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A B D E G H I M N O P Q R S T V W

A

addToAuditTrail(Audit) - Method in class org.biomage.Common.Describable
Method to add Audit to AuditTrail_list
addToAuditTrail(int, Audit) - Method in class org.biomage.Common.Describable
Method to add Audit at position to AuditTrail_list
addToDescriptions(Description) - Method in class org.biomage.Common.Describable
Method to add Description to Descriptions_list
addToDescriptions(int, Description) - Method in class org.biomage.Common.Describable
Method to add Description at position to Descriptions_list
addToPropertySets(NameValueType) - Method in class org.biomage.Common.Extendable
Method to add NameValueType to PropertySets_list
addToPropertySets(int, NameValueType) - Method in class org.biomage.Common.Extendable
Method to add NameValueType at position to PropertySets_list
addToPropertySets(NameValueType) - Method in class org.biomage.Common.NameValueType
Method to add NameValueType to PropertySets_list
addToPropertySets(int, NameValueType) - Method in class org.biomage.Common.NameValueType
Method to add NameValueType at position to PropertySets_list
arrayDesign_package - Variable in class org.biomage.Common.MAGEJava
Describes a microarray design that can be printed and then, in the case of gene expression, hybridized.
array_package - Variable in class org.biomage.Common.MAGEJava
Describes the process of creating arrays from array designs.
auditAndSecurity_package - Variable in class org.biomage.Common.MAGEJava
Specifies classes that allow tracking of changes and information on user permissions to view the data and annotation.
auditTrail - Variable in class org.biomage.Common.Describable
A list of Audit instances that track changes to the instance of Describable.

B

bQS_package - Variable in class org.biomage.Common.MAGEJava
Allows a reference to an article, book or other publication to be specified for searching repositories.
bioAssayData_package - Variable in class org.biomage.Common.MAGEJava
The classes defined here provide data and the information and annotation on the derivation of that data.
bioAssay_package - Variable in class org.biomage.Common.MAGEJava
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.
bioEvent_package - Variable in class org.biomage.Common.MAGEJava
An abstract class representing an event that takes sources of some type to produce a target of some type.
bioMaterial_package - Variable in class org.biomage.Common.MAGEJava
The classes in this package describe how a BioSource is treated to obtain the BioMaterial (typically a LabeledExtract) that is used by a BioAssayCreation in combination with an Array to produce a PhysicalBioAssay.
bioSequence_package - Variable in class org.biomage.Common.MAGEJava
Describes a known gene or sequence.

D

Describable - class org.biomage.Common.Describable.
Abstract class that allows subclasses to inherit the association to Description, for detailed annotations such as Ontology entries and Database references, the association to Audit, for tracking changes, and the association to Security for indicating permissions.
Describable() - Constructor for class org.biomage.Common.Describable
Default constructor.
Describable(Attributes) - Constructor for class org.biomage.Common.Describable
Attribute constructor.
description_package - Variable in class org.biomage.Common.MAGEJava
The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter.
descriptions - Variable in class org.biomage.Common.Describable
Free hand text descriptions.
designElement_package - Variable in class org.biomage.Common.MAGEJava
The classes of this package are the contained classes of the ArrayDesign and describe through the DesignElements what is intended to be at each location of the Array.

E

Extendable - class org.biomage.Common.Extendable.
Abstract class that specifies for subclasses an association to NameValueTypes.
Extendable() - Constructor for class org.biomage.Common.Extendable
Default constructor.
Extendable(Attributes) - Constructor for class org.biomage.Common.Extendable
Attribute constructor.
experiment_package - Variable in class org.biomage.Common.MAGEJava
Represents the container for a hierarchical grouping of BioAssays.

