offer.Builder(Customer, ProjectManager, String, String, Affiliation) - Constructor in Offer.Builder

Offer(Date, Date, Customer, ProjectManager, String, String, List<ProductItem>, double, OfferId) - Constructor in Offer

OfferId - Class in life.qbic.datamodel.dtos.business

A DTO describing the offer identifier

OfferId(String, String, String) - Constructor in OfferId

offset - Field in SRMAnalysisParameters

Offset applied in the analysis This is e.g. 100 ADU The collected signal from the light source can be shifted via an offset amount through pre-amplification

OpenbisBiologicalEntity - Class in life.qbic.datamodel.samples

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

OpenbisBiologicalEntity(String, String, String, String, String, List<Property>, String, String, String) - Constructor in OpenbisBiologicalEntity

Create a new Biological Entity

OpenbisBiologicalSample - Class in life.qbic.datamodel.samples

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

OpenbisBiologicalSample(int, List<AOpenbisSample>, String, String, String, String, List<Property>, String) - Constructor in OpenbisBiologicalSample

openbisCode - Field in CollaboratorWithResponsibility

OpenbisExperiment - Class in life.qbic.datamodel.experiments

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

OpenbisExperiment(String, ExperimentType, int, Map<String, Object>) - Constructor in OpenbisExperiment

Creates a new Openbis Experiment

openbisIdentifier - Field in CollaboratorWithResponsibility

OpenbisMHCExtractSample - Class in life.qbic.datamodel.samples

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

OpenbisMHCExtractSample(int, List<AOpenbisSample>, String, String, String, List<Property>, String) - Constructor in OpenbisMHCExtractSample

OpenbisMSSample - Class in life.qbic.datamodel.samples

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

OpenbisMSSample(int, List<AOpenbisSample>, String, String, List<Property>, String) - Constructor in OpenbisMSSample

OpenbisSpaceUserRole - Enum in life.qbic.datamodel.persons

Stores the roles of users that can be added to a space in openBIS

OpenbisTestSample - Class in life.qbic.datamodel.samples

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

OpenbisTestSample(int, List<AOpenbisSample>, String, String, String, List<Property>, String) - Constructor in OpenbisTestSample

openbisType - Field in CollaboratorWithResponsibility

organisation - Property in Affiliation

The organisation label of an affiliation.

organisation - Property in Affiliation.Builder

organization - Field in Affiliation

overheadRatio - Property in Offer

The overhead ratio applied to the pricing dependent on the customer affiliation

overheadRatio - Property in Offer.Builder

overheads - Property in Offer

The amount of overheads part, of the total price

overheads - Property in Offer.Builder

OxfordNanoporeExperiment - Class in life.qbic.datamodel.datasets

Class that holds information about an Oxford Nanopore Experiment.

OxfordNanoporeExperiment(String, List<OxfordNanoporeMeasurement>) - Constructor in OxfordNanoporeExperiment

OxfordNanoporeInstrumentOutput - Class in life.qbic.datamodel.instruments

Represents the Nanopore instrument output data structure schema.

OxfordNanoporeInstrumentOutput() - Constructor in OxfordNanoporeInstrumentOutput

OxfordNanoporeMeasurement - Class in life.qbic.datamodel.datasets

A dataset that represents a Oxford Nanopore Measurement.

OxfordNanoporeMeasurement.MetaData - Class in life.qbic.datamodel.datasets

OxfordNanoporeMeasurement.METADATA_FIELD - Enum in life.qbic.datamodel.datasets

OxfordNanoporeMeasurement.MetaData() - Constructor in OxfordNanoporeMeasurement.MetaData

OxfordNanoporeMeasurement(String, String, List, Map) - Constructor in OxfordNanoporeMeasurement

P

parent - Property in AOpenbisSample

parentIDs - Field in SampleSummary

parentIDs - Field in TSVSampleBean

parents - Field in AOpenbisSample

parents - Field in NewModelBarcodeBean

parseChildren(List<Map>) - Method in NfCorePipelineResult

parseChildren(List<Map>) - Method in OxfordNanoporeExperiment

parseDate(Date) - Method in Location

parseFile(Map) - Method in NfCorePipelineResult

parseFile(Map) - Method in OxfordNanoporeExperiment

parseFolder(Map) - Method in NfCorePipelineResult

parseFolder(Map) - Method in OxfordNanoporeExperiment

parseMeasurementItems(List<Map>) - Method in OxfordNanoporeExperiment

parseMeasurements(Map) - Method in OxfordNanoporeExperiment

Helper method that creates the measurements from the sequencer output

parseQbicIdFromRootFolder(Map) - Method in OxfordNanoporeExperiment

Helper method that parses the QBiC identifier from the root folder name

PartialProduct - Class in life.qbic.datamodel.dtos.business.services

Describes a product type that can only have positive natural unit multipliers (N={0,1...

PartialProduct(String, String, double, ProductUnit, ProductId) - Constructor in PartialProduct

Basic product constructor.

pass - Field in AttachmentConfig

password - Field in ServiceUser

pastLocations - Field in Sample

PER_100_MICROGRAM_PEPTIDE_CHANNEL - Enum Constant in ProductUnit

PER_10_MG - Enum Constant in ProductUnit

PER_500_ML - Enum Constant in ProductUnit

PER_BATCH - Enum Constant in ProductUnit

PER_CHANNEL - Enum Constant in ProductUnit

PER_COMPARISON - Enum Constant in ProductUnit

PER_CYCLE - Enum Constant in ProductUnit

PER_DATASET - Enum Constant in ProductUnit

PER_FLOW_CELL - Enum Constant in ProductUnit

PER_GEL - Enum Constant in ProductUnit

PER_GIGABYTE - Enum Constant in ProductUnit

PER_HOUR - Enum Constant in ProductUnit

PER_MEASUREMENT - Enum Constant in ProductUnit

PER_PROJECT - Enum Constant in ProductUnit

PER_RUN - Enum Constant in ProductUnit

PER_SAMPLE - Enum Constant in ProductUnit

Person - Class in life.qbic.datamodel.people

Person.Builder - Class in life.qbic.datamodel.dtos.general

Person.Builder(String, String, String) - Constructor in Person.Builder

person - Field in CollaboratorWithResponsibility

person_id - Field in PersonAffiliationConnectionInfo

Person(String, String, String) - Constructor in Person

PersonAffiliationConnectionInfo - Class in life.qbic.datamodel.persons

*************************************************************************** QBiC User DB Tools enables users to add people and affiliations to our mysql user database.

