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A
- addToBioAssayFactorValues(FactorValue) - Method in class org.biomage.BioAssay.BioAssay
- Method to add FactorValue to BioAssayFactorValues_list
- addToBioAssayFactorValues(int, FactorValue) - Method in class org.biomage.BioAssay.BioAssay
- Method to add FactorValue at position to BioAssayFactorValues_list
- addToBioAssayTreatments(BioAssayTreatment) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Method to add BioAssayTreatment to BioAssayTreatments_list
- addToBioAssayTreatments(int, BioAssayTreatment) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Method to add BioAssayTreatment at position to BioAssayTreatments_list
- addToBioAssay_list(BioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to add BioAssay to BioAssay_list
- addToBioAssay_list(int, BioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to add BioAssay at position to BioAssay_list
- addToChannel_list(Channel) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to add Channel to Channel_list
- addToChannel_list(int, Channel) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to add Channel at position to Channel_list
- addToChannels(Channel) - Method in class org.biomage.BioAssay.BioAssay
- Method to add Channel to Channels_list
- addToChannels(int, Channel) - Method in class org.biomage.BioAssay.BioAssay
- Method to add Channel at position to Channels_list
- addToChannels(Channel) - Method in class org.biomage.BioAssay.Image
- Method to add Channel to Channels_list
- addToChannels(int, Channel) - Method in class org.biomage.BioAssay.Image
- Method to add Channel at position to Channels_list
- addToDerivedBioAssayData(DerivedBioAssayData) - Method in class org.biomage.BioAssay.DerivedBioAssay
- Method to add DerivedBioAssayData to DerivedBioAssayData_list
- addToDerivedBioAssayData(int, DerivedBioAssayData) - Method in class org.biomage.BioAssay.DerivedBioAssay
- Method to add DerivedBioAssayData at position to DerivedBioAssayData_list
- addToDerivedBioAssay_list(DerivedBioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to add DerivedBioAssay to DerivedBioAssay_list
- addToDerivedBioAssay_list(int, DerivedBioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to add DerivedBioAssay at position to DerivedBioAssay_list
- addToImages(Image) - Method in class org.biomage.BioAssay.ImageAcquisition
- Method to add Image to Images_list
- addToImages(int, Image) - Method in class org.biomage.BioAssay.ImageAcquisition
- Method to add Image at position to Images_list
- addToLabels(Compound) - Method in class org.biomage.BioAssay.Channel
- Method to add Compound to Labels_list
- addToLabels(int, Compound) - Method in class org.biomage.BioAssay.Channel
- Method to add Compound at position to Labels_list
- addToMeasuredBioAssayData(MeasuredBioAssayData) - Method in class org.biomage.BioAssay.MeasuredBioAssay
- Method to add MeasuredBioAssayData to MeasuredBioAssayData_list
- addToMeasuredBioAssayData(int, MeasuredBioAssayData) - Method in class org.biomage.BioAssay.MeasuredBioAssay
- Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list
- addToMeasuredBioAssay_list(MeasuredBioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to add MeasuredBioAssay to MeasuredBioAssay_list
- addToMeasuredBioAssay_list(int, MeasuredBioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to add MeasuredBioAssay at position to MeasuredBioAssay_list
- addToPhysicalBioAssayData(Image) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Method to add Image to PhysicalBioAssayData_list
- addToPhysicalBioAssayData(int, Image) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Method to add Image at position to PhysicalBioAssayData_list
- addToPhysicalBioAssay_list(PhysicalBioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to add PhysicalBioAssay to PhysicalBioAssay_list
- addToPhysicalBioAssay_list(int, PhysicalBioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to add PhysicalBioAssay at position to PhysicalBioAssay_list
- addToSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in class org.biomage.BioAssay.BioAssayCreation
- Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list
- addToSourceBioMaterialMeasurements(int, BioMaterialMeasurement) - Method in class org.biomage.BioAssay.BioAssayCreation
- Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list
- array - Variable in class org.biomage.BioAssay.BioAssayCreation
- The array used in the BioAssayCreation event.
B
- BioAssay - class org.biomage.BioAssay.BioAssay.
- An abstract class which represents both physical and computational groupings of arrays and biomaterials.
- BioAssay() - Constructor for class org.biomage.BioAssay.BioAssay
- Default constructor.
- BioAssay(Attributes) - Constructor for class org.biomage.BioAssay.BioAssay
- Attribute constructor.
