org.biomage.Common
Class MAGEJava

java.lang.Object
  |
  +--org.biomage.Common.MAGEJava

All Implemented Interfaces:

java.io.Serializable

public class MAGEJava

extends java.lang.Object

implements java.io.Serializable

Top-level object that represents the model. Contains the packages.

See Also:

Serialized Form

Field Summary

Array_package	array_package Describes the process of creating arrays from array designs.
ArrayDesign_package	arrayDesign_package Describes a microarray design that can be printed and then, in the case of gene expression, hybridized.
AuditAndSecurity_package	auditAndSecurity_package Specifies classes that allow tracking of changes and information on user permissions to view the data and annotation.
BioAssay_package	bioAssay_package 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.
BioAssayData_package	bioAssayData_package The classes defined here provide data and the information and annotation on the derivation of that data.
BioEvent_package	bioEvent_package An abstract class representing an event that takes sources of some type to produce a target of some type.
BioMaterial_package	bioMaterial_package 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	bioSequence_package Describes a known gene or sequence.
BQS_package	bQS_package Allows a reference to an article, book or other publication to be specified for searching repositories.
Description_package	description_package The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter.
DesignElement_package	designElement_package 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.
Experiment_package	experiment_package Represents the container for a hierarchical grouping of BioAssays.
HigherLevelAnalysis_package	higherLevelAnalysis_package Describes the results of performing analysis on the result of the BioAssayData from an Experiment.
Measurement_package	measurement_package The classes of this package provide utility information on the quantities of other classes to each other.
Protocol_package	protocol_package 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.
QuantitationType_package	quantitationType_package This Package defines the classes for quantitations, such as measured and derived signal, error, and pvalue.

Constructor Summary

MAGEJava()
Default constructor.

MAGEJava(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

Array_package	getArray_package() Get method for array_package
ArrayDesign_package	getArrayDesign_package() Get method for arrayDesign_package
AuditAndSecurity_package	getAuditAndSecurity_package() Get method for auditAndSecurity_package
BioAssay_package	getBioAssay_package() Get method for bioAssay_package
BioAssayData_package	getBioAssayData_package() Get method for bioAssayData_package
BioEvent_package	getBioEvent_package() Get method for bioEvent_package
BioMaterial_package	getBioMaterial_package() Get method for bioMaterial_package
BioSequence_package	getBioSequence_package() Get method for bioSequence_package
BQS_package	getBQS_package() Get method for bQS_package
java.lang.Class	getClassWithModelName(java.lang.String modelName) getClassWithModelName(String modelName) This method returns a MAGE class given it's common Model name.
Description_package	getDescription_package() Get method for description_package
DesignElement_package	getDesignElement_package() Get method for designElement_package
Experiment_package	getExperiment_package() Get method for experiment_package
HigherLevelAnalysis_package	getHigherLevelAnalysis_package() Get method for higherLevelAnalysis_package
Measurement_package	getMeasurement_package() Get method for measurement_package
Protocol_package	getProtocol_package() Get method for protocol_package
QuantitationType_package	getQuantitationType_package() Get method for quantitationType_package
void	setArray_package(Array_package array_package) Set method for array_package
void	setArrayDesign_package(ArrayDesign_package arrayDesign_package) Set method for arrayDesign_package
void	setAuditAndSecurity_package(AuditAndSecurity_package auditAndSecurity_package) Set method for auditAndSecurity_package
void	setBioAssay_package(BioAssay_package bioAssay_package) Set method for bioAssay_package
void	setBioAssayData_package(BioAssayData_package bioAssayData_package) Set method for bioAssayData_package
void	setBioEvent_package(BioEvent_package bioEvent_package) Set method for bioEvent_package
void	setBioMaterial_package(BioMaterial_package bioMaterial_package) Set method for bioMaterial_package
void	setBioSequence_package(BioSequence_package bioSequence_package) Set method for bioSequence_package
void	setBQS_package(BQS_package bQS_package) Set method for bQS_package
void	setDescription_package(Description_package description_package) Set method for description_package
void	setDesignElement_package(DesignElement_package designElement_package) Set method for designElement_package
void	setExperiment_package(Experiment_package experiment_package) Set method for experiment_package
void	setHigherLevelAnalysis_package(HigherLevelAnalysis_package higherLevelAnalysis_package) Set method for higherLevelAnalysis_package
void	setMeasurement_package(Measurement_package measurement_package) Set method for measurement_package
void	setProtocol_package(Protocol_package protocol_package) Set method for protocol_package
void	setQuantitationType_package(QuantitationType_package quantitationType_package) Set method for quantitationType_package
void	writeAssociations(java.io.Writer out) writeAssociations This method is responsible for assembling the association data into XML.
void	writeAttributes(java.io.Writer out) writeAttributes This method is responsible for assembling the attribute data into XML.
void	writeMAGEML(java.io.Writer out) writeMAGEML This method is responsible for assembling the attribute and association data into XML.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

