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org.biomage.Common
Class MAGEJava
java.lang.Objectorg.biomage.Common.MAGEJava
- All Implemented Interfaces:
- java.io.Serializable
- public class MAGEJava
- extends java.lang.Object
- implements java.io.Serializable
- extends java.lang.Object
| Nested Class Summary | |
private class |
MAGEJava.ModelNameToClassMap
Inner class to store Model to Class mappings |
| Field Summary | |
org.biomage.Array.Array_package |
array_package
Describes the process of creating arrays from array designs. |
org.biomage.ArrayDesign.ArrayDesign_package |
arrayDesign_package
Describes a microarray design that can be printed and then, in the case of gene expression, hybridized. |
org.biomage.AuditAndSecurity.AuditAndSecurity_package |
auditAndSecurity_package
Specifies classes that allow tracking of changes and information on user permissions to view the data and annotation. |
org.biomage.BioAssay.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. |
org.biomage.BioAssayData.BioAssayData_package |
bioAssayData_package
The classes defined here provide data and the information and annotation on the derivation of that data. |
org.biomage.BioEvent.BioEvent_package |
bioEvent_package
An abstract class representing an event that takes sources of some type to produce a target of some type. |
org.biomage.BioMaterial.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. |
org.biomage.BioSequence.BioSequence_package |
bioSequence_package
Describes a known gene or sequence. |
org.biomage.BQS.BQS_package |
bQS_package
Allows a reference to an article, book or other publication to be specified for searching repositories. |
org.biomage.Description.Description_package |
description_package
The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter. |
org.biomage.DesignElement.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. |
org.biomage.Experiment.Experiment_package |
experiment_package
Represents the container for a hierarchical grouping of BioAssays. |
org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package |
higherLevelAnalysis_package
Describes the results of performing analysis on the result of the BioAssayData from an Experiment. |
org.biomage.Measurement.Measurement_package |
measurement_package
The classes of this package provide utility information on the quantities of other classes to each other. |
(package private) MAGEJava.ModelNameToClassMap |
modelToClass
Instantiate the ModelNameToClassMap |
org.biomage.Protocol.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. |
org.biomage.QuantitationType.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. |
|
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
bioEvent_package
public org.biomage.BioEvent.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.
array_package
public org.biomage.Array.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.
bioAssayData_package
public org.biomage.BioAssayData.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.
bioAssay_package
public org.biomage.BioAssay.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.
description_package
public org.biomage.Description.Description_package description_package
- The classes in this package allow a variety of references to
third party annotation and direct annotation by the experimenter.
quantitationType_package
public org.biomage.QuantitationType.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.
protocol_package
public org.biomage.Protocol.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.
measurement_package
public org.biomage.Measurement.Measurement_package measurement_package
- The classes of this package provide utility information on the
quantities of other classes to each other.
bioSequence_package
public org.biomage.BioSequence.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.
bQS_package
public org.biomage.BQS.BQS_package bQS_package
- Allows a reference to an article, book or other publication to be
specified for searching repositories.
experiment_package
public org.biomage.Experiment.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.
auditAndSecurity_package
public org.biomage.AuditAndSecurity.AuditAndSecurity_package auditAndSecurity_package
- Specifies classes that allow tracking of changes and information
on user permissions to view the data and annotation.
higherLevelAnalysis_package
public org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package higherLevelAnalysis_package
- Describes the results of performing analysis on the result of the
BioAssayData from an Experiment.
designElement_package
public org.biomage.DesignElement.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 org.biomage.ArrayDesign.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.
bioMaterial_package
public org.biomage.BioMaterial.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.
modelToClass
MAGEJava.ModelNameToClassMap modelToClass
- Instantiate the ModelNameToClassMap
| 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.
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.
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.
