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org.biomage.Common
Class MAGEJava  view MAGEJava download MAGEJava.java

java.lang.Object
  extended byorg.biomage.Common.MAGEJava
All Implemented Interfaces:
java.io.Serializable

public class MAGEJava
extends java.lang.Object
implements java.io.Serializable


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.
 
Method Summary
 org.biomage.Array.Array_package getArray_package()
          Get method for array_package
 org.biomage.ArrayDesign.ArrayDesign_package getArrayDesign_package()
          Get method for arrayDesign_package
 org.biomage.AuditAndSecurity.AuditAndSecurity_package getAuditAndSecurity_package()
          Get method for auditAndSecurity_package
 org.biomage.BioAssay.BioAssay_package getBioAssay_package()
          Get method for bioAssay_package
 org.biomage.BioAssayData.BioAssayData_package getBioAssayData_package()
          Get method for bioAssayData_package
 org.biomage.BioEvent.BioEvent_package getBioEvent_package()
          Get method for bioEvent_package
 org.biomage.BioMaterial.BioMaterial_package getBioMaterial_package()
          Get method for bioMaterial_package
 org.biomage.BioSequence.BioSequence_package getBioSequence_package()
          Get method for bioSequence_package
 org.biomage.BQS.BQS_package getBQS_package()
          Get method for bQS_package
 java.lang.Class getClassWithModelName(java.lang.String modelName)
          getClassWithModelName(String modelName)
 org.biomage.Description.Description_package getDescription_package()
          Get method for description_package
 org.biomage.DesignElement.DesignElement_package getDesignElement_package()
          Get method for designElement_package
 org.biomage.Experiment.Experiment_package getExperiment_package()
          Get method for experiment_package
 org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package getHigherLevelAnalysis_package()
          Get method for higherLevelAnalysis_package
 org.biomage.Measurement.Measurement_package getMeasurement_package()
          Get method for measurement_package
 org.biomage.Protocol.Protocol_package getProtocol_package()
          Get method for protocol_package
 org.biomage.QuantitationType.QuantitationType_package getQuantitationType_package()
          Get method for quantitationType_package
 void setArray_package(org.biomage.Array.Array_package array_package)
          Set method for array_package
 void setArrayDesign_package(org.biomage.ArrayDesign.ArrayDesign_package arrayDesign_package)
          Set method for arrayDesign_package
 void setAuditAndSecurity_package(org.biomage.AuditAndSecurity.AuditAndSecurity_package auditAndSecurity_package)
          Set method for auditAndSecurity_package
 void setBioAssay_package(org.biomage.BioAssay.BioAssay_package bioAssay_package)
          Set method for bioAssay_package
 void setBioAssayData_package(org.biomage.BioAssayData.BioAssayData_package bioAssayData_package)
          Set method for bioAssayData_package
 void setBioEvent_package(org.biomage.BioEvent.BioEvent_package bioEvent_package)
          Set method for bioEvent_package
 void setBioMaterial_package(org.biomage.BioMaterial.BioMaterial_package bioMaterial_package)
          Set method for bioMaterial_package
 void setBioSequence_package(org.biomage.BioSequence.BioSequence_package bioSequence_package)
          Set method for bioSequence_package
 void setBQS_package(org.biomage.BQS.BQS_package bQS_package)
          Set method for bQS_package
 void setDescription_package(org.biomage.Description.Description_package description_package)
          Set method for description_package
 void setDesignElement_package(org.biomage.DesignElement.DesignElement_package designElement_package)
          Set method for designElement_package
 void setExperiment_package(org.biomage.Experiment.Experiment_package experiment_package)
          Set method for experiment_package
 void setHigherLevelAnalysis_package(org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package higherLevelAnalysis_package)
          Set method for higherLevelAnalysis_package
 void setMeasurement_package(org.biomage.Measurement.Measurement_package measurement_package)
          Set method for measurement_package
 void setProtocol_package(org.biomage.Protocol.Protocol_package protocol_package)
          Set method for protocol_package
 void setQuantitationType_package(org.biomage.QuantitationType.QuantitationType_package quantitationType_package)
          Set method for quantitationType_package
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
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