- BioAssayCreation - class org.biomage.BioAssay.BioAssayCreation.
- The process by which an array and one or more biomaterials are combined to create a bioAssayCreation.
- BioAssayCreation() - Constructor for class org.biomage.BioAssay.BioAssayCreation
- Default constructor.
- BioAssayCreation(Attributes) - Constructor for class org.biomage.BioAssay.BioAssayCreation
- Attribute constructor.
- BioAssayTreatment - class org.biomage.BioAssay.BioAssayTreatment.
- The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...).
- BioAssayTreatment() - Constructor for class org.biomage.BioAssay.BioAssayTreatment
- Default constructor.
- BioAssayTreatment(Attributes) - Constructor for class org.biomage.BioAssay.BioAssayTreatment
- Attribute constructor.
- BioAssay_package - class org.biomage.BioAssay.BioAssay_package.
- Provides classes that contain information and annotation on the event of joining an Array with a BioMaterial preparation, the acquisition of images and the extraction of data on a per feature basis from those images.
- BioAssay_package() - Constructor for class org.biomage.BioAssay.BioAssay_package
- Default constructor.
- BioAssay_package(Attributes) - Constructor for class org.biomage.BioAssay.BioAssay_package
- Attribute constructor.
- BioAssay_package.BioAssay_list - class org.biomage.BioAssay.BioAssay_package.BioAssay_list.
- Inner list class for holding multiple entries for attribute bioAssay_list.
- BioAssay_package.BioAssay_list() - Constructor for class org.biomage.BioAssay.BioAssay_package.BioAssay_list
- BioAssay_package.Channel_list - class org.biomage.BioAssay.BioAssay_package.Channel_list.
- Inner list class for holding multiple entries for attribute channel_list.
- BioAssay_package.Channel_list() - Constructor for class org.biomage.BioAssay.BioAssay_package.Channel_list
- BioAssay_package.DerivedBioAssay_list - class org.biomage.BioAssay.BioAssay_package.DerivedBioAssay_list.
- Inner list class for holding multiple entries for attribute derivedBioAssay_list.
- BioAssay_package.DerivedBioAssay_list() - Constructor for class org.biomage.BioAssay.BioAssay_package.DerivedBioAssay_list
- BioAssay_package.MeasuredBioAssay_list - class org.biomage.BioAssay.BioAssay_package.MeasuredBioAssay_list.
- Inner list class for holding multiple entries for attribute measuredBioAssay_list.
- BioAssay_package.MeasuredBioAssay_list() - Constructor for class org.biomage.BioAssay.BioAssay_package.MeasuredBioAssay_list
- BioAssay_package.PhysicalBioAssay_list - class org.biomage.BioAssay.BioAssay_package.PhysicalBioAssay_list.
- Inner list class for holding multiple entries for attribute physicalBioAssay_list.
- BioAssay_package.PhysicalBioAssay_list() - Constructor for class org.biomage.BioAssay.BioAssay_package.PhysicalBioAssay_list
- bioAssayCreation - Variable in class org.biomage.BioAssay.PhysicalBioAssay
- The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.
- bioAssayFactorValues - Variable in class org.biomage.BioAssay.BioAssay
- The values that this BioAssay is associated with for the experiment.
- bioAssayTreatments - Variable in class org.biomage.BioAssay.PhysicalBioAssay
- The set of treatments undergone by this PhysicalBioAssay.
- bioAssay_list - Variable in class org.biomage.BioAssay.BioAssay_package
- An abstract class which represents both physical and computational groupings of arrays and biomaterials.
C
- Channel - class org.biomage.BioAssay.Channel.
- A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.
- Channel() - Constructor for class org.biomage.BioAssay.Channel
- Default constructor.
- Channel(Attributes) - Constructor for class org.biomage.BioAssay.Channel
- Attribute constructor.
- channel_list - Variable in class org.biomage.BioAssay.BioAssay_package
- A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.
- channels - Variable in class org.biomage.BioAssay.BioAssay
- Channels can be non-null for all subclasses.
- channels - Variable in class org.biomage.BioAssay.Image
- The channels captured in this image.
D
- DerivedBioAssay - class org.biomage.BioAssay.DerivedBioAssay.
- A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.
- DerivedBioAssay() - Constructor for class org.biomage.BioAssay.DerivedBioAssay
- Default constructor.
- DerivedBioAssay(Attributes) - Constructor for class org.biomage.BioAssay.DerivedBioAssay
- Attribute constructor.