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.
setBioEvent_package
public void setBioEvent_package(org.biomage.BioEvent.BioEvent_package bioEvent_package)
- Set method for bioEvent_package
getBioEvent_package
public org.biomage.BioEvent.BioEvent_package getBioEvent_package()
- Get method for bioEvent_package
setArray_package
public void setArray_package(org.biomage.Array.Array_package array_package)
- Set method for array_package
getArray_package
public org.biomage.Array.Array_package getArray_package()
- Get method for array_package
setBioAssayData_package
public void setBioAssayData_package(org.biomage.BioAssayData.BioAssayData_package bioAssayData_package)
- Set method for bioAssayData_package
getBioAssayData_package
public org.biomage.BioAssayData.BioAssayData_package getBioAssayData_package()
- Get method for bioAssayData_package
setBioAssay_package
public void setBioAssay_package(org.biomage.BioAssay.BioAssay_package bioAssay_package)
- Set method for bioAssay_package
getBioAssay_package
public org.biomage.BioAssay.BioAssay_package getBioAssay_package()
- Get method for bioAssay_package
setDescription_package
public void setDescription_package(org.biomage.Description.Description_package description_package)
- Set method for description_package
getDescription_package
public org.biomage.Description.Description_package getDescription_package()
- Get method for description_package
setQuantitationType_package
public void setQuantitationType_package(org.biomage.QuantitationType.QuantitationType_package quantitationType_package)
- Set method for quantitationType_package
getQuantitationType_package
public org.biomage.QuantitationType.QuantitationType_package getQuantitationType_package()
- Get method for quantitationType_package
setProtocol_package
public void setProtocol_package(org.biomage.Protocol.Protocol_package protocol_package)
- Set method for protocol_package
getProtocol_package
public org.biomage.Protocol.Protocol_package getProtocol_package()
- Get method for protocol_package
setMeasurement_package
public void setMeasurement_package(org.biomage.Measurement.Measurement_package measurement_package)
- Set method for measurement_package
getMeasurement_package
public org.biomage.Measurement.Measurement_package getMeasurement_package()
- Get method for measurement_package
setBioSequence_package
public void setBioSequence_package(org.biomage.BioSequence.BioSequence_package bioSequence_package)
- Set method for bioSequence_package
getBioSequence_package
public org.biomage.BioSequence.BioSequence_package getBioSequence_package()
- Get method for bioSequence_package
setBQS_package
public void setBQS_package(org.biomage.BQS.BQS_package bQS_package)
- Set method for bQS_package
getBQS_package
public org.biomage.BQS.BQS_package getBQS_package()
- Get method for bQS_package
setExperiment_package
public void setExperiment_package(org.biomage.Experiment.Experiment_package experiment_package)
- Set method for experiment_package
getExperiment_package
public org.biomage.Experiment.Experiment_package getExperiment_package()
- Get method for experiment_package
setAuditAndSecurity_package
public void setAuditAndSecurity_package(org.biomage.AuditAndSecurity.AuditAndSecurity_package auditAndSecurity_package)
- Set method for auditAndSecurity_package
getAuditAndSecurity_package
public org.biomage.AuditAndSecurity.AuditAndSecurity_package getAuditAndSecurity_package()
- Get method for auditAndSecurity_package
setHigherLevelAnalysis_package
public void setHigherLevelAnalysis_package(org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package higherLevelAnalysis_package)
- Set method for higherLevelAnalysis_package
getHigherLevelAnalysis_package
public org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package getHigherLevelAnalysis_package()
- Get method for higherLevelAnalysis_package
setDesignElement_package
public void setDesignElement_package(org.biomage.DesignElement.DesignElement_package designElement_package)
- Set method for designElement_package
getDesignElement_package
public org.biomage.DesignElement.DesignElement_package getDesignElement_package()
- Get method for designElement_package
setArrayDesign_package
public void setArrayDesign_package(org.biomage.ArrayDesign.ArrayDesign_package arrayDesign_package)
- Set method for arrayDesign_package
getArrayDesign_package
public org.biomage.ArrayDesign.ArrayDesign_package getArrayDesign_package()
- Get method for arrayDesign_package
setBioMaterial_package
public void setBioMaterial_package(org.biomage.BioMaterial.BioMaterial_package bioMaterial_package)
- Set method for bioMaterial_package
getBioMaterial_package
public org.biomage.BioMaterial.BioMaterial_package getBioMaterial_package()
- Get method for bioMaterial_package
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SUMMARY: JAVADOC | SOURCE | DOWNLOAD | NESTED | FIELD | CONSTR | METHOD |
DETAIL: FIELD | CONSTR | METHOD | ||||||||