PersonAffiliationConnectionInfo(int, int, String) - Constructor in PersonAffiliationConnectionInfo

personID - Field in OpenbisExperiment

PersonType - Enum in life.qbic.datamodel.persons

personType - Property in Person

Person type.

PHD - Enum Constant in AcademicTitle

phone - Property in Person

piezoScanner - Field in SRMHardware

Scanner to detect fast, high precision motion in one or more axes

piezoScanner - Property in SRMHardware.Builder

piezoTableController - Field in SRMHardware

Piezo is greek and means 'to squeeze or press' Its the stage which 'holds' the specimen

piezoTableController - Property in SRMHardware.Builder

pilot - Field in ExperimentBean

pinholeSize - Field in SRMHardware

This variable describes the size of the pinhole, which helps to focus the light and eliminate stray light

pinholeSize - Property in SRMHardware.Builder

PipelineInformationFolder - Class in life.qbic.datamodel.datasets.datastructure.folders.nfcore

A special case of a DataFolder, its name is always pipeline_info.

pipelineInformationFolder - Field in NfCorePipelineResult

PipelineInformationFolder(String, String, List<DataFile>) - Constructor in PipelineInformationFolder

PipelineOutput - Class in life.qbic.datamodel.pipelines

PipelineOutput() - Constructor in PipelineOutput

PipelineReport - Class in life.qbic.datamodel.datasets.datastructure.files.nfcore

A specialisation of a DataFile, represents a nf-core Pipeline report file

pipelineReport - Property in PipelineInformationFolder

PipelineReport(String, String) - Constructor in PipelineReport

PixelSize - Class in life.qbic.datamodel.dtos.imaging.properties

A DTO describing pixel size in images

pixelSize - Property in Image

Information about the time and spacial distribution of a pixel.

PixelSize(Float, Float, Float, Float) - Constructor in PixelSize

A DTO describing pixel size in images

pixelSize - Field in SRMAnalysisParameters

Describes the size of the image pixels.

plane - Property in Area

Describes the image plane of the area

POINT - Enum Constant in ScanMode

polarizationOptics - Field in SRMHardware

Polarization optics change the state of polarization of incident radiation

polarizationOptics - Property in SRMHardware.Builder

pooledSamplesMeasurement - Field in OxfordNanoporeMeasurement

Porsche - Class in life.qbic.example

Porsche() - Constructor in Porsche

PortalUser - Class in life.qbic.datamodel.dtos.portal

PortalUser.Builder - Class in life.qbic.datamodel.dtos.portal

PortalUser.Builder(String, String, String, String, String) - Constructor in PortalUser.Builder

PortalUser(ProjectManager.Builder) - Constructor in PortalUser

Position - Class in life.qbic.datamodel.dtos.imaging.properties

DTO that describes a position on an image

position - Property in LightMicroscopyParameters

Position of the light beam on the scanning area

Position(Float, Float, Float) - Constructor in Position

DTO that describes a position on an image

postalCode - Property in Affiliation

The affiliation postal code

postalCode - Property in Affiliation.Builder

POWERUSER - Enum Constant in OpenbisSpaceUserRole

prepareRawData(String) - Method in OxfordNanoporeMeasurement

prepareRawDataFromPooledMeasurement() - Method in OxfordNanoporeMeasurement

prepareUnclassifiedData() - Method in OxfordNanoporeMeasurement

prepDate - Field in LigandPrepRun

PRIMARY_BIOINFO - Enum Constant in ProductCategory

PRIMARY_BIOINFO - Enum Constant in ProductType

PrimaryAnalysis - Class in life.qbic.datamodel.dtos.business.services

Describes a product for primary bioinformatic analysis services.

PrimaryAnalysis(String, String, double, ProductUnit, long) - Constructor in PrimaryAnalysis

Basic product constructor.

primaryTissue - Field in OpenbisBiologicalSample

Printer - Class in life.qbic.datamodel.printing

Printer.PrinterType - Enum in life.qbic.datamodel.printing

Printer(String, String, String, Printer.PrinterType, boolean, String) - Constructor in Printer

PrinterType(String) - Method in Printer.PrinterType

PROCESSED - Enum Constant in Status

ProcessFolder - Class in life.qbic.datamodel.datasets.datastructure.folders.nfcore

A special case of a DataFolder,

ProcessFolder(String, String, List<?>) - Constructor in ProcessFolder

processFolders - Field in NfCorePipelineResult

PROCESSING - Enum Constant in Status

Product - Class in life.qbic.datamodel.accounting

Describes an entity which packages all ProductItems of the same type

Product(ProductCategory, Currency, String, String, Double, String, Boolean) - Constructor in Product

product - Property in ProductItem

Describes the which product type of the current item

ProductCategory - Enum in life.qbic.datamodel.dtos.business

Lists all packages that bundle the offer items

productCategory - Property in Product

Describes the category of the product

ProductCategory(String) - Constructor in ProductCategory

ProductCategoryFactory - Class in life.qbic.datamodel.dtos.business

This class provides functionality for enum key retrieval

ProductCategoryFactory() - Constructor in ProductCategoryFactory

ProductId - Class in life.qbic.datamodel.dtos.business

A DTO describing Product Identifiers

ProductId.Builder - Class in life.qbic.datamodel.dtos.business

A builder for ProductId instances.

