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org.biomage.ArrayDesign
Class ArrayDesign_package  view ArrayDesign_package download ArrayDesign_package.java

java.lang.Object
  extended byorg.biomage.ArrayDesign.ArrayDesign_package
All Implemented Interfaces:
java.io.Serializable

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

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.


Nested Class Summary
 class ArrayDesign_package.ArrayDesign_list
          Inner list class for holding multiple entries for attribute arrayDesign_list.
 class ArrayDesign_package.CompositeGroup_list
          Inner list class for holding multiple entries for attribute compositeGroup_list.
 class ArrayDesign_package.DesignElementGroup_list
          Inner list class for holding multiple entries for attribute designElementGroup_list.
 class ArrayDesign_package.PhysicalArrayDesign_list
          Inner list class for holding multiple entries for attribute physicalArrayDesign_list.
 class ArrayDesign_package.ReporterGroup_list
          Inner list class for holding multiple entries for attribute reporterGroup_list.
 
Field Summary
 ArrayDesign_package.ArrayDesign_list arrayDesign_list
          Describes the design of an gene expression layout.
 ArrayDesign_package.CompositeGroup_list compositeGroup_list
          Allows specification of the type of Composite Design Element.
 ArrayDesign_package.DesignElementGroup_list designElementGroup_list
          The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.
 ArrayDesign_package.PhysicalArrayDesign_list physicalArrayDesign_list
          A design that is expected to be used to manufacture physical arrays.
 ArrayDesign_package.ReporterGroup_list reporterGroup_list
          Allows specification of the type of Reporter Design Element.
 
Constructor Summary
ArrayDesign_package()
          Default constructor.
ArrayDesign_package(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToArrayDesign_list(ArrayDesign arrayDesign)
          Method to add ArrayDesign to ArrayDesign_list
 void addToArrayDesign_list(int position, ArrayDesign arrayDesign)
          Method to add ArrayDesign at position to ArrayDesign_list
 void addToCompositeGroup_list(CompositeGroup compositeGroup)
          Method to add CompositeGroup to CompositeGroup_list
 void addToCompositeGroup_list(int position, CompositeGroup compositeGroup)
          Method to add CompositeGroup at position to CompositeGroup_list
 void addToDesignElementGroup_list(DesignElementGroup designElementGroup)
          Method to add DesignElementGroup to DesignElementGroup_list
 void addToDesignElementGroup_list(int position, DesignElementGroup designElementGroup)
          Method to add DesignElementGroup at position to DesignElementGroup_list
 void addToPhysicalArrayDesign_list(int position, PhysicalArrayDesign physicalArrayDesign)
          Method to add PhysicalArrayDesign at position to PhysicalArrayDesign_list
 void addToPhysicalArrayDesign_list(PhysicalArrayDesign physicalArrayDesign)
          Method to add PhysicalArrayDesign to PhysicalArrayDesign_list
 void addToReporterGroup_list(int position, ReporterGroup reporterGroup)
          Method to add ReporterGroup at position to ReporterGroup_list
 void addToReporterGroup_list(ReporterGroup reporterGroup)
          Method to add ReporterGroup to ReporterGroup_list
 ArrayDesign_package.ArrayDesign_list getArrayDesign_list()
          Get method for arrayDesign_list
 ArrayDesign_package.CompositeGroup_list getCompositeGroup_list()
          Get method for compositeGroup_list
 ArrayDesign_package.DesignElementGroup_list getDesignElementGroup_list()
          Get method for designElementGroup_list
 ArrayDesign getFromArrayDesign_list(int position)
          Method to get ArrayDesign from ArrayDesign_list
 CompositeGroup getFromCompositeGroup_list(int position)
          Method to get CompositeGroup from CompositeGroup_list
 DesignElementGroup getFromDesignElementGroup_list(int position)
          Method to get DesignElementGroup from DesignElementGroup_list
 PhysicalArrayDesign getFromPhysicalArrayDesign_list(int position)
          Method to get PhysicalArrayDesign from PhysicalArrayDesign_list
 ReporterGroup getFromReporterGroup_list(int position)
          Method to get ReporterGroup from ReporterGroup_list
 ArrayDesign_package.PhysicalArrayDesign_list getPhysicalArrayDesign_list()
          Get method for physicalArrayDesign_list
 ArrayDesign_package.ReporterGroup_list getReporterGroup_list()
          Get method for reporterGroup_list
 void removeElementAtFromArrayDesign_list(int position)
          Method to remove by position from ArrayDesign_list
 void removeElementAtFromCompositeGroup_list(int position)
          Method to remove by position from CompositeGroup_list
 void removeElementAtFromDesignElementGroup_list(int position)
          Method to remove by position from DesignElementGroup_list
 void removeElementAtFromPhysicalArrayDesign_list(int position)
          Method to remove by position from PhysicalArrayDesign_list
 void removeElementAtFromReporterGroup_list(int position)
          Method to remove by position from ReporterGroup_list
 void removeFromArrayDesign_list(ArrayDesign arrayDesign)
          Method to remove first ArrayDesign from ArrayDesign_list
 void removeFromCompositeGroup_list(CompositeGroup compositeGroup)
          Method to remove first CompositeGroup from CompositeGroup_list
 void removeFromDesignElementGroup_list(DesignElementGroup designElementGroup)
          Method to remove first DesignElementGroup from DesignElementGroup_list
 void removeFromPhysicalArrayDesign_list(PhysicalArrayDesign physicalArrayDesign)
          Method to remove first PhysicalArrayDesign from PhysicalArrayDesign_list
 void removeFromReporterGroup_list(ReporterGroup reporterGroup)
          Method to remove first ReporterGroup from ReporterGroup_list
 void setArrayDesign_list(ArrayDesign_package.ArrayDesign_list arrayDesign_list)
          Set method for arrayDesign_list
 void setCompositeGroup_list(ArrayDesign_package.CompositeGroup_list compositeGroup_list)
          Set method for compositeGroup_list
 void setDesignElementGroup_list(ArrayDesign_package.DesignElementGroup_list designElementGroup_list)
          Set method for designElementGroup_list
 void setPhysicalArrayDesign_list(ArrayDesign_package.PhysicalArrayDesign_list physicalArrayDesign_list)
          Set method for physicalArrayDesign_list
 void setReporterGroup_list(ArrayDesign_package.ReporterGroup_list reporterGroup_list)
          Set method for reporterGroup_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

