Docjar: A Java Source and Docuemnt Enginecom.*    java.*    javax.*    org.*    all    new    plug-in

Quick Search    Search Deep
A B D F G I L M N O P Q R S T V W Z

A

Array - class org.biomage.Array.Array.
The physical substrate along with its features and their annotation
Array() - Constructor for class org.biomage.Array.Array
Default constructor.
Array(Attributes) - Constructor for class org.biomage.Array.Array
Attribute constructor.
ArrayGroup - class org.biomage.Array.ArrayGroup.
An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.
ArrayGroup() - Constructor for class org.biomage.Array.ArrayGroup
Default constructor.
ArrayGroup(Attributes) - Constructor for class org.biomage.Array.ArrayGroup
Attribute constructor.
ArrayGroup.OrientationMarkPosition - class org.biomage.Array.ArrayGroup.OrientationMarkPosition.
Inner class for the enumeration values that the attribute orientationMarkPosition can assume.
ArrayGroup.OrientationMarkPosition() - Constructor for class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
ArrayManufacture - class org.biomage.Array.ArrayManufacture.
Describes the process by which arrays are produced.
ArrayManufacture() - Constructor for class org.biomage.Array.ArrayManufacture
Default constructor.
ArrayManufacture(Attributes) - Constructor for class org.biomage.Array.ArrayManufacture
Attribute constructor.
ArrayManufactureDeviation - class org.biomage.Array.ArrayManufactureDeviation.
Stores information of the potential difference between an array design and arrays that have been manufactured using that design (e.g.
ArrayManufactureDeviation() - Constructor for class org.biomage.Array.ArrayManufactureDeviation
Default constructor.
ArrayManufactureDeviation(Attributes) - Constructor for class org.biomage.Array.ArrayManufactureDeviation
Attribute constructor.
Array_package - class org.biomage.Array.Array_package.
Describes the process of creating arrays from array designs.
Array_package() - Constructor for class org.biomage.Array.Array_package
Default constructor.
Array_package(Attributes) - Constructor for class org.biomage.Array.Array_package
Attribute constructor.
Array_package.ArrayGroup_list - class org.biomage.Array.Array_package.ArrayGroup_list.
Inner list class for holding multiple entries for attribute arrayGroup_list.
Array_package.ArrayGroup_list() - Constructor for class org.biomage.Array.Array_package.ArrayGroup_list
 
Array_package.ArrayManufacture_list - class org.biomage.Array.Array_package.ArrayManufacture_list.
Inner list class for holding multiple entries for attribute arrayManufacture_list.
Array_package.ArrayManufacture_list() - Constructor for class org.biomage.Array.Array_package.ArrayManufacture_list
 
Array_package.Array_list - class org.biomage.Array.Array_package.Array_list.
Inner list class for holding multiple entries for attribute array_list.
Array_package.Array_list() - Constructor for class org.biomage.Array.Array_package.Array_list
 