ProductId.Builder(String, long) - Constructor in ProductId.Builder

@param productType

productId - Property in Product

The Id of the product.

ProductId(ProjectManager.Builder) - Constructor in ProductId

ProductItem - Class in life.qbic.datamodel.dtos.business

An item with associated costs and quantity

ProductItem(double, Product) - Constructor in ProductItem

productName - Property in Product

The name of the product

ProductType - Enum in life.qbic.datamodel.dtos.business.services

Lists the abbreviation for each Product used as a type specification by the ProductIdentifier ProductId

productType - Field in ProductId.Builder

ProductType(String) - Constructor in ProductType

Private constructor to create different ProductType enum items

ProductUnit - Enum in life.qbic.datamodel.dtos.business.services

Describes available product units.

ProductUnit(String) - Constructor in ProductUnit

Private constructor to create different ProductUnit enum items

ProductUnitFactory - Class in life.qbic.datamodel.dtos.business.services

This class provides functionality for enum key retrieval

ProductUnitFactory() - Constructor in ProductUnitFactory

PROFESSOR - Enum Constant in AcademicTitle

Project - Class in life.qbic.datamodel.dtos.projectmanagement

A typical scientific QBiC project.

Project.Builder - Class in life.qbic.datamodel.dtos.projectmanagement

Project.Builder(ProjectIdentifier, String) - Constructor in Project.Builder

project - Field in AExperiment

project - Property in ISampleBean

PROJECT_MANAGEMENT - Enum Constant in ProductCategory

PROJECT_MANAGEMENT - Enum Constant in ProductType

Project(ProjectManager.Builder) - Constructor in Project

project - Property in TSVSampleBean

ProjectApplication - Class in life.qbic.datamodel.dtos.business

Information about a desired project registration in QBiC's project management system.

ProjectApplication(OfferId, String, String, String, ProjectManager, ProjectSpace, Customer, ProjectCode) - Constructor in ProjectApplication

ProjectCode - Class in life.qbic.datamodel.dtos.projectmanagement

Describes the project code, that identifies the project within a project space.

projectCode - Property in ProjectApplication

The desired project code

ProjectCode(String) - Constructor in ProjectCode

Constructs a project code instance based on the given code string.

projectCode - Property in ProjectIdentifier

The associated project code within the project space

projectCode - Field in ProjectInfo

projectConserved - Field in TomatoId

Conserved part of a project which is the name of the customer

projectDescription - Property in CostEstimate

A short description of the project

projectDescription - Property in CostEstimate.Builder

projectDescription - Property in Offer

A short description of the project

projectDescription - Property in Offer.Builder

@deprecated Replaced with projectObjective, since 2.1.0

projectId - Property in Project

QBiC's internal project identifier

projectID - Field in ProjectInfo

ProjectIdentifier - Class in life.qbic.datamodel.dtos.projectmanagement

Global project identifier for QBiC projects

projectIdentifier - Field in Project.Builder

ProjectIdentifier(ProjectSpace, ProjectCode) - Constructor in ProjectIdentifier

Constructor for a project identifier.

ProjectInfo - Class in life.qbic.datamodel.projects

ProjectInfo(String, String, String, String, int) - Constructor in ProjectInfo

ProjectManagement - Class in life.qbic.datamodel.dtos.business.services

Describes a product for project management services.

ProjectManagement(String, String, double, ProductUnit, long) - Constructor in ProjectManagement

Basic product constructor.

ProjectManager - Class in life.qbic.datamodel.dtos.business

A project manager specialisation.

ProjectManager.Builder - Class in life.qbic.datamodel.dtos.business

ProjectManager.Builder(String, String, String) - Constructor in ProjectManager.Builder

projectManager - Property in CostEstimate

The QBiC project manager who was assigned to the project

projectManager - Property in CostEstimate.Builder

projectManager - Property in Offer

The QBiC project manager who was assigned to the project

projectManager - Property in Offer.Builder

projectManager - Property in ProjectApplication

The associated project manager

ProjectManager(ProjectManager.Builder) - Constructor in ProjectManager

projectObjective - Property in Offer

A short objective of the project

projectObjective - Property in Offer.Builder

projectObjective - Property in ProjectApplication

A descriptive project objective

ProjectSpace - Class in life.qbic.datamodel.dtos.projectmanagement

Represents a QBiC project space

projectSpace - Property in ProjectApplication

The requested project space the project shall be associated with

projectSpace - Property in ProjectIdentifier

The associated project space

ProjectSpace(String) - Constructor in ProjectSpace

projectTitle - Property in CostEstimate

The title of the project

projectTitle - Property in CostEstimate.Builder

projectTitle - Property in Offer

The title of the project

projectTitle - Property in Offer.Builder

projectTitle - Property in Project

A short but descriptive project title

projectTitle - Field in Project.Builder

projectTitle - Property in ProjectApplication

A short and precise project title

properties - Property in ExperimentModel

properties - Field in OpenbisExperiment

proportionateAllowed - Property in Product

States if the product can be proportioned or not

PROTEOMIC - Enum Constant in ProductCategory

PROTEOMIC - Enum Constant in ProductType

ProteomicAnalysis - Class in life.qbic.datamodel.dtos.business.services

Describes a product for proteomics services.

ProteomicAnalysis(String, String, double, ProductUnit, long) - Constructor in ProteomicAnalysis

Basic product constructor.

Q

Q__WF_NGS_MAPPING - Enum Constant in ExperimentType

Q_ACT_DATA_VOLUME - Enum Constant in QbicPropertyType

Q_ADAPTER_INDEX - Enum Constant in QbicPropertyType

Q_ADAPTER_SEQUENCE - Enum Constant in QbicPropertyType

Q_ADDITIONAL_DATA_INFO - Enum Constant in QbicPropertyType

Q_ADDITIONAL_INFO - Enum Constant in QbicPropertyType

q_ADDITIONAL_NOTES - Property in AOpenbisSample

Q_ADDITIONAL_NOTES - Field in OpenbisExperiment

Q_ANTIBODY - Enum Constant in QbicPropertyType

Q_ATTACHMENT_SAMPLE - Enum Constant in SampleType

Q_ATTACHMENT_TYPE - Enum Constant in QbicPropertyType

Q_BIOLOGICAL_ENTITY - Enum Constant in SampleType

Q_BIOLOGICAL_SAMPLE - Enum Constant in SampleType

Q_BMI_GENERIC_IMAGING - Enum Constant in ExperimentType

Q_BMI_GENERIC_IMAGING_RUN - Enum Constant in SampleType

Q_BMI_MODALITY - Enum Constant in QbicPropertyType

Q_BMI_PET_TRACER - Enum Constant in QbicPropertyType

Q_CELL_COUNT - Enum Constant in QbicPropertyType

Q_CHROMATOGRAPHY_COLUMN_NAME - Enum Constant in QbicPropertyType

Q_CHROMATOGRAPHY_PROPERTIES - Enum Constant in QbicPropertyType

Q_CHROMATOGRAPHY_TYPE - Enum Constant in QbicPropertyType

Q_CONDUCTED_BY_EMAIL - Enum Constant in QbicPropertyType

Q_CONDUCTED_BY_NAME - Enum Constant in QbicPropertyType

Q_CONDUCTED_BY_PHONE - Enum Constant in QbicPropertyType

Q_CREATION_TIME - Enum Constant in QbicPropertyType

Q_CURRENT_PROCESS_STATE - Enum Constant in QbicPropertyType

Q_CURRENT_STATUS - Enum Constant in QbicPropertyType

Q_DEEP_SEQUENCING - Enum Constant in QbicPropertyType

Q_DEMUX_SOFTWARE - Enum Constant in QbicPropertyType

Q_DIGNITY - Enum Constant in QbicPropertyType

Q_EDDA_BENCHMARK - Enum Constant in SampleType

Q_EST_DATA_VOLUME - Enum Constant in QbicPropertyType

Q_EXPERIMENTAL_DESIGN - Enum Constant in ExperimentType

Q_EXPERIMENTAL_SETUP - Enum Constant in QbicPropertyType

Q_EXT_MS_QUALITYCONTROL_RUN - Enum Constant in SampleType

Q_EXT_NGS_QUALITYCONTROL_RUN - Enum Constant in SampleType

q_EXTERNALDB_ID - Property in AOpenbisSample

Q_EXTERNALDB_ID - Enum Constant in QbicPropertyType

Q_EXTRACT_SHARE - Enum Constant in QbicPropertyType

Q_FASTA - Enum Constant in SampleType

Q_FILE_PROPERTIES - Enum Constant in QbicPropertyType

Q_FLOWCELL_BARCODE - Enum Constant in QbicPropertyType

Q_FLOWLANE_INDEX - Enum Constant in QbicPropertyType

Q_GENDER - Enum Constant in QbicPropertyType

Q_HISTOLOGY - Enum Constant in QbicPropertyType

Q_HLA_CLASS - Enum Constant in QbicPropertyType

Q_HLA_TYPING_METHOD - Enum Constant in QbicPropertyType

Q_HLA_TYPING - Enum Constant in QbicPropertyType

Q_HT_QPCR_RUN - Enum Constant in SampleType

Q_ILLUMINA_RUN_MODE - Enum Constant in QbicPropertyType

Q_IMAGED_TISSUE - Enum Constant in QbicPropertyType

Q_IONIZATION_MODE - Enum Constant in QbicPropertyType

Q_IS_METASTASIS - Enum Constant in QbicPropertyType

Q_IS_PILOT - Enum Constant in QbicPropertyType

Q_LIBRARY_PREPKIT - Enum Constant in QbicPropertyType

Q_LOCI - Enum Constant in QbicPropertyType

Q_MAXQUANT_IDENT_ONLY - Enum Constant in QbicPropertyType

Q_MEASUREMENT_FINISH_DATE - Enum Constant in QbicPropertyType

Q_MEASUREMENT_START_DATE - Enum Constant in QbicPropertyType

Q_MHC_ANTIBODY_COL1 - Enum Constant in QbicPropertyType

Q_MHC_ANTIBODY_COL2 - Enum Constant in QbicPropertyType

Q_MHC_ANTIBODY_COL3 - Enum Constant in QbicPropertyType

Q_MHC_ANTIBODY_MASS_COL1 - Enum Constant in QbicPropertyType

Q_MHC_ANTIBODY_MASS_COL2 - Enum Constant in QbicPropertyType

Q_MHC_ANTIBODY_MASS_COL3 - Enum Constant in QbicPropertyType

Q_MHC_ANTIBODY - Field in OpenbisMHCExtractSample

Q_MHC_CLASS - Field in OpenbisMHCExtractSample

Q_MHC_CLASS - Enum Constant in QbicPropertyType

Q_MHC_LIGAND_EXTRACT - Enum Constant in SampleType

Q_MHC_LIGAND_EXTRACTION - Enum Constant in ExperimentType

Q_MICROARRAY_MEASUREMENT - Enum Constant in ExperimentType

Q_MICROARRAY_RUN - Enum Constant in SampleType

Q_MS_CONTROL_SOFTWARE - Enum Constant in QbicPropertyType

Q_MS_CONVERSION_SOFTWARE - Enum Constant in QbicPropertyType

Q_MS_DEVICE - Enum Constant in QbicPropertyType

Q_MS_ENRICHMENT_METHOD - Enum Constant in QbicPropertyType

Q_MS_FRACTIONATION_METHOD - Enum Constant in QbicPropertyType

