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org.biomage.DesignElement
Class DesignElement_package  

java.lang.Object
  org.biomage.DesignElement.DesignElement_package

All Implemented Interfaces:

java.io.Serializable

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public class DesignElement_package

extends java.lang.Object

implements java.io.Serializable

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.

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Nested Class Summary
class	DesignElement_package.CompositeCompositeMap_list           Inner list class for holding multiple entries for attribute compositeCompositeMap_list.
class	DesignElement_package.CompositeSequence_list           Inner list class for holding multiple entries for attribute compositeSequence_list.
class	DesignElement_package.DesignElement_list           Inner list class for holding multiple entries for attribute designElement_list.
class	DesignElement_package.FeatureReporterMap_list           Inner list class for holding multiple entries for attribute featureReporterMap_list.
class	DesignElement_package.Reporter_list           Inner list class for holding multiple entries for attribute reporter_list.
class	DesignElement_package.ReporterCompositeMap_list           Inner list class for holding multiple entries for attribute reporterCompositeMap_list.

 

Field Summary
DesignElement_package.CompositeCompositeMap_list	compositeCompositeMap_list           A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence.
DesignElement_package.CompositeSequence_list	compositeSequence_list           A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.
DesignElement_package.DesignElement_list	designElement_list           An element of an array.
DesignElement_package.FeatureReporterMap_list	featureReporterMap_list           A FeatureReporterMap is the description of how source features are transformed into a target reporter.
DesignElement_package.Reporter_list	reporter_list           A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.
DesignElement_package.ReporterCompositeMap_list	reporterCompositeMap_list           A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences.

 

Constructor Summary

DesignElement_package()           Default constructor.

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

 