addToAdjustments(ZoneDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to add ZoneDefect to Adjustments_list
addToAdjustments(int, ZoneDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to add ZoneDefect at position to Adjustments_list
addToArrayGroup_list(ArrayGroup) - Method in class org.biomage.Array.Array_package
Method to add ArrayGroup to ArrayGroup_list
addToArrayGroup_list(int, ArrayGroup) - Method in class org.biomage.Array.Array_package
Method to add ArrayGroup at position to ArrayGroup_list
addToArrayManufactureDeviations(ArrayManufactureDeviation) - Method in class org.biomage.Array.Array
Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list
addToArrayManufactureDeviations(int, ArrayManufactureDeviation) - Method in class org.biomage.Array.Array
Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list
addToArrayManufacture_list(ArrayManufacture) - Method in class org.biomage.Array.Array_package
Method to add ArrayManufacture to ArrayManufacture_list
addToArrayManufacture_list(int, ArrayManufacture) - Method in class org.biomage.Array.Array_package
Method to add ArrayManufacture at position to ArrayManufacture_list
addToArrayManufacturers(Contact) - Method in class org.biomage.Array.ArrayManufacture
Method to add Contact to ArrayManufacturers_list
addToArrayManufacturers(int, Contact) - Method in class org.biomage.Array.ArrayManufacture
Method to add Contact at position to ArrayManufacturers_list
addToArray_list(Array) - Method in class org.biomage.Array.Array_package
Method to add Array to Array_list
addToArray_list(int, Array) - Method in class org.biomage.Array.Array_package
Method to add Array at position to Array_list
addToArrays(Array) - Method in class org.biomage.Array.ArrayGroup
Method to add Array to Arrays_list
addToArrays(int, Array) - Method in class org.biomage.Array.ArrayGroup
Method to add Array at position to Arrays_list
addToArrays(Array) - Method in class org.biomage.Array.ArrayManufacture
Method to add Array to Arrays_list
addToArrays(int, Array) - Method in class org.biomage.Array.ArrayManufacture
Method to add Array at position to Arrays_list
addToFeatureDefects(FeatureDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to add FeatureDefect to FeatureDefects_list
addToFeatureDefects(int, FeatureDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to add FeatureDefect at position to FeatureDefects_list
addToFeatureLIMSs(ManufactureLIMS) - Method in class org.biomage.Array.ArrayManufacture
Method to add ManufactureLIMS to FeatureLIMSs_list
addToFeatureLIMSs(int, ManufactureLIMS) - Method in class org.biomage.Array.ArrayManufacture
Method to add ManufactureLIMS at position to FeatureLIMSs_list
addToFiducials(Fiducial) - Method in class org.biomage.Array.ArrayGroup
Method to add Fiducial to Fiducials_list
addToFiducials(int, Fiducial) - Method in class org.biomage.Array.ArrayGroup
Method to add Fiducial at position to Fiducials_list
addToProtocolApplications(ProtocolApplication) - Method in class org.biomage.Array.ArrayManufacture
Method to add ProtocolApplication to ProtocolApplications_list
addToProtocolApplications(int, ProtocolApplication) - Method in class org.biomage.Array.ArrayManufacture
Method to add ProtocolApplication at position to ProtocolApplications_list
addToQualityControlStatistics(NameValueType) - Method in class org.biomage.Array.ArrayManufacture
Method to add NameValueType to QualityControlStatistics_list
addToQualityControlStatistics(int, NameValueType) - Method in class org.biomage.Array.ArrayManufacture
Method to add NameValueType at position to QualityControlStatistics_list
adjustments - Variable in class org.biomage.Array.ArrayManufactureDeviation
Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.
arrayDesign - Variable in class org.biomage.Array.Array
The association of a physical array with its array design.
arrayGroup - Variable in class org.biomage.Array.Array
Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.
arrayGroup_list - Variable in class org.biomage.Array.Array_package
An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.
arrayIdentifier - Variable in class org.biomage.Array.Array
An identifying string, e.g.
arrayManufactureDeviations - Variable in class org.biomage.Array.Array
Association to classes to describe deviations from the ArrayDesign.
arrayManufacture_list - Variable in class org.biomage.Array.Array_package
Describes the process by which arrays are produced.
arrayManufacturers - Variable in class org.biomage.Array.ArrayManufacture
The person or organization to contact for information concerning the ArrayManufacture.
arraySpacingX - Variable in class org.biomage.Array.ArrayGroup
If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.
arraySpacingY - Variable in class org.biomage.Array.ArrayGroup
If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.
arrayXOrigin - Variable in class org.biomage.Array.Array
This can indicate the x position on a slide, chip, etc.
arrayYOrigin - Variable in class org.biomage.Array.Array
This can indicate the y position on a slide, chip, etc.
array_list - Variable in class org.biomage.Array.Array_package
The physical substrate along with its features and their annotation
arrays - Variable in class org.biomage.Array.ArrayGroup
Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.
arrays - Variable in class org.biomage.Array.ArrayManufacture
Association between the manufactured array and the information on that manufacture.

