A B C D E F G H I J K L M N O P Q R S T U V W Y Z

F

FactorValue - class org.biomage.Experiment.FactorValue.

The value for a ExperimentalFactor

FactorValue() - Constructor for class org.biomage.Experiment.FactorValue

Default constructor.

FactorValue(Attributes) - Constructor for class org.biomage.Experiment.FactorValue

Attribute constructor.

factorValues - Variable in class org.biomage.Experiment.ExperimentalFactor

The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.

failTypes - Variable in class org.biomage.DesignElement.Reporter

If at some time the reporter is determined to be failed this indicts the failure (doesn't report on what it was intended to report on, etc.)

FALSE - Static variable in class org.biomage.tools.generate_er.CreateMageER

the foreign key does not cause a cascade action

feature - Variable in class org.biomage.Array.ManufactureLIMS

The feature whose LIMS information is being described.

feature - Variable in class org.biomage.Array.FeatureDefect

The feature that was manufactured defectively.

feature - Variable in class org.biomage.DesignElement.FeatureInformation

The feature the FeatureInformation is supplying information for.

Feature - class org.biomage.DesignElement.Feature.

An intended position on an array.

Feature() - Constructor for class org.biomage.DesignElement.Feature

Default constructor.

Feature(Attributes) - Constructor for class org.biomage.DesignElement.Feature

Attribute constructor.

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.

featureDefects - Variable in class org.biomage.Array.ArrayManufactureDeviation

Description on features who are manufactured in a different location than specified in the ArrayDesign.

FeatureDimension - class org.biomage.BioAssayData.FeatureDimension.

Specialized DesignElementDimension to hold Features.

FeatureDimension() - Constructor for class org.biomage.BioAssayData.FeatureDimension

Default constructor.

FeatureDimension(Attributes) - Constructor for class org.biomage.BioAssayData.FeatureDimension

Attribute constructor.

featureExtraction - Variable in class org.biomage.BioAssay.MeasuredBioAssay

The association between the MeasuredBioAssay and the FeatureExtraction Event.

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.

featureGroup - Variable in class org.biomage.DesignElement.Feature

The features that belong to this group.

FeatureGroup - class org.biomage.ArrayDesign.FeatureGroup.

A collection of like features.

FeatureGroup() - Constructor for class org.biomage.ArrayDesign.FeatureGroup

Default constructor.

FeatureGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.FeatureGroup

Attribute constructor.

featureGroups - Variable in class org.biomage.ArrayDesign.ArrayDesign

The grouping of like Features together.

FeatureInformation - class org.biomage.DesignElement.FeatureInformation.

As part of the map information, allows the association of one or more differences in the BioMaterial on a feature from the BioMaterial of the Reporter.

FeatureInformation() - Constructor for class org.biomage.DesignElement.FeatureInformation

Default constructor.

FeatureInformation(Attributes) - Constructor for class org.biomage.DesignElement.FeatureInformation

Attribute constructor.

featureInformationSources - Variable in class org.biomage.DesignElement.FeatureReporterMap

Typically, the features on an array that are manufactured with this reporter's BioSequence.

featureLIMSs - Variable in class org.biomage.Array.ArrayManufacture

Information on the manufacture of the features.

featureLocation - Variable in class org.biomage.DesignElement.Feature

Location of this feature relative to a grid.

FeatureLocation - class org.biomage.DesignElement.FeatureLocation.

Specifies where a feature is located relative to a grid.

FeatureLocation() - Constructor for class org.biomage.DesignElement.FeatureLocation

Default constructor.

FeatureLocation(Attributes) - Constructor for class org.biomage.DesignElement.FeatureLocation

Attribute constructor.

FeatureReporterMap - class org.biomage.DesignElement.FeatureReporterMap.

A FeatureReporterMap is the description of how source features are transformed into a target reporter.

featureReporterMap_list - Variable in class org.biomage.DesignElement.DesignElement_package

A FeatureReporterMap is the description of how source features are transformed into a target reporter.

FeatureReporterMap() - Constructor for class org.biomage.DesignElement.FeatureReporterMap

Default constructor.

FeatureReporterMap(Attributes) - Constructor for class org.biomage.DesignElement.FeatureReporterMap

Attribute constructor.

featureReporterMaps - Variable in class org.biomage.DesignElement.Reporter

Associates features with their reporter.

features - Variable in class org.biomage.ArrayDesign.FeatureGroup

The features that belong to this group.

featureShape - Variable in class org.biomage.ArrayDesign.FeatureGroup

The expected shape of the feature on the array: circular, oval, square, etc.

FG - Variable in class org.biomage.Measurement.MassUnit.UnitNameCV

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.

fiducials - Variable in class org.biomage.Array.ArrayGroup

Association to the marks on the Array for alignment for the scanner.

fiducialType - Variable in class org.biomage.Array.Fiducial

A descriptive string that indicates the type of a fiducial (e.g.

FIRSTLINE - Static variable in class org.biomage.tools.generate_er.CreateMageER

first line in the MAGE_ER.xml file

FL - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV

FM - Variable in class org.biomage.Measurement.DistanceUnit.UnitNameCV

FM - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV

FMOL - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV

ForeignKey - class org.biomage.tools.generate_er.ForeignKey.

FOREIGNKEY - Static variable in class org.biomage.tools.generate_er.CreateMageER

indicate the column is a one_to_one foreign key.

ForeignKey() - Constructor for class org.biomage.tools.generate_er.ForeignKey

Description: Constructor for the ForeignKey object.

ForeignKey(ForeignKey) - Constructor for class org.biomage.tools.generate_er.ForeignKey

Description: Constructor for the ForeignKey object.

ForeignKey(String, String, String, String, String) - Constructor for class org.biomage.tools.generate_er.ForeignKey

Description: Constructor for the ForeignKey object.

format - Variable in class org.biomage.BioAssay.Image

The file format of the image typically a TIF or a JPEG.