- derivedBioAssayData - Variable in class org.biomage.BioAssay.DerivedBioAssay
- The data associated with the DerivedBioAssay.
- derivedBioAssay_list - Variable in class org.biomage.BioAssay.BioAssay_package
- A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.
F
- FeatureExtraction - class org.biomage.BioAssay.FeatureExtraction.
- The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay.
- FeatureExtraction() - Constructor for class org.biomage.BioAssay.FeatureExtraction
- Default constructor.
- FeatureExtraction(Attributes) - Constructor for class org.biomage.BioAssay.FeatureExtraction
- Attribute constructor.
- featureExtraction - Variable in class org.biomage.BioAssay.MeasuredBioAssay
- The association between the MeasuredBioAssay and the FeatureExtraction Event.
- format - Variable in class org.biomage.BioAssay.Image
- The file format of the image typically a TIF or a JPEG.
G
- getArray() - Method in class org.biomage.BioAssay.BioAssayCreation
- Get method for array
- getBioAssayCreation() - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Get method for bioAssayCreation
- getBioAssayFactorValues() - Method in class org.biomage.BioAssay.BioAssay
- Get method for bioAssayFactorValues
- getBioAssayTreatments() - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Get method for bioAssayTreatments
- getBioAssay_list() - Method in class org.biomage.BioAssay.BioAssay_package
- Get method for bioAssay_list
- getChannel_list() - Method in class org.biomage.BioAssay.BioAssay_package
- Get method for channel_list
- getChannels() - Method in class org.biomage.BioAssay.BioAssay
- Get method for channels
- getChannels() - Method in class org.biomage.BioAssay.Image
- Get method for channels
- getDerivedBioAssayData() - Method in class org.biomage.BioAssay.DerivedBioAssay
- Get method for derivedBioAssayData
- getDerivedBioAssay_list() - Method in class org.biomage.BioAssay.BioAssay_package
- Get method for derivedBioAssay_list
- getFeatureExtraction() - Method in class org.biomage.BioAssay.MeasuredBioAssay
- Get method for featureExtraction
- getFormat() - Method in class org.biomage.BioAssay.Image
- Get method for format
- getFromBioAssayFactorValues(int) - Method in class org.biomage.BioAssay.BioAssay
- Method to get FactorValue from BioAssayFactorValues_list
- getFromBioAssayTreatments(int) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Method to get BioAssayTreatment from BioAssayTreatments_list
- getFromBioAssay_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to get BioAssay from BioAssay_list
- getFromChannel_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to get Channel from Channel_list
- getFromChannels(int) - Method in class org.biomage.BioAssay.BioAssay
- Method to get Channel from Channels_list
- getFromChannels(int) - Method in class org.biomage.BioAssay.Image
- Method to get Channel from Channels_list
- getFromDerivedBioAssayData(int) - Method in class org.biomage.BioAssay.DerivedBioAssay
- Method to get DerivedBioAssayData from DerivedBioAssayData_list
- getFromDerivedBioAssay_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to get DerivedBioAssay from DerivedBioAssay_list
- getFromImages(int) - Method in class org.biomage.BioAssay.ImageAcquisition
- Method to get Image from Images_list
- getFromLabels(int) - Method in class org.biomage.BioAssay.Channel
- Method to get Compound from Labels_list
- getFromMeasuredBioAssayData(int) - Method in class org.biomage.BioAssay.MeasuredBioAssay
- Method to get MeasuredBioAssayData from MeasuredBioAssayData_list
- getFromMeasuredBioAssay_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to get MeasuredBioAssay from MeasuredBioAssay_list
- getFromPhysicalBioAssayData(int) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Method to get Image from PhysicalBioAssayData_list
- getFromPhysicalBioAssay_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to get PhysicalBioAssay from PhysicalBioAssay_list
- getFromSourceBioMaterialMeasurements(int) - Method in class org.biomage.BioAssay.BioAssayCreation
- Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list
- getImages() - Method in class org.biomage.BioAssay.ImageAcquisition
- Get method for images
- getLabels() - Method in class org.biomage.BioAssay.Channel
- Get method for labels
- getMeasuredBioAssayData() - Method in class org.biomage.BioAssay.MeasuredBioAssay
- Get method for measuredBioAssayData
- getMeasuredBioAssayTarget() - Method in class org.biomage.BioAssay.FeatureExtraction
- Get method for measuredBioAssayTarget
- getMeasuredBioAssay_list() - Method in class org.biomage.BioAssay.BioAssay_package
- Get method for measuredBioAssay_list
- getPhysicalBioAssay() - Method in class org.biomage.BioAssay.BioAssayTreatment
- Get method for physicalBioAssay
- getPhysicalBioAssayData() - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Get method for physicalBioAssayData
- getPhysicalBioAssaySource() - Method in class org.biomage.BioAssay.FeatureExtraction
- Get method for physicalBioAssaySource
- getPhysicalBioAssayTarget() - Method in class org.biomage.BioAssay.BioAssayCreation
- Get method for physicalBioAssayTarget
- getPhysicalBioAssay_list() - Method in class org.biomage.BioAssay.BioAssay_package
- Get method for physicalBioAssay_list
- getSourceBioMaterialMeasurements() - Method in class org.biomage.BioAssay.BioAssayCreation
- Get method for sourceBioMaterialMeasurements
- getTarget() - Method in class org.biomage.BioAssay.BioAssayTreatment
- Get method for target
- getType() - Method in class org.biomage.BioAssay.DerivedBioAssay
- Get method for type
- getURI() - Method in class org.biomage.BioAssay.Image
- Get method for URI
H
- Hybridization - class org.biomage.BioAssay.Hybridization.