G

getArrayDesign_package() - Method in class org.biomage.Common.MAGEJava
Get method for arrayDesign_package
getArray_package() - Method in class org.biomage.Common.MAGEJava
Get method for array_package
getAuditAndSecurity_package() - Method in class org.biomage.Common.MAGEJava
Get method for auditAndSecurity_package
getAuditTrail() - Method in class org.biomage.Common.Describable
Get method for auditTrail
getBQS_package() - Method in class org.biomage.Common.MAGEJava
Get method for bQS_package
getBioAssayData_package() - Method in class org.biomage.Common.MAGEJava
Get method for bioAssayData_package
getBioAssay_package() - Method in class org.biomage.Common.MAGEJava
Get method for bioAssay_package
getBioEvent_package() - Method in class org.biomage.Common.MAGEJava
Get method for bioEvent_package
getBioMaterial_package() - Method in class org.biomage.Common.MAGEJava
Get method for bioMaterial_package
getBioSequence_package() - Method in class org.biomage.Common.MAGEJava
Get method for bioSequence_package
getClassWithModelName(String) - Method in class org.biomage.Common.MAGEJava
getClassWithModelName(String modelName)
getDescription_package() - Method in class org.biomage.Common.MAGEJava
Get method for description_package
getDescriptions() - Method in class org.biomage.Common.Describable
Get method for descriptions
getDesignElement_package() - Method in class org.biomage.Common.MAGEJava
Get method for designElement_package
getExperiment_package() - Method in class org.biomage.Common.MAGEJava
Get method for experiment_package
getFromAuditTrail(int) - Method in class org.biomage.Common.Describable
Method to get Audit from AuditTrail_list
getFromDescriptions(int) - Method in class org.biomage.Common.Describable
Method to get Description from Descriptions_list
getFromPropertySets(int) - Method in class org.biomage.Common.Extendable
Method to get NameValueType from PropertySets_list
getFromPropertySets(int) - Method in class org.biomage.Common.NameValueType
Method to get NameValueType from PropertySets_list
getHigherLevelAnalysis_package() - Method in class org.biomage.Common.MAGEJava
Get method for higherLevelAnalysis_package
getIdentifier() - Method in class org.biomage.Common.Identifiable
Get method for identifier
getMeasurement_package() - Method in class org.biomage.Common.MAGEJava
Get method for measurement_package
getName() - Method in class org.biomage.Common.Identifiable
Get method for name
getName() - Method in class org.biomage.Common.NameValueType
Get method for name
getPropertySets() - Method in class org.biomage.Common.Extendable
Get method for propertySets
getPropertySets() - Method in class org.biomage.Common.NameValueType
Get method for propertySets
getProtocol_package() - Method in class org.biomage.Common.MAGEJava
Get method for protocol_package
getQuantitationType_package() - Method in class org.biomage.Common.MAGEJava
Get method for quantitationType_package
getSecurity() - Method in class org.biomage.Common.Describable
Get method for security
getType() - Method in class org.biomage.Common.NameValueType
Get method for type
getValue() - Method in class org.biomage.Common.NameValueType
Get method for value

H

higherLevelAnalysis_package - Variable in class org.biomage.Common.MAGEJava
Describes the results of performing analysis on the result of the BioAssayData from an Experiment.

I

Identifiable - class org.biomage.Common.Identifiable.
An Identifiable class is one that has an unambiguous reference within the scope.
Identifiable() - Constructor for class org.biomage.Common.Identifiable
Default constructor.
Identifiable(Attributes) - Constructor for class org.biomage.Common.Identifiable
Attribute constructor.
identifier - Variable in class org.biomage.Common.Identifiable
An identifier is an unambiguous string that is unique within the scope (i.e.

M

MAGEException - exception org.biomage.Common.MAGEException.
 
MAGEException(String) - Constructor for class org.biomage.Common.MAGEException
Description: Constructor for the MAGEException object.
MAGEException() - Constructor for class org.biomage.Common.MAGEException
Description: Default constructor for the MAGEException object.
MAGEException(Throwable, String) - Constructor for class org.biomage.Common.MAGEException
Description: Specialized constructor for the MAGEException object.
MAGEJava - class org.biomage.Common.MAGEJava.
 
MAGEJava() - Constructor for class org.biomage.Common.MAGEJava
Default constructor.
MAGEJava(Attributes) - Constructor for class org.biomage.Common.MAGEJava
Attribute constructor.
MAGEJava.ModelNameToClassMap - class org.biomage.Common.MAGEJava.ModelNameToClassMap.
Inner class to store Model to Class mappings
MAGEJava.ModelNameToClassMap() - Constructor for class org.biomage.Common.MAGEJava.ModelNameToClassMap
 
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.
modelToClass - Variable in class org.biomage.Common.MAGEJava
Instantiate the ModelNameToClassMap

N

NameValueType - class org.biomage.Common.NameValueType.
A tuple designed to store data, keyed by a name and type.
NameValueType() - Constructor for class org.biomage.Common.NameValueType
Default constructor.
NameValueType(Attributes) - Constructor for class org.biomage.Common.NameValueType
Attribute constructor.
name - Variable in class org.biomage.Common.Identifiable
The potentially ambiguous common identifier.
name - Variable in class org.biomage.Common.NameValueType
The name of the key.

O

org.biomage.Common - package org.biomage.Common
 

P

propertySets - Variable in class org.biomage.Common.Extendable
Allows specification of name/value pairs.
propertySets - Variable in class org.biomage.Common.NameValueType
Allows nested specification of name/value pairs
protocol_package - Variable in class org.biomage.Common.MAGEJava
Provides a relatively immutable class, Protocol, that can describe a generic laboratory procedure or analysis algorithm, for example, and an instance class, ProtocolApplication, which can describe the actual application of a protocol.

Q

quantitationType_package - Variable in class org.biomage.Common.MAGEJava
This Package defines the classes for quantitations, such as measured and derived signal, error, and pvalue.