Q_MS_LCMS_METHOD_INFO - Enum Constant in QbicPropertyType

Q_MS_LCMS_METHOD - Enum Constant in QbicPropertyType

Q_MS_MEASUREMENT - Enum Constant in ExperimentType

Q_MS_PROTOCOL - Enum Constant in QbicPropertyType

Q_MS_PURIFICATION_METHOD - Enum Constant in QbicPropertyType

Q_MS_RAW_VENDOR_TYPE - Enum Constant in QbicPropertyType

Q_MS_RUN - Enum Constant in SampleType

Q_MSDEV_PROPERTIES - Enum Constant in QbicPropertyType

Q_MSHCC_IMAGING_DATE - Enum Constant in QbicPropertyType

Q_NCBI_ORGANISM - Enum Constant in QbicPropertyType

Q_NGS_EPITOPE_PREDICTION - Enum Constant in ExperimentType

Q_NGS_EPITOPES - Enum Constant in SampleType

Q_NGS_FLOWCELL_RUN - Enum Constant in ExperimentType

Q_NGS_FLOWCELL_RUN - Enum Constant in SampleType

Q_NGS_HLATYPING - Enum Constant in ExperimentType

Q_NGS_HLATYPING - Enum Constant in SampleType

Q_NGS_IMMUNE_MONITORING - Enum Constant in ExperimentType

Q_NGS_IMMUNE_MONITORING - Enum Constant in SampleType

Q_NGS_IONTORRENT_RUN - Enum Constant in SampleType

Q_NGS_MAPPING - Enum Constant in ExperimentType

Q_NGS_MAPPING - Enum Constant in SampleType

Q_NGS_MEASUREMENT - Enum Constant in ExperimentType

Q_NGS_MTB_DIAGNOSIS_RUN - Enum Constant in SampleType

Q_NGS_READ_MATCH_ALIGNMENT_RUN - Enum Constant in SampleType

Q_NGS_SINGLE_SAMPLE_RUN - Enum Constant in ExperimentType

Q_NGS_SINGLE_SAMPLE_RUN - Enum Constant in SampleType

Q_NGS_VARIANT_CALLING - Enum Constant in ExperimentType

Q_NGS_VARIANT_CALLING - Enum Constant in SampleType

Q_NOTES - Enum Constant in QbicPropertyType

Q_ONTOLOGY_INSTRUMENT_ID - Enum Constant in QbicPropertyType

Q_ORGANISM_DETAILED - Enum Constant in QbicPropertyType

Q_PGM_TOTAL_SAMPLES - Enum Constant in QbicPropertyType

Q_PREPARATION_DATE - Enum Constant in QbicPropertyType

Q_PRIMARY_TISSUE - Enum Constant in QbicPropertyType

Q_PROJECT_DETAILS - Enum Constant in ExperimentType

Q_PROPERTIES - Enum Constant in QbicPropertyType

Q_PROTEASE_1 - Enum Constant in QbicPropertyType

Q_PROTEASE_2 - Enum Constant in QbicPropertyType

Q_PROTEASE_3 - Enum Constant in QbicPropertyType

Q_PROTEASE_4 - Enum Constant in QbicPropertyType

Q_PROTEASE_DIGESTION - Enum Constant in QbicPropertyType

Q_READ_LENGTH - Enum Constant in QbicPropertyType

Q_READ_MATCH_ARCHIVE_FORMAT - Enum Constant in QbicPropertyType

Q_READS_COUNT - Enum Constant in QbicPropertyType

Q_RNA_INTEGRITY_NUMBER - Enum Constant in QbicPropertyType

Q_SAMPLE_EXTRACTION - Enum Constant in ExperimentType

Q_SAMPLE_MASS - Enum Constant in QbicPropertyType

Q_SAMPLE_PREPARATION - Enum Constant in ExperimentType

Q_SAMPLE_TYPE - Field in OpenbisTestSample

Q_SAMPLE_TYPE - Enum Constant in QbicPropertyType

Q_SAMPLE_VOLUME - Enum Constant in QbicPropertyType

q_SECONDARY_NAME - Property in AOpenbisSample

Q_SECONDARY_NAME - Field in OpenbisExperiment

Q_SECONDARY_NAME - Enum Constant in QbicPropertyType

Q_SEQUENCER_DEVICE - Enum Constant in QbicPropertyType

Q_SEQUENCER_PARAMS - Enum Constant in QbicPropertyType

Q_SEQUENCER_SOFTWARE - Enum Constant in QbicPropertyType

Q_SEQUENCING_CHEMISTRY - Enum Constant in QbicPropertyType

Q_SEQUENCING_CYCLES - Enum Constant in QbicPropertyType

Q_SEQUENCING_MODE - Enum Constant in QbicPropertyType

Q_SEQUENCING_TYPE - Enum Constant in QbicPropertyType

Q_SEX - Enum Constant in QbicPropertyType

Q_TARBALL_SHA256SUM - Enum Constant in QbicPropertyType

Q_TEST_SAMPLE - Enum Constant in SampleType

Q_TILE_INDEX - Enum Constant in QbicPropertyType

Q_TIMEPOINT - Enum Constant in QbicPropertyType

Q_TISSUE_DETAILED - Enum Constant in QbicPropertyType

Q_TISSUE_LOCATION - Enum Constant in QbicPropertyType

Q_TUMOR_STAGE - Enum Constant in QbicPropertyType

Q_TUMOR_TYPE - Enum Constant in QbicPropertyType

Q_VACCINE_CONSTRUCT - Enum Constant in SampleType

Q_WF_EXECUTED_BY - Enum Constant in QbicPropertyType

Q_WF_FINISHED_AT - Enum Constant in QbicPropertyType

Q_WF_ID - Enum Constant in QbicPropertyType

Q_WF_MA_QUALITYCONTROL_RUN - Enum Constant in SampleType

Q_WF_MS_INDIVIDUALIZED_PROTEOME_RUN - Enum Constant in SampleType

Q_WF_MS_LIGANDOMICS_ID_RUN - Enum Constant in SampleType

Q_WF_MS_LIGANDOMICS_QC_RUN - Enum Constant in SampleType

Q_WF_MS_MAXQUANT - Enum Constant in ExperimentType