auditAndSecurity_package

public AuditAndSecurity_package auditAndSecurity_package

Specifies classes that allow tracking of changes and information on user permissions to view the data and annotation.

description_package

public Description_package description_package

The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter.

measurement_package

public Measurement_package measurement_package

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

bQS_package

public BQS_package bQS_package

Allows a reference to an article, book or other publication to be specified for searching repositories.

bioEvent_package

public BioEvent_package bioEvent_package

An abstract class representing an event that takes sources of some type to produce a target of some type. Each of the realized subclasses determines the type of the sources and the target. The association to a protocol application allows specification of how the event was performed.

protocol_package

public Protocol_package protocol_package

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. The ProtocolApplication provides values for the replaceable parameters of the Protocol and, through the Description association of Describable, any variation from the Protocol.

bioMaterial_package

public BioMaterial_package bioMaterial_package

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. A set of treatments are typically linear in time but can form a Directed Acyclic Graph.

bioSequence_package

public BioSequence_package bioSequence_package

Describes a known gene or sequence. BioAssays typically seek to identify what BioSequences are expressed in a BioMaterial after treatments, the expression level measured from the association between the BioMaterial and the Array. The Array's Features typically provide known locations for this association to occur. Most often, the Reporter and CompositeSequence are known and the presence or absence of a particular BioSequence in the BioMaterial is based on whether there as been an association to the DesignElement targeted for it. Some other experiments may not know the DesignElement's target but can discover it with known properties of the BioSequences in the BioMaterial.

designElement_package

public DesignElement_package designElement_package

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. The Feature describes an intended location on the Array, the Reporter the Oligo, Clone, PCR Product that is on a Feature and the CompositeSequence which combines Reporters or CompositeSequences into what the child DesignElements are meant to represent biologically, e.g. a Gene, Exon, SpliceVariant, etc.

arrayDesign_package

public ArrayDesign_package arrayDesign_package

Describes a microarray design that can be printed and then, in the case of gene expression, hybridized. An array design consists of several features (also called spots) in which reporter sequences are placed. Many features may have the same reporter replicated and a reporter may be specified in one or more array designs. The nature of the reporter's biosequence placed on a spot will depend on the technology. Two well-known technologies differ significantly-spotter arrays draw material from a well and place a spot on the array whereas in situ oligo arrays are created through the synthesis of many, short (~20-100mer) nucleotide sequences onto the features. Reporters can be grouped together into CompositeSequences, typically representing a gene or one or more splice variants in gene expression experiments. There are then two distinct ways that DesignElements are grouped. The one described in the ArrayDesign package by FeatureGroup, ReporterGroup and CompositeGroup is by technology type, that is, one might want to segregate the controls to a Group and all the non-controls to another. Or if PCR Product and Oligos are both used on an array they would likely be in different groups. The grouping described in the DesignElement package by the mappings relates the Features to the Reporter, the Reporters to CompositeSequence, and at higher levels, CompositeSequences to CompositeSequence.

