org.biomage.BioAssayData
Class CompositeSequenceDimension

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioAssayData.DesignElementDimension
                          |
                          +--org.biomage.BioAssayData.CompositeSequenceDimension

All Implemented Interfaces:

HasAuditTrail, HasCompositeSequences, HasDescriptions, HasPropertySets, HasSecurity, java.io.Serializable

public class CompositeSequenceDimension

extends DesignElementDimension

implements java.io.Serializable, HasCompositeSequences

Specialized DesignElementDimension to hold CompositeSequences.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasCompositeSequences

HasCompositeSequences.CompositeSequences_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected HasCompositeSequences.CompositeSequences_list

compositeSequences The CompositeSequences for this Dimension.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

CompositeSequenceDimension()
Default constructor.

CompositeSequenceDimension(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

void	addToCompositeSequences(CompositeSequence compositeSequence) Method to add CompositeSequence to CompositeSequences_list
void	addToCompositeSequences(int position, CompositeSequence compositeSequence) Method to add CompositeSequence at position to CompositeSequences_list
HasCompositeSequences.CompositeSequences_list	getCompositeSequences() Get method for compositeSequences
CompositeSequence	getFromCompositeSequences(int position) Method to get CompositeSequence from CompositeSequences_list
void	removeElementAtFromCompositeSequences(int position) Method to remove by position from CompositeSequences_list
void	removeFromCompositeSequences(CompositeSequence compositeSequence) Method to remove first CompositeSequence from CompositeSequences_list
void	setCompositeSequences(HasCompositeSequences.CompositeSequences_list compositeSequences) Set method for compositeSequences
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 org.biomage.Common.Identifiable

getIdentifier, getName, setIdentifier, setName

Methods inherited from class org.biomage.Common.Describable

addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity

Methods inherited from class org.biomage.Common.Extendable

addToPropertySets, addToPropertySets, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

compositeSequences

protected HasCompositeSequences.CompositeSequences_list compositeSequences

The CompositeSequences for this Dimension.

Constructor Detail

CompositeSequenceDimension

public CompositeSequenceDimension()

Default constructor.

CompositeSequenceDimension

public CompositeSequenceDimension(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.

Overrides:

writeMAGEML in class DesignElementDimension

java.io.IOException

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.

Overrides:

writeAttributes in class DesignElementDimension

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.

Overrides:

writeAssociations in class DesignElementDimension

java.io.IOException

setCompositeSequences

public void setCompositeSequences(HasCompositeSequences.CompositeSequences_list compositeSequences)

Set method for compositeSequences

Specified by:

setCompositeSequences in interface HasCompositeSequences

getCompositeSequences

public HasCompositeSequences.CompositeSequences_list getCompositeSequences()

Get method for compositeSequences

Specified by:

getCompositeSequences in interface HasCompositeSequences

Returns:

value of the attribute

addToCompositeSequences

public void addToCompositeSequences(CompositeSequence compositeSequence)

Method to add CompositeSequence to CompositeSequences_list

Specified by:

addToCompositeSequences in interface HasCompositeSequences

addToCompositeSequences

public void addToCompositeSequences(int position,
                                    CompositeSequence compositeSequence)

Method to add CompositeSequence at position to CompositeSequences_list

Specified by:

addToCompositeSequences in interface HasCompositeSequences

getFromCompositeSequences

public CompositeSequence getFromCompositeSequences(int position)

Method to get CompositeSequence from CompositeSequences_list

Specified by:

getFromCompositeSequences in interface HasCompositeSequences

removeElementAtFromCompositeSequences

public void removeElementAtFromCompositeSequences(int position)

Method to remove by position from CompositeSequences_list

Specified by:

removeElementAtFromCompositeSequences in interface HasCompositeSequences

removeFromCompositeSequences

public void removeFromCompositeSequences(CompositeSequence compositeSequence)

Method to remove first CompositeSequence from CompositeSequences_list

Specified by:

removeFromCompositeSequences in interface HasCompositeSequences