Q_WF_MS_MAXQUANT_RUN - Enum Constant in SampleType

Q_WF_MS_PEPTIDEID_RUN - Enum Constant in SampleType

Q_WF_MS_QUALITYCONTROL - Enum Constant in ExperimentType

Q_WF_MS_QUALITYCONTROL_RUN - Enum Constant in SampleType

Q_WF_NAME - Enum Constant in QbicPropertyType

Q_WF_NGS_16S_TAXONOMIC_PROFILING - Enum Constant in SampleType

Q_WF_NGS_EPITOPE_PREDICTION - Enum Constant in ExperimentType

Q_WF_NGS_EPITOPE_PREDICTION_RUN - Enum Constant in SampleType

Q_WF_NGS_HLATYPING - Enum Constant in ExperimentType

Q_WF_NGS_HLATYPING_RUN - Enum Constant in SampleType

Q_WF_NGS_MAPPING_RUN - Enum Constant in SampleType

Q_WF_NGS_QUALITYCONTROL - Enum Constant in ExperimentType

Q_WF_NGS_QUALITYCONTROL_RUN - Enum Constant in SampleType

Q_WF_NGS_RNA_EXPRESSION_ANALYSIS_RUN - Enum Constant in SampleType

Q_WF_NGS_SHRNA_COUNTING_RUN - Enum Constant in SampleType

Q_WF_NGS_VARIANT_ANNOTATION - Enum Constant in ExperimentType

Q_WF_NGS_VARIANT_ANNOTATION_RUN - Enum Constant in SampleType

Q_WF_NGS_VARIANT_CALLING_RUN - Enum Constant in SampleType

Q_WF_RNASEQ - Enum Constant in QbicPropertyType

Q_WF_RUNTIME - Enum Constant in QbicPropertyType

Q_WF_STARTED_AT - Enum Constant in QbicPropertyType

Q_WF_STATUS - Enum Constant in QbicPropertyType

Q_WF_VERSION - Enum Constant in QbicPropertyType

QBIC_ENTITY_SAMPLE_CODE_SCHEMA - Field in SampleCodeFunctions

QBIC_SAMPLE_BARCODE_SCHEMA - Field in SampleCodeFunctions

QBIC_SAMPLE_ID_SCHEMA - Field in SampleCodeFunctions

@deprecated this is deprecated since 2.4.0 please use QBIC_SAMPLE_BARCODE_SCHEMA instead

QbicPropertyType - Enum in life.qbic.datamodel

QualityControlFolder - Class in life.qbic.datamodel.datasets.datastructure.folders.nfcore

A special case of a DataFolder, its name is always multiqc.

qualityControlFolder - Field in NfCorePipelineResult

QualityControlFolder(String, String, List<?>) - Constructor in QualityControlFolder

quantity - Property in ProductItem

Describes the amount of a given item

R

random - Field in TomatoId

Random part of the identifier which should follow the Regex [a-x0-9]{4}

readMetaData(Map<String, String>) - Method in OxfordNanoporeMeasurement

REGEX - Field in ProjectCode

RegExHelper - Class in life.qbic.datamodel

*************************************************************************** QBiC User DB Tools enables users to add people and affiliations to our mysql user database.

RegExHelper() - Constructor in RegExHelper

registrationDate - Field in ExperimentBean

relativePath - Field in DataFile

The relative file path

relativePath - Field in DataFolder

removeItem(ProductItem) - Method in CostEstimate

Removes an item from the list of items of the offer

removeItem(ProductItem) - Method in Offer

Removes an item from the list of items of the offer

replaceMetadataValues(String, Map<String, String>) - Method in ISampleBean

replace metadata values relating to a certain property

replaceMetadataValues(String, Map<String, String>) - Method in TSVSampleBean

ReportMdLog - Class in life.qbic.datamodel.datasets.datastructure.files.nanopore

A specialisation of a DataFile, represents an Oxford Nanopore report markdown data log file

ReportMdLog(String, String) - Constructor in ReportMdLog

ReportPDFLog - Class in life.qbic.datamodel.datasets.datastructure.files.nanopore

A specialisation of a DataFile, represents an Oxford Nanopore report PDF log file

ReportPDFLog(String, String) - Constructor in ReportPDFLog

requestCar() - Method in Garage

resolution - Property in Image

Describes the resolution of the image.

responsibleEmail - Property in Location

responsiblePerson - Property in Location

roiSize - Field in SRMAnalysisParameters

ROI stands for region of interest.

role - Field in CollaboratorWithResponsibility

role - Field in PersonAffiliationConnectionInfo

role - Field in RoleAt

RoleAt - Class in life.qbic.datamodel.persons

*************************************************************************** QBiC User DB Tools enables users to add people and affiliations to our mysql user database.

RoleAt(String, String) - Constructor in RoleAt

roomId - Property in Location

An identifier for a room an instrument is located at.

