|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biomage.Common.MAGEJava
public class MAGEJava
Top-level object that represents the model. Contains the packages.
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 |
java.lang.String |
getIdentifier()
|
Measurement_package |
getMeasurement_package()
Get method for measurement_package |
java.lang.String |
getModelClassName()
|
java.lang.String |
getName()
|
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 |
setIdentifier(java.lang.String identifier)
|
void |
setMeasurement_package(Measurement_package measurement_package)
Set method for measurement_package |
void |
setName(java.lang.String name)
|
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 |
---|
public AuditAndSecurity_package auditAndSecurity_package
public Description_package description_package
public Measurement_package measurement_package
public BQS_package bQS_package
public BioEvent_package bioEvent_package
public Protocol_package protocol_package
public BioMaterial_package bioMaterial_package
public BioSequence_package bioSequence_package
public DesignElement_package designElement_package
public ArrayDesign_package arrayDesign_package
public Array_package array_package
public BioAssay_package bioAssay_package
public QuantitationType_package quantitationType_package
public BioAssayData_package bioAssayData_package
public Experiment_package experiment_package
public HigherLevelAnalysis_package higherLevelAnalysis_package
Constructor Detail |
---|
public MAGEJava()
public MAGEJava(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
---|
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
java.io.IOException
public void writeAttributes(java.io.Writer out) throws java.io.IOException
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
java.io.IOException
public java.lang.Class getClassWithModelName(java.lang.String modelName)
public java.lang.String getModelClassName()
public void setAuditAndSecurity_package(AuditAndSecurity_package auditAndSecurity_package)
value
- to setpublic AuditAndSecurity_package getAuditAndSecurity_package()
public void setDescription_package(Description_package description_package)
value
- to setpublic Description_package getDescription_package()
public void setMeasurement_package(Measurement_package measurement_package)
value
- to setpublic Measurement_package getMeasurement_package()
public void setBQS_package(BQS_package bQS_package)
value
- to setpublic BQS_package getBQS_package()
public void setBioEvent_package(BioEvent_package bioEvent_package)
value
- to setpublic BioEvent_package getBioEvent_package()
public void setProtocol_package(Protocol_package protocol_package)
value
- to setpublic Protocol_package getProtocol_package()
public void setBioMaterial_package(BioMaterial_package bioMaterial_package)
value
- to setpublic BioMaterial_package getBioMaterial_package()
public void setBioSequence_package(BioSequence_package bioSequence_package)
value
- to setpublic BioSequence_package getBioSequence_package()
public void setDesignElement_package(DesignElement_package designElement_package)
value
- to setpublic DesignElement_package getDesignElement_package()
public void setArrayDesign_package(ArrayDesign_package arrayDesign_package)
value
- to setpublic ArrayDesign_package getArrayDesign_package()
public void setArray_package(Array_package array_package)
value
- to setpublic Array_package getArray_package()
public void setBioAssay_package(BioAssay_package bioAssay_package)
value
- to setpublic BioAssay_package getBioAssay_package()
public void setQuantitationType_package(QuantitationType_package quantitationType_package)
value
- to setpublic QuantitationType_package getQuantitationType_package()
public void setBioAssayData_package(BioAssayData_package bioAssayData_package)
value
- to setpublic BioAssayData_package getBioAssayData_package()
public void setExperiment_package(Experiment_package experiment_package)
value
- to setpublic Experiment_package getExperiment_package()
public void setHigherLevelAnalysis_package(HigherLevelAnalysis_package higherLevelAnalysis_package)
value
- to setpublic HigherLevelAnalysis_package getHigherLevelAnalysis_package()
public java.lang.String getIdentifier()
public void setIdentifier(java.lang.String identifier)
identifier
- public java.lang.String getName()
public void setName(java.lang.String name)
name
-
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |