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

M

M - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV

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

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

MAGEContentHandler - class org.biomage.tools.xmlutils.MAGEContentHandler.

Description: Content handler for MAGE.

MAGEContentHandler.UnresolvedRef - class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef.

Basic structure to hold unresolved references.

MAGEContentHandler.UnresolvedRef(MAGEContentHandler.Association, Object, String, String) - Constructor for class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef

MAGEContentHandler() - Constructor for class org.biomage.tools.xmlutils.MAGEContentHandler

MAGEException - exception org.biomage.Common.MAGEException.

MAGEException() - Constructor for class org.biomage.Common.MAGEException

Description: Default constructor for the MAGEException object.

MAGEException(String) - Constructor for class org.biomage.Common.MAGEException

Description: Constructor for the MAGEException object.

MAGEException(Throwable, String) - Constructor for class org.biomage.Common.MAGEException

Description: Specialized constructor for the MAGEException object.

mageJava - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler

MAGEJava - class org.biomage.Common.MAGEJava.

Top-level object that represents the model.

MAGEJava() - Constructor for class org.biomage.Common.MAGEJava

Default constructor.

MAGEJava(Attributes) - Constructor for class org.biomage.Common.MAGEJava

Attribute constructor.

main(String[]) - Static method in class org.biomage.tools.xmlutils.Importer

Description: Program entry point.

main(String[]) - Static method in class org.biomage.tools.xmlutils.ImportExportTest

Description: Program entry point.

makeAssociation(MAGEContentHandler.Association, Object, Object) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

Method to make an association between object via reflection.

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.

ManyToMany(CreateFile, String) - Method in class org.biomage.tools.generate_er.CreateMageER

Description: create an association column for many to many relationship

ManyToOne(Table, AssociationColumn, CreateFile, CreateFile.AssociationAttrInformation, FileWriter) - Method in class org.biomage.tools.generate_er.CreateMageER

Description: create an association column for one to one relationship

Map - class org.biomage.BioEvent.Map.

A Map is the description of how sources are transformed into a target.

Map() - Constructor for class org.biomage.BioEvent.Map

Default constructor.

Map(Attributes) - Constructor for class org.biomage.BioEvent.Map

Attribute constructor.

MASS - Variable in class org.biomage.Measurement.Measurement.KindCV

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

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

MassUnit - class org.biomage.Measurement.MassUnit.

Mass

MassUnit.UnitNameCV - class org.biomage.Measurement.MassUnit.UnitNameCV.

Inner class for the enumeration values that the attribute unitNameCV can assume.

MassUnit() - Constructor for class org.biomage.Measurement.MassUnit

Default constructor.

MassUnit(Attributes) - Constructor for class org.biomage.Measurement.MassUnit

Attribute constructor.

materialType - Variable in class org.biomage.BioMaterial.BioMaterial

The type of material used, i.e.

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.

MeasuredBioAssayData - class org.biomage.BioAssayData.MeasuredBioAssayData.

The data associated with the MeasuredBioAssay produced by FeatureExtraction.

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

Default constructor.

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

Attribute constructor.

measuredBioAssayTarget - Variable in class org.biomage.BioAssay.FeatureExtraction

The association between the MeasuredBioAssay and the FeatureExtraction Event.

MeasuredSignal - class org.biomage.QuantitationType.MeasuredSignal.

Best measure from feature extraction as to the presence and intensity of the signal.

MeasuredSignal() - Constructor for class org.biomage.QuantitationType.MeasuredSignal

Default constructor.

MeasuredSignal(Attributes) - Constructor for class org.biomage.QuantitationType.MeasuredSignal

Attribute constructor.

measurement - Variable in class org.biomage.BioMaterial.CompoundMeasurement

The amount of the Compound.

measurement - Variable in class org.biomage.BioMaterial.BioMaterialMeasurement

The amount of the BioMaterial.

measurement - Variable in class org.biomage.Experiment.FactorValue

The measured value for this factor.

Measurement - class org.biomage.Measurement.Measurement.