- The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array.
- Hybridization() - Constructor for class org.biomage.BioAssay.Hybridization
- Default constructor.
- Hybridization(Attributes) - Constructor for class org.biomage.BioAssay.Hybridization
- Attribute constructor.
I
- Image - class org.biomage.BioAssay.Image.
- An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay).
- Image() - Constructor for class org.biomage.BioAssay.Image
- Default constructor.
- Image(Attributes) - Constructor for class org.biomage.BioAssay.Image
- Attribute constructor.
- ImageAcquisition - class org.biomage.BioAssay.ImageAcquisition.
- The process by which an image is generated (typically scanning).
- ImageAcquisition() - Constructor for class org.biomage.BioAssay.ImageAcquisition
- Default constructor.
- ImageAcquisition(Attributes) - Constructor for class org.biomage.BioAssay.ImageAcquisition
- Attribute constructor.
- images - Variable in class org.biomage.BioAssay.ImageAcquisition
- The images produced by the ImageAcquisition event.
L
M
- MeasuredBioAssay - class org.biomage.BioAssay.MeasuredBioAssay.
- A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event.
- MeasuredBioAssay() - Constructor for class org.biomage.BioAssay.MeasuredBioAssay
- Default constructor.
- MeasuredBioAssay(Attributes) - Constructor for class org.biomage.BioAssay.MeasuredBioAssay
- Attribute constructor.
- measuredBioAssayData - Variable in class org.biomage.BioAssay.MeasuredBioAssay
- The data associated with the MeasuredBioAssay.
- measuredBioAssayTarget - Variable in class org.biomage.BioAssay.FeatureExtraction
- The association between the MeasuredBioAssay and the FeatureExtraction Event.
- measuredBioAssay_list - Variable in class org.biomage.BioAssay.BioAssay_package
- A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event.
O
- org.biomage.BioAssay - package org.biomage.BioAssay
P
- PhysicalBioAssay - class org.biomage.BioAssay.PhysicalBioAssay.
- A bioAssay created by the bioAssayCreation event (e.g.
- PhysicalBioAssay() - Constructor for class org.biomage.BioAssay.PhysicalBioAssay
- Default constructor.
- PhysicalBioAssay(Attributes) - Constructor for class org.biomage.BioAssay.PhysicalBioAssay
- Attribute constructor.
- physicalBioAssay - Variable in class org.biomage.BioAssay.BioAssayTreatment
- The set of treatments undergone by this PhysicalBioAssay.
- physicalBioAssayData - Variable in class org.biomage.BioAssay.PhysicalBioAssay
- The Images associated with this PhysicalBioAssay by ImageAcquisition.
- physicalBioAssaySource - Variable in class org.biomage.BioAssay.FeatureExtraction
- The PhysicalBioAssay used in the FeatureExtraction event.
- physicalBioAssayTarget - Variable in class org.biomage.BioAssay.BioAssayCreation
- The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.
- physicalBioAssay_list - Variable in class org.biomage.BioAssay.BioAssay_package
- A bioAssay created by the bioAssayCreation event (e.g.