B

BOTTOM - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
barcode - Variable in class org.biomage.Array.ArrayGroup
Identifier for the ArrayGroup.
bioMaterial - Variable in class org.biomage.Array.ManufactureLIMS
The BioMaterial used for the feature.
bioMaterialPlateCol - Variable in class org.biomage.Array.ManufactureLIMSBiomaterial
The plate column from which a biomaterial was obtained.
bioMaterialPlateIdentifier - Variable in class org.biomage.Array.ManufactureLIMSBiomaterial
The plate from which a biomaterial was obtained.
bioMaterialPlateRow - Variable in class org.biomage.Array.ManufactureLIMSBiomaterial
The plate row from which a biomaterial was obtained.

D

defectType - Variable in class org.biomage.Array.FeatureDefect
Indicates the type of defect (e.g.
defectType - Variable in class org.biomage.Array.ZoneDefect
Indicates the type of defect (e.g.
deltaX - Variable in class org.biomage.Array.PositionDelta
Deviation from the y coordinate of this feature's position.
deltaY - Variable in class org.biomage.Array.PositionDelta
Deviation from the y coordinate of this feature's position.
distanceUnit - Variable in class org.biomage.Array.ArrayGroup
The unit of the measurement attributes.
distanceUnit - Variable in class org.biomage.Array.Fiducial
The units the fiducial is measured in.
distanceUnit - Variable in class org.biomage.Array.PositionDelta
The unit for the attributes.

F

FeatureDefect - class org.biomage.Array.FeatureDefect.
Stores the defect information for a feature.
FeatureDefect() - Constructor for class org.biomage.Array.FeatureDefect
Default constructor.
FeatureDefect(Attributes) - Constructor for class org.biomage.Array.FeatureDefect
Attribute constructor.
Fiducial - class org.biomage.Array.Fiducial.
A marking on the surface of the array that can be used to identify the array's origin, the coordinates of which are the fiducial's centroid.
Fiducial() - Constructor for class org.biomage.Array.Fiducial
Default constructor.
Fiducial(Attributes) - Constructor for class org.biomage.Array.Fiducial
Attribute constructor.
feature - Variable in class org.biomage.Array.FeatureDefect
The feature that was manufactured defectively.
feature - Variable in class org.biomage.Array.ManufactureLIMS
The feature whose LIMS information is being described.
featureDefects - Variable in class org.biomage.Array.ArrayManufactureDeviation
Description on features who are manufactured in a different location than specified in the ArrayDesign.
featureLIMSs - Variable in class org.biomage.Array.ArrayManufacture
Information on the manufacture of the features.
fiducialType - Variable in class org.biomage.Array.Fiducial
A descriptive string that indicates the type of a fiducial (e.g.
fiducials - Variable in class org.biomage.Array.ArrayGroup
Association to the marks on the Array for alignment for the scanner.

