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org.biomage.Experiment
Class Experiment_package  view Experiment_package download Experiment_package.java

java.lang.Object
  extended byorg.biomage.Experiment.Experiment_package
All Implemented Interfaces:
java.io.Serializable

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

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.


Nested Class Summary
 class Experiment_package.Experiment_list
          Inner list class for holding multiple entries for attribute experiment_list.
 
Field Summary
 Experiment_package.Experiment_list experiment_list
          The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
 
Constructor Summary
Experiment_package()
          Default constructor.
Experiment_package(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToExperiment_list(Experiment experiment)
          Method to add Experiment to Experiment_list
 void addToExperiment_list(int position, Experiment experiment)
          Method to add Experiment at position to Experiment_list
 Experiment_package.Experiment_list getExperiment_list()
          Get method for experiment_list
 Experiment getFromExperiment_list(int position)
          Method to get Experiment from Experiment_list
 void removeElementAtFromExperiment_list(int position)
          Method to remove by position from Experiment_list
 void removeFromExperiment_list(Experiment experiment)
          Method to remove first Experiment from Experiment_list
 void setExperiment_list(Experiment_package.Experiment_list experiment_list)
          Set method for experiment_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

experiment_list

public Experiment_package.Experiment_list experiment_list
The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.

Constructor Detail

Experiment_package

public Experiment_package()
Default constructor.


Experiment_package

public Experiment_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.


setExperiment_list

public void setExperiment_list(Experiment_package.Experiment_list experiment_list)
Set method for experiment_list


getExperiment_list

public Experiment_package.Experiment_list getExperiment_list()
Get method for experiment_list


addToExperiment_list

public void addToExperiment_list(Experiment experiment)
Method to add Experiment to Experiment_list


addToExperiment_list

public void addToExperiment_list(int position,
                                 Experiment experiment)
Method to add Experiment at position to Experiment_list


getFromExperiment_list

public Experiment getFromExperiment_list(int position)
Method to get Experiment from Experiment_list


removeElementAtFromExperiment_list

public void removeElementAtFromExperiment_list(int position)
Method to remove by position from Experiment_list


removeFromExperiment_list

public void removeFromExperiment_list(Experiment experiment)
Method to remove first Experiment from Experiment_list