arrayDesign_list

public ArrayDesign_package.ArrayDesign_list arrayDesign_list
Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features.


physicalArrayDesign_list

public ArrayDesign_package.PhysicalArrayDesign_list physicalArrayDesign_list
A design that is expected to be used to manufacture physical arrays.


reporterGroup_list

public ArrayDesign_package.ReporterGroup_list reporterGroup_list
Allows specification of the type of Reporter Design Element.


designElementGroup_list

public ArrayDesign_package.DesignElementGroup_list designElementGroup_list
The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.


compositeGroup_list

public ArrayDesign_package.CompositeGroup_list compositeGroup_list
Allows specification of the type of Composite Design Element.

Constructor Detail

ArrayDesign_package

public ArrayDesign_package()
Default constructor.


ArrayDesign_package

public ArrayDesign_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.


setArrayDesign_list

public void setArrayDesign_list(ArrayDesign_package.ArrayDesign_list arrayDesign_list)
Set method for arrayDesign_list


getArrayDesign_list

public ArrayDesign_package.ArrayDesign_list getArrayDesign_list()
Get method for arrayDesign_list


addToArrayDesign_list

public void addToArrayDesign_list(ArrayDesign arrayDesign)
Method to add ArrayDesign to ArrayDesign_list


addToArrayDesign_list

public void addToArrayDesign_list(int position,
                                  ArrayDesign arrayDesign)
Method to add ArrayDesign at position to ArrayDesign_list


getFromArrayDesign_list

public ArrayDesign getFromArrayDesign_list(int position)
Method to get ArrayDesign from ArrayDesign_list


removeElementAtFromArrayDesign_list

public void removeElementAtFromArrayDesign_list(int position)
Method to remove by position from ArrayDesign_list


removeFromArrayDesign_list

public void removeFromArrayDesign_list(ArrayDesign arrayDesign)
Method to remove first ArrayDesign from ArrayDesign_list


setPhysicalArrayDesign_list

public void setPhysicalArrayDesign_list(ArrayDesign_package.PhysicalArrayDesign_list physicalArrayDesign_list)
Set method for physicalArrayDesign_list


getPhysicalArrayDesign_list

public ArrayDesign_package.PhysicalArrayDesign_list getPhysicalArrayDesign_list()
Get method for physicalArrayDesign_list