G

getAdjustments() - Method in class org.biomage.Array.ArrayManufactureDeviation
Get method for adjustments
getArrayDesign() - Method in class org.biomage.Array.Array
Get method for arrayDesign
getArrayGroup() - Method in class org.biomage.Array.Array
Get method for arrayGroup
getArrayGroup_list() - Method in class org.biomage.Array.Array_package
Get method for arrayGroup_list
getArrayIdentifier() - Method in class org.biomage.Array.Array
Get method for arrayIdentifier
getArrayManufactureDeviations() - Method in class org.biomage.Array.Array
Get method for arrayManufactureDeviations
getArrayManufacture_list() - Method in class org.biomage.Array.Array_package
Get method for arrayManufacture_list
getArrayManufacturers() - Method in class org.biomage.Array.ArrayManufacture
Get method for arrayManufacturers
getArraySpacingX() - Method in class org.biomage.Array.ArrayGroup
Get method for arraySpacingX
getArraySpacingY() - Method in class org.biomage.Array.ArrayGroup
Get method for arraySpacingY
getArrayXOrigin() - Method in class org.biomage.Array.Array
Get method for arrayXOrigin
getArrayYOrigin() - Method in class org.biomage.Array.Array
Get method for arrayYOrigin
getArray_list() - Method in class org.biomage.Array.Array_package
Get method for array_list
getArrays() - Method in class org.biomage.Array.ArrayGroup
Get method for arrays
getArrays() - Method in class org.biomage.Array.ArrayManufacture
Get method for arrays
getBarcode() - Method in class org.biomage.Array.ArrayGroup
Get method for barcode
getBioMaterial() - Method in class org.biomage.Array.ManufactureLIMS
Get method for bioMaterial
getBioMaterialPlateCol() - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Get method for bioMaterialPlateCol
getBioMaterialPlateIdentifier() - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Get method for bioMaterialPlateIdentifier
getBioMaterialPlateRow() - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Get method for bioMaterialPlateRow
getDefectType() - Method in class org.biomage.Array.FeatureDefect
Get method for defectType
getDefectType() - Method in class org.biomage.Array.ZoneDefect
Get method for defectType
getDeltaX() - Method in class org.biomage.Array.PositionDelta
Get method for deltaX
getDeltaY() - Method in class org.biomage.Array.PositionDelta
Get method for deltaY
getDistanceUnit() - Method in class org.biomage.Array.ArrayGroup
Get method for distanceUnit
getDistanceUnit() - Method in class org.biomage.Array.Fiducial
Get method for distanceUnit
getDistanceUnit() - Method in class org.biomage.Array.PositionDelta
Get method for distanceUnit
getFeature() - Method in class org.biomage.Array.FeatureDefect
Get method for feature
getFeature() - Method in class org.biomage.Array.ManufactureLIMS
Get method for feature
getFeatureDefects() - Method in class org.biomage.Array.ArrayManufactureDeviation
Get method for featureDefects
getFeatureLIMSs() - Method in class org.biomage.Array.ArrayManufacture
Get method for featureLIMSs
getFiducialType() - Method in class org.biomage.Array.Fiducial
Get method for fiducialType
getFiducials() - Method in class org.biomage.Array.ArrayGroup
Get method for fiducials
getFromAdjustments(int) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to get ZoneDefect from Adjustments_list
getFromArrayGroup_list(int) - Method in class org.biomage.Array.Array_package
Method to get ArrayGroup from ArrayGroup_list
getFromArrayManufactureDeviations(int) - Method in class org.biomage.Array.Array
Method to get ArrayManufactureDeviation from ArrayManufactureDeviations_list
getFromArrayManufacture_list(int) - Method in class org.biomage.Array.Array_package
Method to get ArrayManufacture from ArrayManufacture_list
getFromArrayManufacturers(int) - Method in class org.biomage.Array.ArrayManufacture
Method to get Contact from ArrayManufacturers_list
getFromArray_list(int) - Method in class org.biomage.Array.Array_package
Method to get Array from Array_list
getFromArrays(int) - Method in class org.biomage.Array.ArrayGroup
Method to get Array from Arrays_list
getFromArrays(int) - Method in class org.biomage.Array.ArrayManufacture
Method to get Array from Arrays_list
getFromFeatureDefects(int) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to get FeatureDefect from FeatureDefects_list
getFromFeatureLIMSs(int) - Method in class org.biomage.Array.ArrayManufacture
Method to get ManufactureLIMS from FeatureLIMSs_list
getFromFiducials(int) - Method in class org.biomage.Array.ArrayGroup
Method to get Fiducial from Fiducials_list
getFromProtocolApplications(int) - Method in class org.biomage.Array.ArrayManufacture
Method to get ProtocolApplication from ProtocolApplications_list
getFromQualityControlStatistics(int) - Method in class org.biomage.Array.ArrayManufacture
Method to get NameValueType from QualityControlStatistics_list
getIdentifierLIMS() - Method in class org.biomage.Array.ManufactureLIMS
Get method for identifierLIMS
getInformation() - Method in class org.biomage.Array.Array
Get method for information
getLength() - Method in class org.biomage.Array.ArrayGroup
Get method for length
getManufacturingDate() - Method in class org.biomage.Array.ArrayManufacture
Get method for manufacturingDate
getNumArrays() - Method in class org.biomage.Array.ArrayGroup
Get method for numArrays
getOrientationMark() - Method in class org.biomage.Array.ArrayGroup
Get method for orientationMark
getOrientationMarkPosition() - Method in class org.biomage.Array.ArrayGroup
Get method for orientationMarkPosition
getOriginRelativeTo() - Method in class org.biomage.Array.Array
Get method for originRelativeTo
getPosition() - Method in class org.biomage.Array.Fiducial
Get method for position
getPositionDelta() - Method in class org.biomage.Array.FeatureDefect
Get method for positionDelta
getPositionDelta() - Method in class org.biomage.Array.ZoneDefect
Get method for positionDelta
getProtocolApplications() - Method in class org.biomage.Array.ArrayManufacture
Get method for protocolApplications
getQuality() - Method in class org.biomage.Array.ManufactureLIMS
Get method for quality
getQualityControlStatistics() - Method in class org.biomage.Array.ArrayManufacture
Get method for qualityControlStatistics
getSubstrateType() - Method in class org.biomage.Array.ArrayGroup
Get method for substrateType
getTolerance() - Method in class org.biomage.Array.ArrayManufacture
Get method for tolerance
getWidth() - Method in class org.biomage.Array.ArrayGroup
Get method for width
getZone() - Method in class org.biomage.Array.ZoneDefect
Get method for zone

