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org.biomage.BioSequence
Class BioSequence_package  

java.lang.Object
  org.biomage.BioSequence.BioSequence_package

All Implemented Interfaces:

java.io.Serializable

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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.

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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.

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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.

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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.

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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.

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setBioSequence_list

public void setBioSequence_list(BioSequence_package.BioSequence_list bioSequence_list)

Set method for bioSequence_list

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getBioSequence_list

public BioSequence_package.BioSequence_list getBioSequence_list()

Get method for bioSequence_list

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addToBioSequence_list

public void addToBioSequence_list(BioSequence bioSequence)

Method to add BioSequence to BioSequence_list

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addToBioSequence_list

public void addToBioSequence_list(int position,
                                  BioSequence bioSequence)

Method to add BioSequence at position to BioSequence_list

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getFromBioSequence_list

public BioSequence getFromBioSequence_list(int position)

Method to get BioSequence from BioSequence_list

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removeElementAtFromBioSequence_list

public void removeElementAtFromBioSequence_list(int position)

Method to remove by position from BioSequence_list

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removeFromBioSequence_list

public void removeFromBioSequence_list(BioSequence bioSequence)

Method to remove first BioSequence from BioSequence_list

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioSequence overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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