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org.biomage.DesignElement
Class DesignElement_package  view DesignElement_package download DesignElement_package.java

java.lang.Object
  extended byorg.biomage.DesignElement.DesignElement_package
All Implemented Interfaces:
java.io.Serializable

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.


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.


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.


compositeSequence_list

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


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.


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.


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.


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.


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.


setDesignElement_list

public void setDesignElement_list(DesignElement_package.DesignElement_list designElement_list)
Set method for designElement_list


getDesignElement_list

public DesignElement_package.DesignElement_list getDesignElement_list()
Get method for designElement_list


addToDesignElement_list

public void addToDesignElement_list(DesignElement designElement)
Method to add DesignElement to DesignElement_list


addToDesignElement_list

public void addToDesignElement_list(int position,
                                    DesignElement designElement)
Method to add DesignElement at position to DesignElement_list


getFromDesignElement_list

public DesignElement getFromDesignElement_list(int position)
Method to get DesignElement from DesignElement_list


removeElementAtFromDesignElement_list

public void removeElementAtFromDesignElement_list(int position)
Method to remove by position from DesignElement_list


removeFromDesignElement_list

public void removeFromDesignElement_list(DesignElement designElement)
Method to remove first DesignElement from DesignElement_list


setReporter_list

public void setReporter_list(DesignElement_package.Reporter_list reporter_list)
Set method for reporter_list


getReporter_list

public DesignElement_package.Reporter_list getReporter_list()
Get method for reporter_list


addToReporter_list

public void addToReporter_list(Reporter reporter)
Method to add Reporter to Reporter_list


addToReporter_list

public void addToReporter_list(int position,
                               Reporter reporter)
Method to add Reporter at position to Reporter_list


getFromReporter_list

public Reporter getFromReporter_list(int position)
Method to get Reporter from Reporter_list


removeElementAtFromReporter_list

public void removeElementAtFromReporter_list(int position)
Method to remove by position from Reporter_list


removeFromReporter_list

public void removeFromReporter_list(Reporter reporter)
Method to remove first Reporter from Reporter_list


setCompositeSequence_list

public void setCompositeSequence_list(DesignElement_package.CompositeSequence_list compositeSequence_list)
Set method for compositeSequence_list


getCompositeSequence_list

public DesignElement_package.CompositeSequence_list getCompositeSequence_list()
Get method for compositeSequence_list


addToCompositeSequence_list

public void addToCompositeSequence_list(CompositeSequence compositeSequence)
Method to add CompositeSequence to CompositeSequence_list


addToCompositeSequence_list

public void addToCompositeSequence_list(int position,
                                        CompositeSequence compositeSequence)
Method to add CompositeSequence at position to CompositeSequence_list


getFromCompositeSequence_list

public CompositeSequence getFromCompositeSequence_list(int position)
Method to get CompositeSequence from CompositeSequence_list


removeElementAtFromCompositeSequence_list

public void removeElementAtFromCompositeSequence_list(int position)
Method to remove by position from CompositeSequence_list


removeFromCompositeSequence_list

public void removeFromCompositeSequence_list(CompositeSequence compositeSequence)
Method to remove first CompositeSequence from CompositeSequence_list


setCompositeCompositeMap_list

public void setCompositeCompositeMap_list(DesignElement_package.CompositeCompositeMap_list compositeCompositeMap_list)
Set method for compositeCompositeMap_list


getCompositeCompositeMap_list

public DesignElement_package.CompositeCompositeMap_list getCompositeCompositeMap_list()
Get method for compositeCompositeMap_list


addToCompositeCompositeMap_list

public void addToCompositeCompositeMap_list(CompositeCompositeMap compositeCompositeMap)
Method to add CompositeCompositeMap to CompositeCompositeMap_list


addToCompositeCompositeMap_list

public void addToCompositeCompositeMap_list(int position,
                                            CompositeCompositeMap compositeCompositeMap)
Method to add CompositeCompositeMap at position to CompositeCompositeMap_list


getFromCompositeCompositeMap_list

public CompositeCompositeMap getFromCompositeCompositeMap_list(int position)
Method to get CompositeCompositeMap from CompositeCompositeMap_list


removeElementAtFromCompositeCompositeMap_list

public void removeElementAtFromCompositeCompositeMap_list(int position)
Method to remove by position from CompositeCompositeMap_list


removeFromCompositeCompositeMap_list

public void removeFromCompositeCompositeMap_list(CompositeCompositeMap compositeCompositeMap)
Method to remove first CompositeCompositeMap from CompositeCompositeMap_list


setFeatureReporterMap_list

public void setFeatureReporterMap_list(DesignElement_package.FeatureReporterMap_list featureReporterMap_list)
Set method for featureReporterMap_list


getFeatureReporterMap_list

public DesignElement_package.FeatureReporterMap_list getFeatureReporterMap_list()
Get method for featureReporterMap_list


addToFeatureReporterMap_list

public void addToFeatureReporterMap_list(FeatureReporterMap featureReporterMap)
Method to add FeatureReporterMap to FeatureReporterMap_list


addToFeatureReporterMap_list

public void addToFeatureReporterMap_list(int position,
                                         FeatureReporterMap featureReporterMap)
Method to add FeatureReporterMap at position to FeatureReporterMap_list


getFromFeatureReporterMap_list

public FeatureReporterMap getFromFeatureReporterMap_list(int position)
Method to get FeatureReporterMap from FeatureReporterMap_list


removeElementAtFromFeatureReporterMap_list

public void removeElementAtFromFeatureReporterMap_list(int position)
Method to remove by position from FeatureReporterMap_list


removeFromFeatureReporterMap_list

public void removeFromFeatureReporterMap_list(FeatureReporterMap featureReporterMap)
Method to remove first FeatureReporterMap from FeatureReporterMap_list


setReporterCompositeMap_list

public void setReporterCompositeMap_list(DesignElement_package.ReporterCompositeMap_list reporterCompositeMap_list)
Set method for reporterCompositeMap_list


getReporterCompositeMap_list

public DesignElement_package.ReporterCompositeMap_list getReporterCompositeMap_list()
Get method for reporterCompositeMap_list


addToReporterCompositeMap_list

public void addToReporterCompositeMap_list(ReporterCompositeMap reporterCompositeMap)
Method to add ReporterCompositeMap to ReporterCompositeMap_list


addToReporterCompositeMap_list

public void addToReporterCompositeMap_list(int position,
                                           ReporterCompositeMap reporterCompositeMap)
Method to add ReporterCompositeMap at position to ReporterCompositeMap_list


getFromReporterCompositeMap_list

public ReporterCompositeMap getFromReporterCompositeMap_list(int position)
Method to get ReporterCompositeMap from ReporterCompositeMap_list


removeElementAtFromReporterCompositeMap_list

public void removeElementAtFromReporterCompositeMap_list(int position)
Method to remove by position from ReporterCompositeMap_list


removeFromReporterCompositeMap_list

public void removeFromReporterCompositeMap_list(ReporterCompositeMap reporterCompositeMap)
Method to remove first ReporterCompositeMap from ReporterCompositeMap_list