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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

labels - Variable in class org.biomage.BioAssay.Channel
The compound used to label the extract.

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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