array_package

public Array_package array_package

Describes the process of creating arrays from array designs. Includes information on how arrays are grouped together, if relevant, how an array deviates from its array design both in layout and per feature and potentially contains references to LIMS data that might contain more detail on the BioMaterial used to create the reporters.

bioAssay_package

public BioAssay_package bioAssay_package

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. The derived classes of BioAssay represent the base PhysicalBioAssays which lead to the production of Images, the MeasuredBioAssay which is associated with the set of quantitations produced by FeatureExtraction, and DerivedBioAssay (see BioAssayData package) which groups together BioAssays that have been analyzed together to produce further refinement of the quantitations. The design of this package and the related BioAssayData package was driven by the following query considerations and the desire to return as little data as necessary to satisfy a query. Often, the first set of queries for experiments below the Experiment level will want to discover the why of an experiment and this is captured in the BioAssay class through its FactorValue, BioEvent and Description associations. This separates it from the data but allows an overview of the experiment hierarchy. The BioAssayData class association to BioDataValues is optional only to allow queries on them to discover the how of the experiment through the association to the transformation and mappings of the three BioAssayData dimensions and the protocols used. Once a researcher, for instance, has narrowed down the experiments of interest then the actual data, represented by the BioDataValues, can be downloaded. Because these data can be in the hundreds of megabytes to gigabytes range, it was considered desirable to be able to return information and annotation on the experiment without the data.

quantitationType_package

public QuantitationType_package quantitationType_package

This Package defines the classes for quantitations, such as measured and derived signal, error, and pvalue. The subclasses of StandardQuantitationType will be the best fit from FeatureExtraction or Transformation Protocol for the values obtained. Other values can be specified using SpecializedQuantitationType.

bioAssayData_package

public BioAssayData_package bioAssayData_package

The classes defined here provide data and the information and annotation on the derivation of that data. Some of the scenarios that might occur are the following. FeatureExtraction of a single PhysicalBioAssay produces MeasuredBioAssayData that has a single BioAssay on the BioAssayDimension, typically the Features described in the ArrayDesign on the DesignElementDimension, and the Quantitations associated with the application of a FeatureExtraction protocol on the QuantitationDimension. An error model transformation might be applied that doesn't change the BioAssayDimension or the DesignElementDimension but likely changes the QuantitationDimension. A transformation on replicate Reporters or CompositeSequences might be applied on the single BioAssay that would change the DesignElementDimension and the QuantitationDimension both. Replicate and Control BioAssays might be added to the BioAssayDimension and a transformation could change the BioAssayDimension and the QuantitationDimension but not change the DesignElementDimension to produce a new DerivedBioAssayData. Or some combination of the above transformations could be performed at once to change all three dimensions. Because the classes derive from Describable, the Experimenter can provide as much detail at each level of the class hierarchy as desired.

experiment_package

public Experiment_package experiment_package

Represents the container for a hierarchical grouping of BioAssays. Can have the end results of Clustering Analysis specified and, through the ExperimentDesign, a description and annotation of the overall design of the experiment and what it was to show.

higherLevelAnalysis_package

public HigherLevelAnalysis_package higherLevelAnalysis_package

Describes the results of performing analysis on the result of the BioAssayData from an Experiment.

Constructor Detail

MAGEJava

public MAGEJava()

Default constructor.