R

removeElementAtFromAuditTrail(int) - Method in class org.biomage.Common.Describable
Method to remove by position from AuditTrail_list
removeElementAtFromDescriptions(int) - Method in class org.biomage.Common.Describable
Method to remove by position from Descriptions_list
removeElementAtFromPropertySets(int) - Method in class org.biomage.Common.Extendable
Method to remove by position from PropertySets_list
removeElementAtFromPropertySets(int) - Method in class org.biomage.Common.NameValueType
Method to remove by position from PropertySets_list
removeFromAuditTrail(Audit) - Method in class org.biomage.Common.Describable
Method to remove first Audit from AuditTrail_list
removeFromDescriptions(Description) - Method in class org.biomage.Common.Describable
Method to remove first Description from Descriptions_list
removeFromPropertySets(NameValueType) - Method in class org.biomage.Common.Extendable
Method to remove first NameValueType from PropertySets_list
removeFromPropertySets(NameValueType) - Method in class org.biomage.Common.NameValueType
Method to remove first NameValueType from PropertySets_list

S

security - Variable in class org.biomage.Common.Describable
Information on the security for the instance of the class.
setArrayDesign_package(ArrayDesign_package) - Method in class org.biomage.Common.MAGEJava
Set method for arrayDesign_package
setArray_package(Array_package) - Method in class org.biomage.Common.MAGEJava
Set method for array_package
setAuditAndSecurity_package(AuditAndSecurity_package) - Method in class org.biomage.Common.MAGEJava
Set method for auditAndSecurity_package
setAuditTrail(HasAuditTrail.AuditTrail_list) - Method in class org.biomage.Common.Describable
Set method for auditTrail
setBQS_package(BQS_package) - Method in class org.biomage.Common.MAGEJava
Set method for bQS_package
setBioAssayData_package(BioAssayData_package) - Method in class org.biomage.Common.MAGEJava
Set method for bioAssayData_package
setBioAssay_package(BioAssay_package) - Method in class org.biomage.Common.MAGEJava
Set method for bioAssay_package
setBioEvent_package(BioEvent_package) - Method in class org.biomage.Common.MAGEJava
Set method for bioEvent_package
setBioMaterial_package(BioMaterial_package) - Method in class org.biomage.Common.MAGEJava
Set method for bioMaterial_package
setBioSequence_package(BioSequence_package) - Method in class org.biomage.Common.MAGEJava
Set method for bioSequence_package
setDescription_package(Description_package) - Method in class org.biomage.Common.MAGEJava
Set method for description_package
setDescriptions(HasDescriptions.Descriptions_list) - Method in class org.biomage.Common.Describable
Set method for descriptions
setDesignElement_package(DesignElement_package) - Method in class org.biomage.Common.MAGEJava
Set method for designElement_package
setExperiment_package(Experiment_package) - Method in class org.biomage.Common.MAGEJava
Set method for experiment_package
setHigherLevelAnalysis_package(HigherLevelAnalysis_package) - Method in class org.biomage.Common.MAGEJava
Set method for higherLevelAnalysis_package
setIdentifier(String) - Method in class org.biomage.Common.Identifiable
Set method for identifier
setMeasurement_package(Measurement_package) - Method in class org.biomage.Common.MAGEJava
Set method for measurement_package
setName(String) - Method in class org.biomage.Common.Identifiable
Set method for name
setName(String) - Method in class org.biomage.Common.NameValueType
Set method for name
setPropertySets(HasPropertySets.PropertySets_list) - Method in class org.biomage.Common.Extendable
Set method for propertySets
setPropertySets(HasPropertySets.PropertySets_list) - Method in class org.biomage.Common.NameValueType
Set method for propertySets
setProtocol_package(Protocol_package) - Method in class org.biomage.Common.MAGEJava
Set method for protocol_package
setQuantitationType_package(QuantitationType_package) - Method in class org.biomage.Common.MAGEJava
Set method for quantitationType_package
setSecurity(Security) - Method in class org.biomage.Common.Describable
Set method for security
setType(String) - Method in class org.biomage.Common.NameValueType
Set method for type
setValue(String) - Method in class org.biomage.Common.NameValueType
Set method for value

T

type - Variable in class org.biomage.Common.NameValueType
The type of the key.

V

value - Variable in class org.biomage.Common.NameValueType
The value of the name.

W

writeAssociations(Writer) - Method in class org.biomage.Common.Describable
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Common.Extendable
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Common.Identifiable
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Common.MAGEJava
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.Common.NameValueType
writeAssociations
writeAttributes(Writer) - Method in class org.biomage.Common.Describable
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Common.Extendable
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Common.Identifiable
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Common.MAGEJava
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.Common.NameValueType
writeAttributes
writeMAGEML(Writer) - Method in class org.biomage.Common.Describable
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Common.Extendable
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Common.Identifiable
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Common.MAGEJava
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.Common.NameValueType
writeMAGEML

A B D E G H I M N O P Q R S T V W