Method Summary
void	addToCompositeCompositeMap_list(CompositeCompositeMap compositeCompositeMap)           Method to add CompositeCompositeMap to CompositeCompositeMap_list
void	addToCompositeCompositeMap_list(int position, CompositeCompositeMap compositeCompositeMap)           Method to add CompositeCompositeMap at position to CompositeCompositeMap_list
void	addToCompositeSequence_list(CompositeSequence compositeSequence)           Method to add CompositeSequence to CompositeSequence_list
void	addToCompositeSequence_list(int position, CompositeSequence compositeSequence)           Method to add CompositeSequence at position to CompositeSequence_list
void	addToDesignElement_list(DesignElement designElement)           Method to add DesignElement to DesignElement_list
void	addToDesignElement_list(int position, DesignElement designElement)           Method to add DesignElement at position to DesignElement_list
void	addToFeatureReporterMap_list(FeatureReporterMap featureReporterMap)           Method to add FeatureReporterMap to FeatureReporterMap_list
void	addToFeatureReporterMap_list(int position, FeatureReporterMap featureReporterMap)           Method to add FeatureReporterMap at position to FeatureReporterMap_list
void	addToReporter_list(int position, Reporter reporter)           Method to add Reporter at position to Reporter_list
void	addToReporter_list(Reporter reporter)           Method to add Reporter to Reporter_list
void	addToReporterCompositeMap_list(int position, ReporterCompositeMap reporterCompositeMap)           Method to add ReporterCompositeMap at position to ReporterCompositeMap_list
void	addToReporterCompositeMap_list(ReporterCompositeMap reporterCompositeMap)           Method to add ReporterCompositeMap to ReporterCompositeMap_list
DesignElement_package.CompositeCompositeMap_list	getCompositeCompositeMap_list()           Get method for compositeCompositeMap_list
DesignElement_package.CompositeSequence_list	getCompositeSequence_list()           Get method for compositeSequence_list
DesignElement_package.DesignElement_list	getDesignElement_list()           Get method for designElement_list
DesignElement_package.FeatureReporterMap_list	getFeatureReporterMap_list()           Get method for featureReporterMap_list
CompositeCompositeMap	getFromCompositeCompositeMap_list(int position)           Method to get CompositeCompositeMap from CompositeCompositeMap_list
CompositeSequence	getFromCompositeSequence_list(int position)           Method to get CompositeSequence from CompositeSequence_list
DesignElement	getFromDesignElement_list(int position)           Method to get DesignElement from DesignElement_list
FeatureReporterMap	getFromFeatureReporterMap_list(int position)           Method to get FeatureReporterMap from FeatureReporterMap_list
Reporter	getFromReporter_list(int position)           Method to get Reporter from Reporter_list
ReporterCompositeMap	getFromReporterCompositeMap_list(int position)           Method to get ReporterCompositeMap from ReporterCompositeMap_list
DesignElement_package.Reporter_list	getReporter_list()           Get method for reporter_list
DesignElement_package.ReporterCompositeMap_list	getReporterCompositeMap_list()           Get method for reporterCompositeMap_list
void	removeElementAtFromCompositeCompositeMap_list(int position)           Method to remove by position from CompositeCompositeMap_list
void	removeElementAtFromCompositeSequence_list(int position)           Method to remove by position from CompositeSequence_list
void	removeElementAtFromDesignElement_list(int position)           Method to remove by position from DesignElement_list
void	removeElementAtFromFeatureReporterMap_list(int position)           Method to remove by position from FeatureReporterMap_list
void	removeElementAtFromReporter_list(int position)           Method to remove by position from Reporter_list
void	removeElementAtFromReporterCompositeMap_list(int position)           Method to remove by position from ReporterCompositeMap_list
void	removeFromCompositeCompositeMap_list(CompositeCompositeMap compositeCompositeMap)           Method to remove first CompositeCompositeMap from CompositeCompositeMap_list
void	removeFromCompositeSequence_list(CompositeSequence compositeSequence)           Method to remove first CompositeSequence from CompositeSequence_list
void	removeFromDesignElement_list(DesignElement designElement)           Method to remove first DesignElement from DesignElement_list
void	removeFromFeatureReporterMap_list(FeatureReporterMap featureReporterMap)           Method to remove first FeatureReporterMap from FeatureReporterMap_list
void	removeFromReporter_list(Reporter reporter)           Method to remove first Reporter from Reporter_list
void	removeFromReporterCompositeMap_list(ReporterCompositeMap reporterCompositeMap)           Method to remove first ReporterCompositeMap from ReporterCompositeMap_list
void	setCompositeCompositeMap_list(DesignElement_package.CompositeCompositeMap_list compositeCompositeMap_list)           Set method for compositeCompositeMap_list
void	setCompositeSequence_list(DesignElement_package.CompositeSequence_list compositeSequence_list)           Set method for compositeSequence_list
void	setDesignElement_list(DesignElement_package.DesignElement_list designElement_list)           Set method for designElement_list
void	setFeatureReporterMap_list(DesignElement_package.FeatureReporterMap_list featureReporterMap_list)           Set method for featureReporterMap_list
void	setReporter_list(DesignElement_package.Reporter_list reporter_list)           Set method for reporter_list
void	setReporterCompositeMap_list(DesignElement_package.ReporterCompositeMap_list reporterCompositeMap_list)           Set method for reporterCompositeMap_list
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

designElement_list

public DesignElement_package.DesignElement_list designElement_list

An element of an array. This is generally of type feature but can be specified as reporters or compositeSequence for arrays that are abstracted from a physical array.

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reporter_list

public DesignElement_package.Reporter_list reporter_list

A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences. The derived data from the measured data of its Features represents the presence or absence of the biosequence or biosequences it is reporting on in the BioAssay. Reporters are Identifiable and several Features on the same array can be mapped to the same reporter as can Features from a different ArrayDesign. The granularity of the Reporters independence is dependent on the technology and the intent of the ArrayDesign. Oligos using mature technologies can in general be assumed to be safely replicated on many features where as with PCR Products there might be the desire for quality assurence to make reporters one to one with features and use the mappings to CompositeSequences for replication purposes.