runDate - Field in MSRunCollection

RunId - Class in life.qbic.datamodel.datasets.datastructure.files.nfcore

A specialisation of a DataFile, represents a nf-core RunId file

runId - Field in NfCorePipelineResult

RunId(String, String) - Constructor in RunId

S

Sample - Class in life.qbic.datamodel.samples

SAMPLE_QC_FAIL - Enum Constant in Status

SAMPLE_QC_PASS - Enum Constant in Status

SAMPLE_RECEIVED - Enum Constant in Status

Sample() - Constructor in Sample

sampleAmount - Field in LigandPrepRun

SampleCodeComparator - Class in life.qbic.datamodel.sorters

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

SampleCodeComparator() - Constructor in SampleCodeComparator

SampleCodeFunctions - Class in life.qbic.datamodel.identifiers

Helper functions used for sample creation

SampleCodeFunctions() - Constructor in SampleCodeFunctions

SampleExtIDComparator - Class in life.qbic.datamodel.sorters

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

SampleExtIDComparator() - Constructor in SampleExtIDComparator

sampleId - Field in BarcodedFolder

sampleId - Field in OxfordNanoporeExperiment

SampleIds - Class in life.qbic.datamodel.datasets.datastructure.files.nfcore

A specialisation of a DataFile, represents a nf-core InputIds file

sampleIds - Field in NfCorePipelineResult

SampleIds(String, String) - Constructor in SampleIds

samples - Property in AExperiment

samples - Property in ExperimentBean

samples - Field in ExperimentModel

samples - Property in SampleSummary

SampleSecondaryNameComparator - Class in life.qbic.datamodel.sorters

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

SampleSecondaryNameComparator() - Constructor in SampleSecondaryNameComparator

SampleSummary - Class in life.qbic.datamodel.samples

SampleSummary(int, Set<Integer>, List<ISampleBean>, String, String, String, boolean) - Constructor in SampleSummary

SampleType - Enum in life.qbic.datamodel.samples

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

sampleType - Field in AOpenbisSample

sampleType - Field in SampleSummary

sampleType - Field in TSVSampleBean

SampleTypeComparator - Class in life.qbic.datamodel.sorters

*************************************************************************** QBiC Project Wizard enables users to create hierarchical experiments including different study conditions using factorial design.

SampleTypeComparator() - Constructor in SampleTypeComparator

sampleTypesToExpTypes - Field in SampleCodeFunctions

scanAcquisitionRate - Property in LightMicroscopyParameters

Describes the time for the acquisition of an image area in pixels.

ScanMode - Enum in life.qbic.datamodel.dtos.imaging.properties

Enumeration of different microscopy scan modes.

ScanMode(String) - Constructor in ScanMode

Enumeration of different microscopy scan modes.

scanSize - Property in LightMicroscopyParameters

The size of the scanned area e.g. the area (40,40) in µm of on the image plane xy

SCHEMA - Field in OxfordNanoporeMeasurement.MetaData

SCHEMA_PATH - Field in ImageMetadata

SCHEMA_PATH - Field in OxfordNanoporeInstrumentOutput

SCHEMA_PATH - Field in PipelineOutput

sCMOS - Field in SRMAnalysisParameters

sCMOS stands for scientific Complementary metal–oxide–semiconductor, its an image sensor which offers rapid frame rates, a wide dynamic range, high quantum efficiency, high resolution and a large field of view simultaneously in one image

SECONDARY_BIOINFO - Enum Constant in ProductCategory

SECONDARY_BIOINFO - Enum Constant in ProductType

secondary_name - Field in AttachmentInformation

SecondaryAnalysis - Class in life.qbic.datamodel.dtos.business.services

Describes a product for secondary bioinformatic analysis services.

SecondaryAnalysis(String, String, double, ProductUnit, long) - Constructor in SecondaryAnalysis

Basic product constructor.

secondaryName - Field in NewModelBarcodeBean

secondaryName - Property in ProjectInfo

secondaryName - Property in TSVSampleBean

secondDimensionValue - Property in Area

Describes the value in µm of the second dimension of the area, e.g. 40 µm

selectedCustomerAffiliation - Property in CostEstimate

An identifier which makes the CostEstimate distinguishable from other CostEstimates

selectedCustomerAffiliation - Property in CostEstimate.Builder

selectedCustomerAffiliation - Property in Offer

The affiliation of the customer selected for this offer

selectedCustomerAffiliation - Property in Offer.Builder

self() - Method in CommonPerson.Builder

self() - Method in Customer.Builder

self() - Method in ImagingHardware.Builder

self() - Method in Person.Builder

Needs to be overridden my sub classes.

self() - Method in PortalUser.Builder

self() - Method in ProjectManager.Builder

self() - Method in SRMHardware.Builder

SEM - Enum Constant in Modality

Sequencing - Class in life.qbic.datamodel.dtos.business.services

Describes a product for sequencing services.

SEQUENCING_COMPLETE - Enum Constant in Status

SEQUENCING - Enum Constant in ProductCategory

SEQUENCING - Enum Constant in ProductType

Sequencing(String, String, double, ProductUnit, long) - Constructor in Sequencing

Basic product constructor.

SEQUENCING - Enum Constant in Status

SequencingSummaryLog - Class in life.qbic.datamodel.datasets.datastructure.files.nanopore

A specialisation of a DataFile, represents an Oxford Nanopore sequencing summary log file

SequencingSummaryLog(String, String) - Constructor in SequencingSummaryLog

serialNumber - Property in Instrument

The serial number of the instrument.

ServiceUser - Class in life.qbic.datamodel.services

ServiceUser() - Constructor in ServiceUser

setAddress(Address) - Method in Contact

setAddress(Address) - Method in Location

setAffiliation(String) - Method in Address

setAffiliationID(int) - Method in Person

setAmount(int) - Method in SampleSummary

setArrivalDate(Date) - Method in Location

setBeamSplitter(Filter) - Method in SRMHardware.Builder

Sets the beam splitter filter.

setChildIDs(Set<Integer>) - Method in SampleSummary

setCode(String) - Method in AOpenbisSample

setCode(String) - Method in ExperimentBean

setCode(String) - Method in Sample

setCode(String) - Method in TSVSampleBean

setCodes(List<String>) - Method in SampleSummary

setContact(String) - Method in ProjectInfo

setCountry(String) - Method in Address

setCurrentLocation(Location) - Method in Sample

setDate(String) - Method in ExperimentBean

setDescription(String) - Method in ProjectInfo

setEmail(String) - Method in Contact

setEmissionFilter(Filter) - Method in SRMHardware.Builder

Sets the emission filter.

setEmissionFilterChannels(List<Filter>) - Method in SRMHardware.Builder

Sets the emission filter channels.