R
- removeElementAtFromBioAssayFactorValues(int) - Method in class org.biomage.BioAssay.BioAssay
- Method to remove by position from BioAssayFactorValues_list
- removeElementAtFromBioAssayTreatments(int) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Method to remove by position from BioAssayTreatments_list
- removeElementAtFromBioAssay_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to remove by position from BioAssay_list
- removeElementAtFromChannel_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to remove by position from Channel_list
- removeElementAtFromChannels(int) - Method in class org.biomage.BioAssay.BioAssay
- Method to remove by position from Channels_list
- removeElementAtFromChannels(int) - Method in class org.biomage.BioAssay.Image
- Method to remove by position from Channels_list
- removeElementAtFromDerivedBioAssayData(int) - Method in class org.biomage.BioAssay.DerivedBioAssay
- Method to remove by position from DerivedBioAssayData_list
- removeElementAtFromDerivedBioAssay_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to remove by position from DerivedBioAssay_list
- removeElementAtFromImages(int) - Method in class org.biomage.BioAssay.ImageAcquisition
- Method to remove by position from Images_list
- removeElementAtFromLabels(int) - Method in class org.biomage.BioAssay.Channel
- Method to remove by position from Labels_list
- removeElementAtFromMeasuredBioAssayData(int) - Method in class org.biomage.BioAssay.MeasuredBioAssay
- Method to remove by position from MeasuredBioAssayData_list
- removeElementAtFromMeasuredBioAssay_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to remove by position from MeasuredBioAssay_list
- removeElementAtFromPhysicalBioAssayData(int) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Method to remove by position from PhysicalBioAssayData_list
- removeElementAtFromPhysicalBioAssay_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to remove by position from PhysicalBioAssay_list
- removeElementAtFromSourceBioMaterialMeasurements(int) - Method in class org.biomage.BioAssay.BioAssayCreation
- Method to remove by position from SourceBioMaterialMeasurements_list
- removeFromBioAssayFactorValues(FactorValue) - Method in class org.biomage.BioAssay.BioAssay
- Method to remove first FactorValue from BioAssayFactorValues_list
- removeFromBioAssayTreatments(BioAssayTreatment) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Method to remove first BioAssayTreatment from BioAssayTreatments_list
- removeFromBioAssay_list(BioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to remove first BioAssay from BioAssay_list
- removeFromChannel_list(Channel) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to remove first Channel from Channel_list
- removeFromChannels(Channel) - Method in class org.biomage.BioAssay.BioAssay
- Method to remove first Channel from Channels_list
- removeFromChannels(Channel) - Method in class org.biomage.BioAssay.Image
- Method to remove first Channel from Channels_list
- removeFromDerivedBioAssayData(DerivedBioAssayData) - Method in class org.biomage.BioAssay.DerivedBioAssay
- Method to remove first DerivedBioAssayData from DerivedBioAssayData_list
- removeFromDerivedBioAssay_list(DerivedBioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to remove first DerivedBioAssay from DerivedBioAssay_list
- removeFromImages(Image) - Method in class org.biomage.BioAssay.ImageAcquisition
- Method to remove first Image from Images_list
- removeFromLabels(Compound) - Method in class org.biomage.BioAssay.Channel
- Method to remove first Compound from Labels_list
- removeFromMeasuredBioAssayData(MeasuredBioAssayData) - Method in class org.biomage.BioAssay.MeasuredBioAssay
- Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list
- removeFromMeasuredBioAssay_list(MeasuredBioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to remove first MeasuredBioAssay from MeasuredBioAssay_list
- removeFromPhysicalBioAssayData(Image) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Method to remove first Image from PhysicalBioAssayData_list
- removeFromPhysicalBioAssay_list(PhysicalBioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
- Method to remove first PhysicalBioAssay from PhysicalBioAssay_list
- removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in class org.biomage.BioAssay.BioAssayCreation
- Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list
S
- setArray(Array) - Method in class org.biomage.BioAssay.BioAssayCreation
- Set method for array
- setBioAssayCreation(BioAssayCreation) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Set method for bioAssayCreation
- setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list) - Method in class org.biomage.BioAssay.BioAssay
- Set method for bioAssayFactorValues
- setBioAssayTreatments(HasBioAssayTreatments.BioAssayTreatments_list) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Set method for bioAssayTreatments
- setBioAssay_list(BioAssay_package.BioAssay_list) - Method in class org.biomage.BioAssay.BioAssay_package
- Set method for bioAssay_list
- setChannel_list(BioAssay_package.Channel_list) - Method in class org.biomage.BioAssay.BioAssay_package
- Set method for channel_list
- setChannels(HasChannels.Channels_list) - Method in class org.biomage.BioAssay.BioAssay
- Set method for channels
- setChannels(HasChannels.Channels_list) - Method in class org.biomage.BioAssay.Image
- Set method for channels
- setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list) - Method in class org.biomage.BioAssay.DerivedBioAssay
- Set method for derivedBioAssayData
- setDerivedBioAssay_list(BioAssay_package.DerivedBioAssay_list) - Method in class org.biomage.BioAssay.BioAssay_package
- Set method for derivedBioAssay_list
- setFeatureExtraction(FeatureExtraction) - Method in class org.biomage.BioAssay.MeasuredBioAssay
- Set method for featureExtraction
- setFormat(OntologyEntry) - Method in class org.biomage.BioAssay.Image
- Set method for format
- setImages(HasImages.Images_list) - Method in class org.biomage.BioAssay.ImageAcquisition
- Set method for images
- setLabels(HasLabels.Labels_list) - Method in class org.biomage.BioAssay.Channel
- Set method for labels
- setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list) - Method in class org.biomage.BioAssay.MeasuredBioAssay
- Set method for measuredBioAssayData
- setMeasuredBioAssayTarget(MeasuredBioAssay) - Method in class org.biomage.BioAssay.FeatureExtraction
- Set method for measuredBioAssayTarget
- setMeasuredBioAssay_list(BioAssay_package.MeasuredBioAssay_list) - Method in class org.biomage.BioAssay.BioAssay_package
- Set method for measuredBioAssay_list
- setPhysicalBioAssay(PhysicalBioAssay) - Method in class org.biomage.BioAssay.BioAssayTreatment
- Set method for physicalBioAssay
- setPhysicalBioAssayData(HasPhysicalBioAssayData.PhysicalBioAssayData_list) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- Set method for physicalBioAssayData
- setPhysicalBioAssaySource(PhysicalBioAssay) - Method in class org.biomage.BioAssay.FeatureExtraction
- Set method for physicalBioAssaySource
- setPhysicalBioAssayTarget(PhysicalBioAssay) - Method in class org.biomage.BioAssay.BioAssayCreation
- Set method for physicalBioAssayTarget
- setPhysicalBioAssay_list(BioAssay_package.PhysicalBioAssay_list) - Method in class org.biomage.BioAssay.BioAssay_package
- Set method for physicalBioAssay_list
- setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list) - Method in class org.biomage.BioAssay.BioAssayCreation
- Set method for sourceBioMaterialMeasurements
- setTarget(PhysicalBioAssay) - Method in class org.biomage.BioAssay.BioAssayTreatment
- Set method for target
- setType(OntologyEntry) - Method in class org.biomage.BioAssay.DerivedBioAssay
- Set method for type
- setURI(String) - Method in class org.biomage.BioAssay.Image
- Set method for URI
- sourceBioMaterialMeasurements - Variable in class org.biomage.BioAssay.BioAssayCreation
- The BioSample and its amount used in the BioAssayCreation event.
T
- target - Variable in class org.biomage.BioAssay.BioAssayTreatment
- The PhysicalBioAssay that was treated.
- type - Variable in class org.biomage.BioAssay.DerivedBioAssay
- The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.
U
- URI - Variable in class org.biomage.BioAssay.Image
- The file location in which an image may be found.
W
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.BioAssay
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.BioAssayCreation
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.BioAssayTreatment
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.BioAssay_package
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.Channel
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.DerivedBioAssay
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.FeatureExtraction
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.Hybridization
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.Image
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.ImageAcquisition
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.MeasuredBioAssay
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- writeAssociations
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.BioAssay
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.BioAssayCreation
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.BioAssayTreatment
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.BioAssay_package
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.Channel
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.DerivedBioAssay
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.FeatureExtraction
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.Hybridization
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.Image
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.ImageAcquisition
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.MeasuredBioAssay
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- writeAttributes
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.BioAssay
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.BioAssayCreation
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.BioAssayTreatment
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.BioAssay_package
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.Channel
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.DerivedBioAssay
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.FeatureExtraction
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.Hybridization
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.Image
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.ImageAcquisition
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.MeasuredBioAssay
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssay.PhysicalBioAssay
- writeMAGEML
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