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compositeSequence_list

public DesignElement_package.CompositeSequence_list compositeSequence_list

A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.

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compositeCompositeMap_list

public DesignElement_package.CompositeCompositeMap_list compositeCompositeMap_list

A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. For instance, several CompositeSequences could represent different sequence regions for a Gene and could be mapped to different CompositeSequences, each representing a different splice variant for that Gene.

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featureReporterMap_list

public DesignElement_package.FeatureReporterMap_list featureReporterMap_list

A FeatureReporterMap is the description of how source features are transformed into a target reporter. These would map replicate features for a reporter to the reporter.

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reporterCompositeMap_list

public DesignElement_package.ReporterCompositeMap_list reporterCompositeMap_list

A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. For instance, several reporters that tile across a section of a chromosome could be mapped to a CompositeSequence.

Constructor Detail

DesignElement_package

public DesignElement_package()

Default constructor.

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DesignElement_package

public DesignElement_package(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.

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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.

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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.

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setDesignElement_list

public void setDesignElement_list(DesignElement_package.DesignElement_list designElement_list)

Set method for designElement_list

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getDesignElement_list

public DesignElement_package.DesignElement_list getDesignElement_list()

Get method for designElement_list

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addToDesignElement_list

public void addToDesignElement_list(DesignElement designElement)

Method to add DesignElement to DesignElement_list

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addToDesignElement_list

public void addToDesignElement_list(int position,
                                    DesignElement designElement)

Method to add DesignElement at position to DesignElement_list

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getFromDesignElement_list

public DesignElement getFromDesignElement_list(int position)

Method to get DesignElement from DesignElement_list

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removeElementAtFromDesignElement_list

public void removeElementAtFromDesignElement_list(int position)

Method to remove by position from DesignElement_list

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removeFromDesignElement_list

public void removeFromDesignElement_list(DesignElement designElement)

Method to remove first DesignElement from DesignElement_list

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setReporter_list

public void setReporter_list(DesignElement_package.Reporter_list reporter_list)

Set method for reporter_list

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getReporter_list

public DesignElement_package.Reporter_list getReporter_list()

Get method for reporter_list

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addToReporter_list

public void addToReporter_list(Reporter reporter)

Method to add Reporter to Reporter_list

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addToReporter_list

public void addToReporter_list(int position,
                               Reporter reporter)

Method to add Reporter at position to Reporter_list

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getFromReporter_list

public Reporter getFromReporter_list(int position)

Method to get Reporter from Reporter_list

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removeElementAtFromReporter_list

public void removeElementAtFromReporter_list(int position)

Method to remove by position from Reporter_list

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removeFromReporter_list

public void removeFromReporter_list(Reporter reporter)

Method to remove first Reporter from Reporter_list

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setCompositeSequence_list

public void setCompositeSequence_list(DesignElement_package.CompositeSequence_list compositeSequence_list)

Set method for compositeSequence_list

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getCompositeSequence_list

public DesignElement_package.CompositeSequence_list getCompositeSequence_list()

Get method for compositeSequence_list

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addToCompositeSequence_list

public void addToCompositeSequence_list(CompositeSequence compositeSequence)

Method to add CompositeSequence to CompositeSequence_list

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addToCompositeSequence_list

public void addToCompositeSequence_list(int position,
                                        CompositeSequence compositeSequence)

Method to add CompositeSequence at position to CompositeSequence_list

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getFromCompositeSequence_list

public CompositeSequence getFromCompositeSequence_list(int position)

Method to get CompositeSequence from CompositeSequence_list

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removeElementAtFromCompositeSequence_list

public void removeElementAtFromCompositeSequence_list(int position)

Method to remove by position from CompositeSequence_list

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removeFromCompositeSequence_list

public void removeFromCompositeSequence_list(CompositeSequence compositeSequence)

Method to remove first CompositeSequence from CompositeSequence_list

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setCompositeCompositeMap_list

public void setCompositeCompositeMap_list(DesignElement_package.CompositeCompositeMap_list compositeCompositeMap_list)