I

identifierLIMS - Variable in class org.biomage.Array.ManufactureLIMS
Association to a LIMS data source for further information on the manufacturing process.
information - Variable in class org.biomage.Array.Array
Association between the manufactured array and the information on that manufacture.

L

LEFT - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
length - Variable in class org.biomage.Array.ArrayGroup
The length of the platform.

M

ManufactureLIMS - class org.biomage.Array.ManufactureLIMS.
Information on the physical production of arrays within the laboratory.
ManufactureLIMS() - Constructor for class org.biomage.Array.ManufactureLIMS
Default constructor.
ManufactureLIMS(Attributes) - Constructor for class org.biomage.Array.ManufactureLIMS
Attribute constructor.
ManufactureLIMSBiomaterial - class org.biomage.Array.ManufactureLIMSBiomaterial.
Stores the location from which a biomaterial was obtained.
ManufactureLIMSBiomaterial() - Constructor for class org.biomage.Array.ManufactureLIMSBiomaterial
Default constructor.
ManufactureLIMSBiomaterial(Attributes) - Constructor for class org.biomage.Array.ManufactureLIMSBiomaterial
Attribute constructor.
manufacturingDate - Variable in class org.biomage.Array.ArrayManufacture
The date the arrays were manufactured

N

nameToValue - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
numArrays - Variable in class org.biomage.Array.ArrayGroup
This attribute defines the number of arrays on a chip or a slide.

O

org.biomage.Array - package org.biomage.Array
 
orientationMark - Variable in class org.biomage.Array.ArrayGroup
For a human to determine where the top left side of the array is, such as a barcode or frosted side of the glass, etc.
orientationMarkPosition - Variable in class org.biomage.Array.ArrayGroup
One of top, bottom, left or right.
originRelativeTo - Variable in class org.biomage.Array.Array
What the array origin is relative to, e.g.

P

PositionDelta - class org.biomage.Array.PositionDelta.
The delta the feature was actually printed on the array from the position specified for the feature in the array design.
PositionDelta() - Constructor for class org.biomage.Array.PositionDelta
Default constructor.
PositionDelta(Attributes) - Constructor for class org.biomage.Array.PositionDelta
Attribute constructor.
position - Variable in class org.biomage.Array.Fiducial
The position, relative to the upper left corner, of the fiducial
positionDelta - Variable in class org.biomage.Array.FeatureDefect
How the feature deviates in position from the ArrayDesign.
positionDelta - Variable in class org.biomage.Array.ZoneDefect
How the zone deviates in position from the ArrayDesign.
protocolApplications - Variable in class org.biomage.Array.ArrayManufacture
The protocols followed in the manufacturing of the arrays.