A Measurement is a quantity with a unit.

measurement_package - Variable in class org.biomage.Common.MAGEJava

The classes of this package provide utility information on the quantities of other classes to each other.

Measurement_package - class org.biomage.Measurement.Measurement_package.

The classes of this package provide utility information on the quantities of other classes to each other.

Measurement_package() - Constructor for class org.biomage.Measurement.Measurement_package

Default constructor.

Measurement_package(Attributes) - Constructor for class org.biomage.Measurement.Measurement_package

Attribute constructor.

Measurement.KindCV - class org.biomage.Measurement.Measurement.KindCV.

Inner class for the enumeration values that the attribute kindCV can assume.

Measurement.Type - class org.biomage.Measurement.Measurement.Type.

Inner class for the enumeration values that the attribute type can assume.

Measurement() - Constructor for class org.biomage.Measurement.Measurement

Default constructor.

Measurement(Attributes) - Constructor for class org.biomage.Measurement.Measurement

Attribute constructor.

members - Variable in class org.biomage.AuditAndSecurity.SecurityGroup

The members of the Security Group.

merckIndex - Variable in class org.biomage.BioMaterial.Compound

The Merck Index of this Compound.

methodsMap - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler

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

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

mismatchInformation - Variable in class org.biomage.DesignElement.ReporterPosition

Differences in how the reporter matches its compositeSequence's sequence.

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

Differences in how the feature matches the reporter's sequence, typical examples is the Affymetrix probe pair where one of the features is printed with a mismatch to the other feature's perfect match.

mismatchInformation - Variable in class org.biomage.DesignElement.CompositePosition

Differences in how the contained compositeSequence matches its target compositeSequence's sequence.

MismatchInformation - class org.biomage.DesignElement.MismatchInformation.

Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.

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

Default constructor.

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

Attribute constructor.

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

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

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

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

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

MODIFICATION - Variable in class org.biomage.AuditAndSecurity.Audit.Action

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

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

MONTHS - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV

MultiHashMap - class org.biomage.tools.xmlutils.MultiHashMap.

Utility class for associating multiple values with a key in a Synchronized Map.

MultiHashMap() - Constructor for class org.biomage.tools.xmlutils.MultiHashMap

{@inheritDoc}

MultiHashMap(int) - Constructor for class org.biomage.tools.xmlutils.MultiHashMap

{@inheritDoc}

MultiHashMap(int, float) - Constructor for class org.biomage.tools.xmlutils.MultiHashMap

{@inheritDoc}

MultiHashMap(Map) - Constructor for class org.biomage.tools.xmlutils.MultiHashMap

{@inheritDoc}

MultiHashMap(MultiHashMap) - Constructor for class org.biomage.tools.xmlutils.MultiHashMap

Constructs a new MultiHashMap with the same mappings as the given MultiHashMap.

MultiHashMap(MultiMap) - Constructor for class org.biomage.tools.xmlutils.MultiHashMap

Constructs a new MultiHashMap with the same mappings as the given MultiMap.

MultiHashtable - class org.biomage.tools.xmlutils.MultiHashtable.

Utility class for associating multiple values with a key in a Synchronized Map.

MultiHashtable() - Constructor for class org.biomage.tools.xmlutils.MultiHashtable

{@inheritDoc}

MultiHashtable(int) - Constructor for class org.biomage.tools.xmlutils.MultiHashtable

{@inheritDoc}

MultiHashtable(int, float) - Constructor for class org.biomage.tools.xmlutils.MultiHashtable

{@inheritDoc}

MultiHashtable(Map) - Constructor for class org.biomage.tools.xmlutils.MultiHashtable

{@inheritDoc}

MultiHashtable(MultiHashtable) - Constructor for class org.biomage.tools.xmlutils.MultiHashtable

Constructs a new MultiHashtable with the same mappings as the given MultiHashtable.

MultiHashtable(MultiMap) - Constructor for class org.biomage.tools.xmlutils.MultiHashtable

Constructs a new MultiHashtable with the same mappings as the given MultiMap.

MultiMap - interface org.biomage.tools.xmlutils.MultiMap.

Utility interface for associating multiple values with a key.