addToPhysicalArrayDesign_list

public void addToPhysicalArrayDesign_list(PhysicalArrayDesign physicalArrayDesign)
Method to add PhysicalArrayDesign to PhysicalArrayDesign_list


addToPhysicalArrayDesign_list

public void addToPhysicalArrayDesign_list(int position,
                                          PhysicalArrayDesign physicalArrayDesign)
Method to add PhysicalArrayDesign at position to PhysicalArrayDesign_list


getFromPhysicalArrayDesign_list

public PhysicalArrayDesign getFromPhysicalArrayDesign_list(int position)
Method to get PhysicalArrayDesign from PhysicalArrayDesign_list


removeElementAtFromPhysicalArrayDesign_list

public void removeElementAtFromPhysicalArrayDesign_list(int position)
Method to remove by position from PhysicalArrayDesign_list


removeFromPhysicalArrayDesign_list

public void removeFromPhysicalArrayDesign_list(PhysicalArrayDesign physicalArrayDesign)
Method to remove first PhysicalArrayDesign from PhysicalArrayDesign_list


setReporterGroup_list

public void setReporterGroup_list(ArrayDesign_package.ReporterGroup_list reporterGroup_list)
Set method for reporterGroup_list


getReporterGroup_list

public ArrayDesign_package.ReporterGroup_list getReporterGroup_list()
Get method for reporterGroup_list


addToReporterGroup_list

public void addToReporterGroup_list(ReporterGroup reporterGroup)
Method to add ReporterGroup to ReporterGroup_list


addToReporterGroup_list

public void addToReporterGroup_list(int position,
                                    ReporterGroup reporterGroup)
Method to add ReporterGroup at position to ReporterGroup_list


getFromReporterGroup_list

public ReporterGroup getFromReporterGroup_list(int position)
Method to get ReporterGroup from ReporterGroup_list


removeElementAtFromReporterGroup_list

public void removeElementAtFromReporterGroup_list(int position)
Method to remove by position from ReporterGroup_list


removeFromReporterGroup_list

public void removeFromReporterGroup_list(ReporterGroup reporterGroup)
Method to remove first ReporterGroup from ReporterGroup_list


setDesignElementGroup_list

public void setDesignElementGroup_list(ArrayDesign_package.DesignElementGroup_list designElementGroup_list)
Set method for designElementGroup_list


getDesignElementGroup_list

public ArrayDesign_package.DesignElementGroup_list getDesignElementGroup_list()
Get method for designElementGroup_list


addToDesignElementGroup_list

public void addToDesignElementGroup_list(DesignElementGroup designElementGroup)
Method to add DesignElementGroup to DesignElementGroup_list


addToDesignElementGroup_list

public void addToDesignElementGroup_list(int position,
                                         DesignElementGroup designElementGroup)
Method to add DesignElementGroup at position to DesignElementGroup_list


getFromDesignElementGroup_list

public DesignElementGroup getFromDesignElementGroup_list(int position)
Method to get DesignElementGroup from DesignElementGroup_list


removeElementAtFromDesignElementGroup_list

public void removeElementAtFromDesignElementGroup_list(int position)
Method to remove by position from DesignElementGroup_list


removeFromDesignElementGroup_list

public void removeFromDesignElementGroup_list(DesignElementGroup designElementGroup)
Method to remove first DesignElementGroup from DesignElementGroup_list


setCompositeGroup_list

public void setCompositeGroup_list(ArrayDesign_package.CompositeGroup_list compositeGroup_list)
Set method for compositeGroup_list


getCompositeGroup_list

public ArrayDesign_package.CompositeGroup_list getCompositeGroup_list()
Get method for compositeGroup_list


addToCompositeGroup_list

public void addToCompositeGroup_list(CompositeGroup compositeGroup)
Method to add CompositeGroup to CompositeGroup_list


addToCompositeGroup_list

public void addToCompositeGroup_list(int position,
                                     CompositeGroup compositeGroup)
Method to add CompositeGroup at position to CompositeGroup_list


getFromCompositeGroup_list

public CompositeGroup getFromCompositeGroup_list(int position)
Method to get CompositeGroup from CompositeGroup_list


removeElementAtFromCompositeGroup_list

public void removeElementAtFromCompositeGroup_list(int position)
Method to remove by position from CompositeGroup_list


removeFromCompositeGroup_list

public void removeFromCompositeGroup_list(CompositeGroup compositeGroup)
Method to remove first CompositeGroup from CompositeGroup_list