Q

quality - Variable in class org.biomage.Array.ManufactureLIMS
A brief description of the quality of the array manufacture process.
qualityControlStatistics - Variable in class org.biomage.Array.ArrayManufacture
Information on the quality of the ArrayManufacture.

R

RIGHT - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
removeElementAtFromAdjustments(int) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to remove by position from Adjustments_list
removeElementAtFromArrayGroup_list(int) - Method in class org.biomage.Array.Array_package
Method to remove by position from ArrayGroup_list
removeElementAtFromArrayManufactureDeviations(int) - Method in class org.biomage.Array.Array
Method to remove by position from ArrayManufactureDeviations_list
removeElementAtFromArrayManufacture_list(int) - Method in class org.biomage.Array.Array_package
Method to remove by position from ArrayManufacture_list
removeElementAtFromArrayManufacturers(int) - Method in class org.biomage.Array.ArrayManufacture
Method to remove by position from ArrayManufacturers_list
removeElementAtFromArray_list(int) - Method in class org.biomage.Array.Array_package
Method to remove by position from Array_list
removeElementAtFromArrays(int) - Method in class org.biomage.Array.ArrayGroup
Method to remove by position from Arrays_list
removeElementAtFromArrays(int) - Method in class org.biomage.Array.ArrayManufacture
Method to remove by position from Arrays_list
removeElementAtFromFeatureDefects(int) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to remove by position from FeatureDefects_list
removeElementAtFromFeatureLIMSs(int) - Method in class org.biomage.Array.ArrayManufacture
Method to remove by position from FeatureLIMSs_list
removeElementAtFromFiducials(int) - Method in class org.biomage.Array.ArrayGroup
Method to remove by position from Fiducials_list
removeElementAtFromProtocolApplications(int) - Method in class org.biomage.Array.ArrayManufacture
Method to remove by position from ProtocolApplications_list
removeElementAtFromQualityControlStatistics(int) - Method in class org.biomage.Array.ArrayManufacture
Method to remove by position from QualityControlStatistics_list
removeFromAdjustments(ZoneDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to remove first ZoneDefect from Adjustments_list
removeFromArrayGroup_list(ArrayGroup) - Method in class org.biomage.Array.Array_package
Method to remove first ArrayGroup from ArrayGroup_list
removeFromArrayManufactureDeviations(ArrayManufactureDeviation) - Method in class org.biomage.Array.Array
Method to remove first ArrayManufactureDeviation from ArrayManufactureDeviations_list
removeFromArrayManufacture_list(ArrayManufacture) - Method in class org.biomage.Array.Array_package
Method to remove first ArrayManufacture from ArrayManufacture_list
removeFromArrayManufacturers(Contact) - Method in class org.biomage.Array.ArrayManufacture
Method to remove first Contact from ArrayManufacturers_list
removeFromArray_list(Array) - Method in class org.biomage.Array.Array_package
Method to remove first Array from Array_list
removeFromArrays(Array) - Method in class org.biomage.Array.ArrayGroup
Method to remove first Array from Arrays_list
removeFromArrays(Array) - Method in class org.biomage.Array.ArrayManufacture
Method to remove first Array from Arrays_list
removeFromFeatureDefects(FeatureDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to remove first FeatureDefect from FeatureDefects_list
removeFromFeatureLIMSs(ManufactureLIMS) - Method in class org.biomage.Array.ArrayManufacture
Method to remove first ManufactureLIMS from FeatureLIMSs_list
removeFromFiducials(Fiducial) - Method in class org.biomage.Array.ArrayGroup
Method to remove first Fiducial from Fiducials_list
removeFromProtocolApplications(ProtocolApplication) - Method in class org.biomage.Array.ArrayManufacture
Method to remove first ProtocolApplication from ProtocolApplications_list
removeFromQualityControlStatistics(NameValueType) - Method in class org.biomage.Array.ArrayManufacture
Method to remove first NameValueType from QualityControlStatistics_list

