|
|||||||||
| Home >> All >> org >> biomage >> [ Array overview ] | PREV NEXT | ||||||||
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
|
|||||||||
| Home >> All >> org >> biomage >> [ Array overview ] | PREV NEXT | ||||||||