org.biomage.ArrayDesign
Class ArrayDesign_package

java.lang.Object
  extended by org.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.

See Also:
Serialized Form

Nested Class Summary
 class ArrayDesign_package.ArrayDesign_list
          Inner list class for holding multiple entries for attribute arrayDesign.
 class ArrayDesign_package.CompositeGroup_list
          Inner list class for holding multiple entries for attribute compositeGroup.
 class ArrayDesign_package.ReporterGroup_list
          Inner list class for holding multiple entries for attribute reporterGroup.
 
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.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 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
 boolean emptyMAGEobject()
           
 ArrayDesign_package.ArrayDesign_list getArrayDesign_list()
          Get method for arrayDesign_list
 ArrayDesign_package.CompositeGroup_list getCompositeGroup_list()
          Get method for compositeGroup_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
 ReporterGroup getFromReporterGroup_list(int position)
          Method to get ReporterGroup from ReporterGroup_list
 java.lang.String getModelClassName()
           
 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 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 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 setReporterGroup_list(ArrayDesign_package.ReporterGroup_list reporterGroup_list)
          Set method for reporterGroup_list
 void writeAssociations(java.io.Writer out)
          writeAssociations This method is responsible for assembling the association data into XML.
 void writeAttributes(java.io.Writer out)
          writeAttributes This method is responsible for assembling the attribute data into XML.
 void writeMAGEML(java.io.Writer out)
          writeMAGEML This method is responsible for assembling the attribute and association data into XML.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

reporterGroup_list

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


compositeGroup_list

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


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.

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

Parameters:
atts: - the attribute list.
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.

Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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.

Throws:
java.io.IOException

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.

Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()

setReporterGroup_list

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

Parameters:
value - to set

getReporterGroup_list

public ArrayDesign_package.ReporterGroup_list getReporterGroup_list()
Get method for reporterGroup_list

Returns:
value of the attribute

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


setCompositeGroup_list

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

Parameters:
value - to set

getCompositeGroup_list

public ArrayDesign_package.CompositeGroup_list getCompositeGroup_list()
Get method for compositeGroup_list

Returns:
value of the attribute

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


setArrayDesign_list

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

Parameters:
value - to set

getArrayDesign_list

public ArrayDesign_package.ArrayDesign_list getArrayDesign_list()
Get method for arrayDesign_list

Returns:
value of the attribute

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