S

setAdjustments(HasAdjustments.Adjustments_list) - Method in class org.biomage.Array.ArrayManufactureDeviation
Set method for adjustments
setArrayDesign(ArrayDesign) - Method in class org.biomage.Array.Array
Set method for arrayDesign
setArrayGroup(ArrayGroup) - Method in class org.biomage.Array.Array
Set method for arrayGroup
setArrayGroup_list(Array_package.ArrayGroup_list) - Method in class org.biomage.Array.Array_package
Set method for arrayGroup_list
setArrayIdentifier(String) - Method in class org.biomage.Array.Array
Set method for arrayIdentifier
setArrayManufactureDeviations(HasArrayManufactureDeviations.ArrayManufactureDeviations_list) - Method in class org.biomage.Array.Array
Set method for arrayManufactureDeviations
setArrayManufacture_list(Array_package.ArrayManufacture_list) - Method in class org.biomage.Array.Array_package
Set method for arrayManufacture_list
setArrayManufacturers(HasArrayManufacturers.ArrayManufacturers_list) - Method in class org.biomage.Array.ArrayManufacture
Set method for arrayManufacturers
setArraySpacingX(float) - Method in class org.biomage.Array.ArrayGroup
Set method for arraySpacingX
setArraySpacingY(float) - Method in class org.biomage.Array.ArrayGroup
Set method for arraySpacingY
setArrayXOrigin(float) - Method in class org.biomage.Array.Array
Set method for arrayXOrigin
setArrayYOrigin(float) - Method in class org.biomage.Array.Array
Set method for arrayYOrigin
setArray_list(Array_package.Array_list) - Method in class org.biomage.Array.Array_package
Set method for array_list
setArrays(HasArrays.Arrays_list) - Method in class org.biomage.Array.ArrayGroup
Set method for arrays
setArrays(HasArrays.Arrays_list) - Method in class org.biomage.Array.ArrayManufacture
Set method for arrays
setBarcode(String) - Method in class org.biomage.Array.ArrayGroup
Set method for barcode
setBioMaterial(BioMaterial) - Method in class org.biomage.Array.ManufactureLIMS
Set method for bioMaterial
setBioMaterialPlateCol(String) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Set method for bioMaterialPlateCol
setBioMaterialPlateIdentifier(String) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Set method for bioMaterialPlateIdentifier
setBioMaterialPlateRow(String) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Set method for bioMaterialPlateRow
setDefectType(OntologyEntry) - Method in class org.biomage.Array.FeatureDefect
Set method for defectType
setDefectType(OntologyEntry) - Method in class org.biomage.Array.ZoneDefect
Set method for defectType
setDeltaX(float) - Method in class org.biomage.Array.PositionDelta
Set method for deltaX
setDeltaY(float) - Method in class org.biomage.Array.PositionDelta
Set method for deltaY
setDistanceUnit(DistanceUnit) - Method in class org.biomage.Array.ArrayGroup
Set method for distanceUnit
setDistanceUnit(DistanceUnit) - Method in class org.biomage.Array.Fiducial
Set method for distanceUnit
setDistanceUnit(DistanceUnit) - Method in class org.biomage.Array.PositionDelta
Set method for distanceUnit
setFeature(Feature) - Method in class org.biomage.Array.FeatureDefect
Set method for feature
setFeature(Feature) - Method in class org.biomage.Array.ManufactureLIMS
Set method for feature
setFeatureDefects(HasFeatureDefects.FeatureDefects_list) - Method in class org.biomage.Array.ArrayManufactureDeviation
Set method for featureDefects
setFeatureLIMSs(HasFeatureLIMSs.FeatureLIMSs_list) - Method in class org.biomage.Array.ArrayManufacture
Set method for featureLIMSs
setFiducialType(OntologyEntry) - Method in class org.biomage.Array.Fiducial
Set method for fiducialType
setFiducials(HasFiducials.Fiducials_list) - Method in class org.biomage.Array.ArrayGroup
Set method for fiducials
setIdentifierLIMS(DatabaseEntry) - Method in class org.biomage.Array.ManufactureLIMS
Set method for identifierLIMS
setInformation(ArrayManufacture) - Method in class org.biomage.Array.Array
Set method for information
setLength(float) - Method in class org.biomage.Array.ArrayGroup
Set method for length
setManufacturingDate(String) - Method in class org.biomage.Array.ArrayManufacture
Set method for manufacturingDate
setNumArrays(int) - Method in class org.biomage.Array.ArrayGroup
Set method for numArrays
setOrientationMark(String) - Method in class org.biomage.Array.ArrayGroup
Set method for orientationMark
setOrientationMarkPosition(ArrayGroup.OrientationMarkPosition) - Method in class org.biomage.Array.ArrayGroup
Set method for orientationMarkPosition
setOriginRelativeTo(String) - Method in class org.biomage.Array.Array
Set method for originRelativeTo
setPosition(Position) - Method in class org.biomage.Array.Fiducial
Set method for position
setPositionDelta(PositionDelta) - Method in class org.biomage.Array.FeatureDefect
Set method for positionDelta
setPositionDelta(PositionDelta) - Method in class org.biomage.Array.ZoneDefect
Set method for positionDelta
setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in class org.biomage.Array.ArrayManufacture
Set method for protocolApplications
setQuality(String) - Method in class org.biomage.Array.ManufactureLIMS
Set method for quality
setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list) - Method in class org.biomage.Array.ArrayManufacture
Set method for qualityControlStatistics
setSubstrateType(OntologyEntry) - Method in class org.biomage.Array.ArrayGroup
Set method for substrateType
setTolerance(float) - Method in class org.biomage.Array.ArrayManufacture
Set method for tolerance
setValueByName(String) - Method in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
setWidth(float) - Method in class org.biomage.Array.ArrayGroup
Set method for width
setZone(Zone) - Method in class org.biomage.Array.ZoneDefect
Set method for zone
substrateType - Variable in class org.biomage.Array.ArrayGroup
Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case.