MAGEJava

public MAGEJava(org.xml.sax.Attributes atts)

Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Method Detail

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException

writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

java.io.IOException

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException

writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException

writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

java.io.IOException

getClassWithModelName

public java.lang.Class getClassWithModelName(java.lang.String modelName)

getClassWithModelName(String modelName) This method returns a MAGE class given it's common Model name.

setAuditAndSecurity_package

public void setAuditAndSecurity_package(AuditAndSecurity_package auditAndSecurity_package)

Set method for auditAndSecurity_package

getAuditAndSecurity_package

public AuditAndSecurity_package getAuditAndSecurity_package()

Get method for auditAndSecurity_package

Returns:

value of the attribute

setDescription_package

public void setDescription_package(Description_package description_package)

Set method for description_package

getDescription_package

public Description_package getDescription_package()

Get method for description_package

Returns:

value of the attribute

setMeasurement_package

public void setMeasurement_package(Measurement_package measurement_package)

Set method for measurement_package

getMeasurement_package

public Measurement_package getMeasurement_package()

Get method for measurement_package

Returns:

value of the attribute

setBQS_package

public void setBQS_package(BQS_package bQS_package)

Set method for bQS_package

getBQS_package

public BQS_package getBQS_package()

Get method for bQS_package

Returns:

value of the attribute

setBioEvent_package

public void setBioEvent_package(BioEvent_package bioEvent_package)

Set method for bioEvent_package

getBioEvent_package

public BioEvent_package getBioEvent_package()

Get method for bioEvent_package

Returns:

value of the attribute

setProtocol_package

public void setProtocol_package(Protocol_package protocol_package)

Set method for protocol_package

getProtocol_package

public Protocol_package getProtocol_package()

Get method for protocol_package

Returns:

value of the attribute

setBioMaterial_package

public void setBioMaterial_package(BioMaterial_package bioMaterial_package)

Set method for bioMaterial_package

getBioMaterial_package

public BioMaterial_package getBioMaterial_package()

Get method for bioMaterial_package

Returns:

value of the attribute

setBioSequence_package

public void setBioSequence_package(BioSequence_package bioSequence_package)

Set method for bioSequence_package

getBioSequence_package

public BioSequence_package getBioSequence_package()

Get method for bioSequence_package

Returns:

value of the attribute

setDesignElement_package

public void setDesignElement_package(DesignElement_package designElement_package)

Set method for designElement_package

getDesignElement_package

public DesignElement_package getDesignElement_package()

Get method for designElement_package

Returns:

value of the attribute

setArrayDesign_package

public void setArrayDesign_package(ArrayDesign_package arrayDesign_package)

Set method for arrayDesign_package

getArrayDesign_package

public ArrayDesign_package getArrayDesign_package()

Get method for arrayDesign_package

Returns:

value of the attribute

setArray_package

public void setArray_package(Array_package array_package)

Set method for array_package

getArray_package

public Array_package getArray_package()

Get method for array_package

Returns:

value of the attribute

setBioAssay_package

public void setBioAssay_package(BioAssay_package bioAssay_package)

Set method for bioAssay_package

getBioAssay_package

public BioAssay_package getBioAssay_package()

Get method for bioAssay_package

Returns:

value of the attribute

setQuantitationType_package

public void setQuantitationType_package(QuantitationType_package quantitationType_package)

Set method for quantitationType_package

getQuantitationType_package

public QuantitationType_package getQuantitationType_package()

Get method for quantitationType_package

Returns:

value of the attribute

setBioAssayData_package

public void setBioAssayData_package(BioAssayData_package bioAssayData_package)

Set method for bioAssayData_package

getBioAssayData_package

public BioAssayData_package getBioAssayData_package()

Get method for bioAssayData_package

Returns:

value of the attribute

setExperiment_package

public void setExperiment_package(Experiment_package experiment_package)

Set method for experiment_package

getExperiment_package

public Experiment_package getExperiment_package()

Get method for experiment_package

Returns:

value of the attribute

setHigherLevelAnalysis_package

public void setHigherLevelAnalysis_package(HigherLevelAnalysis_package higherLevelAnalysis_package)

Set method for higherLevelAnalysis_package

getHigherLevelAnalysis_package

public HigherLevelAnalysis_package getHigherLevelAnalysis_package()

Get method for higherLevelAnalysis_package

Returns:

value of the attribute