setExcitationBeamSplitter(String) - Method in SRMHardware.Builder

Sets the excitation beam splitter.

setExperiment(String) - Method in AOpenbisSample

setExperiment(String) - Method in ISampleBean

setExperiment(String) - Method in TSVSampleBean

setExperiment_type(String) - Method in ExperimentBean

setFactors(List<Property>) - Method in AOpenbisSample

setforwardDate(Date) - Method in Location

setFullName(String) - Method in Contact

setID(String) - Method in ExperimentModel

setId(int) - Method in SampleSummary

setIlluminationMode(IlluminationMode) - Method in SRMHardware.Builder

Sets the illumination mode.

setInvestigator(String) - Method in ProjectInfo

setLaserLineFilter(Float) - Method in SRMHardware.Builder

Sets the laser line filter.

setLaserLinesCw(Integer) - Method in SRMHardware.Builder

Sets the laser line.

setLaserLinesPulsed(Integer) - Method in SRMHardware.Builder

Sets the laser line pulse.

setLaserRepetitionRate(Integer) - Method in SRMHardware.Builder

Sets the laser repetition rate.

setLeaf(boolean) - Method in SampleSummary

setManager(String) - Method in ProjectInfo

setMeasuredPercent(int) - Method in SampleSummary

setMetadata(Map<String, Object>) - Method in OpenbisExperiment

setMetadata(HashMap<String, Object>) - Method in TSVSampleBean

setName(String) - Method in Location

setName(String) - Method in SampleSummary

setParent(String) - Method in AOpenbisSample

setParents(List<ISampleBean>) - Method in TSVSampleBean

setPastLocations(List<Location>) - Method in Sample

setPhone(String) - Method in Person

setPiezoScanner(String) - Method in SRMHardware.Builder

Sets the piezo scanner.

setPiezoTableController(String) - Method in SRMHardware.Builder

Sets the piezo table controller.

setPinholeSize(Size) - Method in SRMHardware.Builder

Sets the pinhole size.

setPolarizationOptics(String) - Method in SRMHardware.Builder

Sets the polarization optics.

setProject(String) - Method in ISampleBean

setProject(String) - Method in TSVSampleBean

setProperties(Map<String, Object>) - Method in ExperimentModel

setQ_ADDITIONAL_NOTES(String) - Method in AOpenbisSample

setQ_EXTERNALDB_ID(String) - Method in AOpenbisSample

setQ_SECONDARY_NAME(String) - Method in AOpenbisSample

setResponsibleEmail(String) - Method in Location

setResponsiblePerson(String) - Method in Location

setSamples(List<AOpenbisSample>) - Method in AExperiment

Sets the list of samples in this experiment

setSamples(String) - Method in ExperimentBean

setSamples(List<ISampleBean>) - Method in SampleSummary

setSampleType(String) - Method in AOpenbisSample

setSampleType(SampleType) - Method in TSVSampleBean

setSecondaryName(String) - Method in ProjectInfo

setSecondaryName(String) - Method in TSVSampleBean

setSpace(String) - Method in AOpenbisSample

setSpace(String) - Method in ISampleBean

setSpace(String) - Method in TSVSampleBean

setStatus(Status) - Method in Location

setStreet(String) - Method in Address

setTitle(String) - Method in Person

setType(String) - Method in CollaboratorWithResponsibility

setUsername(String) - Method in Person

setZipCode(Integer) - Method in Address

Size - Enum in life.qbic.datamodel.dtos.imaging.properties

DTO to describe the size of an object in context of imaging

Size(String) - Constructor in Size

DTO to describe the size of an object in context of imaging

SoftwareVersions - Class in life.qbic.datamodel.datasets.datastructure.files.nfcore

A specialisation of a DataFile, represents a nf-core SoftwareVersions file

softwareVersions - Property in PipelineInformationFolder

SoftwareVersions(String, String) - Constructor in SoftwareVersions

source - Field in SampleSummary

sourceID - Field in LigandPrepRun

space - Field in AExperiment

space - Property in AOpenbisSample

space - Property in ISampleBean

space - Field in ProjectInfo

space - Property in TSVSampleBean

speciesInfo - Field in OpenbisBiologicalEntity

SPECTROSCOPY - Enum Constant in Modality

SPT_PALM - Enum Constant in Modality

SRMAnalysisParameters - Class in life.qbic.datamodel.dtos.imaging.parameters.srm

Describes super resolution microscope (SRM) analysis parameters during image analysis

SRMAnalysisParameters(Dimensionality, String, Float, Float, Float, PixelSize, Float, Integer, Boolean, Boolean, Boolean, Float, Integer, Integer) - Constructor in SRMAnalysisParameters

Returns a super resolution microscopy parameter.

SRMHardware - Class in life.qbic.datamodel.dtos.imaging.parameters.srm

Describes the properties of the super resolution microscope (SRM) hardware

SRMHardware.Builder - Class in life.qbic.datamodel.dtos.imaging.parameters.srm

SRMHardware.Builder(String, Detector) - Constructor in SRMHardware.Builder

Constructor with mandatory parameters.

SRMHardware(ProjectManager.Builder) - Constructor in SRMHardware

start(BundleContext) - Method in Activator

START_DATE - Enum Constant in OxfordNanoporeMeasurement.METADATA_FIELD

startEngine() - Method in Car

startEngine() - Method in Porsche

startWavelength - Property in EmissionRange

Its the smallest wavelength within the emission range e.g 495 nm

Status - Enum in life.qbic.datamodel.samples

The status of an sample in the context of sample-tracking

status - Property in Location

stop(BundleContext) - Method in Activator

strArrToInt(List<String>) - Method in SampleCodeFunctions

Parses a whole String list to integers and returns them in another list.

street - Property in Address

street - Property in Address.Builder

street - Property in Affiliation

The affiliation street

street - Property in Affiliation.Builder