Set method for compositeCompositeMap_list

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getCompositeCompositeMap_list

public DesignElement_package.CompositeCompositeMap_list getCompositeCompositeMap_list()

Get method for compositeCompositeMap_list

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addToCompositeCompositeMap_list

public void addToCompositeCompositeMap_list(CompositeCompositeMap compositeCompositeMap)

Method to add CompositeCompositeMap to CompositeCompositeMap_list

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addToCompositeCompositeMap_list

public void addToCompositeCompositeMap_list(int position,
                                            CompositeCompositeMap compositeCompositeMap)

Method to add CompositeCompositeMap at position to CompositeCompositeMap_list

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getFromCompositeCompositeMap_list

public CompositeCompositeMap getFromCompositeCompositeMap_list(int position)

Method to get CompositeCompositeMap from CompositeCompositeMap_list

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removeElementAtFromCompositeCompositeMap_list

public void removeElementAtFromCompositeCompositeMap_list(int position)

Method to remove by position from CompositeCompositeMap_list

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removeFromCompositeCompositeMap_list

public void removeFromCompositeCompositeMap_list(CompositeCompositeMap compositeCompositeMap)

Method to remove first CompositeCompositeMap from CompositeCompositeMap_list

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setFeatureReporterMap_list

public void setFeatureReporterMap_list(DesignElement_package.FeatureReporterMap_list featureReporterMap_list)

Set method for featureReporterMap_list

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getFeatureReporterMap_list

public DesignElement_package.FeatureReporterMap_list getFeatureReporterMap_list()

Get method for featureReporterMap_list

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addToFeatureReporterMap_list

public void addToFeatureReporterMap_list(FeatureReporterMap featureReporterMap)

Method to add FeatureReporterMap to FeatureReporterMap_list

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addToFeatureReporterMap_list

public void addToFeatureReporterMap_list(int position,
                                         FeatureReporterMap featureReporterMap)

Method to add FeatureReporterMap at position to FeatureReporterMap_list

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getFromFeatureReporterMap_list

public FeatureReporterMap getFromFeatureReporterMap_list(int position)

Method to get FeatureReporterMap from FeatureReporterMap_list

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removeElementAtFromFeatureReporterMap_list

public void removeElementAtFromFeatureReporterMap_list(int position)

Method to remove by position from FeatureReporterMap_list

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removeFromFeatureReporterMap_list

public void removeFromFeatureReporterMap_list(FeatureReporterMap featureReporterMap)

Method to remove first FeatureReporterMap from FeatureReporterMap_list

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setReporterCompositeMap_list

public void setReporterCompositeMap_list(DesignElement_package.ReporterCompositeMap_list reporterCompositeMap_list)

Set method for reporterCompositeMap_list

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getReporterCompositeMap_list

public DesignElement_package.ReporterCompositeMap_list getReporterCompositeMap_list()

Get method for reporterCompositeMap_list

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addToReporterCompositeMap_list

public void addToReporterCompositeMap_list(ReporterCompositeMap reporterCompositeMap)

Method to add ReporterCompositeMap to ReporterCompositeMap_list

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addToReporterCompositeMap_list

public void addToReporterCompositeMap_list(int position,
                                           ReporterCompositeMap reporterCompositeMap)

Method to add ReporterCompositeMap at position to ReporterCompositeMap_list

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getFromReporterCompositeMap_list

public ReporterCompositeMap getFromReporterCompositeMap_list(int position)

Method to get ReporterCompositeMap from ReporterCompositeMap_list

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removeElementAtFromReporterCompositeMap_list

public void removeElementAtFromReporterCompositeMap_list(int position)

Method to remove by position from ReporterCompositeMap_list

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removeFromReporterCompositeMap_list

public void removeFromReporterCompositeMap_list(ReporterCompositeMap reporterCompositeMap)

Method to remove first ReporterCompositeMap from ReporterCompositeMap_list

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SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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