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org.biomage.BioSequence
Class BioSequence_package  view BioSequence_package download BioSequence_package.java

java.lang.Object
  extended byorg.biomage.BioSequence.BioSequence_package
All Implemented Interfaces:
java.io.Serializable

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

Describes a known gene or sequence. BioAssays typically seek to identify what BioSequences are expressed in a BioMaterial after treatments, the expression level measured from the association between the BioMaterial and the Array. The Array's Features typically provide known locations for this association to occur. Most often, the Reporter and CompositeSequence are known and the presence or absence of a particular BioSequence in the BioMaterial is based on whether there as been an association to the DesignElement targeted for it. Some other experiments may not know the DesignElement's target but can discover it with known properties of the BioSequences in the BioMaterial.


Nested Class Summary
 class BioSequence_package.BioSequence_list
          Inner list class for holding multiple entries for attribute bioSequence_list.
 
Field Summary
 BioSequence_package.BioSequence_list bioSequence_list
          A BioSequence is a representation of a DNA, RNA, or protein sequence.
 
Constructor Summary
BioSequence_package()
          Default constructor.
BioSequence_package(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioSequence_list(BioSequence bioSequence)
          Method to add BioSequence to BioSequence_list
 void addToBioSequence_list(int position, BioSequence bioSequence)
          Method to add BioSequence at position to BioSequence_list
 BioSequence_package.BioSequence_list getBioSequence_list()
          Get method for bioSequence_list
 BioSequence getFromBioSequence_list(int position)
          Method to get BioSequence from BioSequence_list
 void removeElementAtFromBioSequence_list(int position)
          Method to remove by position from BioSequence_list
 void removeFromBioSequence_list(BioSequence bioSequence)
          Method to remove first BioSequence from BioSequence_list
 void setBioSequence_list(BioSequence_package.BioSequence_list bioSequence_list)
          Set method for bioSequence_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

bioSequence_list

public BioSequence_package.BioSequence_list bioSequence_list
A BioSequence is a representation of a DNA, RNA, or protein sequence. It can be represented by a Clone, Gene, or the sequence.

Constructor Detail

BioSequence_package

public BioSequence_package()
Default constructor.


BioSequence_package

public BioSequence_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.


setBioSequence_list

public void setBioSequence_list(BioSequence_package.BioSequence_list bioSequence_list)
Set method for bioSequence_list


getBioSequence_list

public BioSequence_package.BioSequence_list getBioSequence_list()
Get method for bioSequence_list


addToBioSequence_list

public void addToBioSequence_list(BioSequence bioSequence)
Method to add BioSequence to BioSequence_list


addToBioSequence_list

public void addToBioSequence_list(int position,
                                  BioSequence bioSequence)
Method to add BioSequence at position to BioSequence_list


getFromBioSequence_list

public BioSequence getFromBioSequence_list(int position)
Method to get BioSequence from BioSequence_list


removeElementAtFromBioSequence_list

public void removeElementAtFromBioSequence_list(int position)
Method to remove by position from BioSequence_list


removeFromBioSequence_list

public void removeFromBioSequence_list(BioSequence bioSequence)
Method to remove first BioSequence from BioSequence_list