T

TOP - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
tolerance - Variable in class org.biomage.Array.ArrayManufacture
The allowable error of a feature printed to its intended position.

V

value - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 

W

width - Variable in class org.biomage.Array.ArrayGroup
The width of the platform
writeAssociations(Writer) - Method in class org.biomage.Array.Array
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Array.ArrayGroup
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Array.ArrayManufacture
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Array.ArrayManufactureDeviation
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Array.Array_package
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Array.FeatureDefect
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Array.Fiducial
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Array.ManufactureLIMS
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Array.PositionDelta
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Array.ZoneDefect
writeAssociations
writeAttributes(Writer) - Method in class org.biomage.Array.Array
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Array.ArrayGroup
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Array.ArrayManufacture
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Array.ArrayManufactureDeviation
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Array.Array_package
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Array.FeatureDefect
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Array.Fiducial
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Array.ManufactureLIMS
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Array.PositionDelta
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Array.ZoneDefect
writeAttributes
writeMAGEML(Writer) - Method in class org.biomage.Array.Array
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Array.ArrayGroup
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Array.ArrayManufacture
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Array.ArrayManufactureDeviation
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Array.Array_package
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Array.FeatureDefect
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Array.Fiducial
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Array.ManufactureLIMS
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Array.PositionDelta
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Array.ZoneDefect
writeMAGEML

Z

ZoneDefect - class org.biomage.Array.ZoneDefect.
Stores the defect information for a zone.
ZoneDefect() - Constructor for class org.biomage.Array.ZoneDefect
Default constructor.
ZoneDefect(Attributes) - Constructor for class org.biomage.Array.ZoneDefect
Attribute constructor.
zone - Variable in class org.biomage.Array.ZoneDefect
Reference to the Zone that was misprinted.

A B D F G I L M N O P Q R S T V W Z