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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:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasCompositeSequences, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable

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public class CompositeSequenceDimension

extends DesignElementDimension

implements java.io.Serializable, org.biomage.Interface.HasCompositeSequences

Specialized DesignElementDimension to hold CompositeSequences.

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Nested Class Summary

 

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

org.biomage.Interface.HasCompositeSequences.CompositeSequences_list

 

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

org.biomage.Interface.HasAuditTrail.AuditTrail_list

 

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

org.biomage.Interface.HasDescriptions.Descriptions_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  org.biomage.Interface.HasCompositeSequences.CompositeSequences_list	compositeSequences           The CompositeSequences for this Dimension.

 

Fields inherited from class org.biomage.Common.Identifiable

 

Fields inherited from class org.biomage.Common.Describable

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

CompositeSequenceDimension()           Default constructor.

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

 

Method Summary
void	addToCompositeSequences(org.biomage.DesignElement.CompositeSequence compositeSequence)           Method to add CompositeSequence to CompositeSequences_list
void	addToCompositeSequences(int position, org.biomage.DesignElement.CompositeSequence compositeSequence)           Method to add CompositeSequence at position to CompositeSequences_list
org.biomage.Interface.HasCompositeSequences.CompositeSequences_list	getCompositeSequences()           Get method for compositeSequences
org.biomage.DesignElement.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(org.biomage.DesignElement.CompositeSequence compositeSequence)           Method to remove first CompositeSequence from CompositeSequences_list
void	setCompositeSequences(org.biomage.Interface.HasCompositeSequences.CompositeSequences_list compositeSequences)           Set method for compositeSequences
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 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

private org.biomage.Interface.HasCompositeSequences.CompositeSequences_list compositeSequences

The CompositeSequences for this Dimension.

Constructor Detail

CompositeSequenceDimension

public CompositeSequenceDimension()

Default constructor.

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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

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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.

Overrides:

writeAttributes in class DesignElementDimension

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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.

Overrides:

writeAssociations in class DesignElementDimension

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setCompositeSequences

public void setCompositeSequences(org.biomage.Interface.HasCompositeSequences.CompositeSequences_list compositeSequences)

Set method for compositeSequences

Specified by:

setCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

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getCompositeSequences

public org.biomage.Interface.HasCompositeSequences.CompositeSequences_list getCompositeSequences()

Get method for compositeSequences

Specified by:

getCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

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addToCompositeSequences

public void addToCompositeSequences(org.biomage.DesignElement.CompositeSequence compositeSequence)

Method to add CompositeSequence to CompositeSequences_list

Specified by:

addToCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

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addToCompositeSequences

public void addToCompositeSequences(int position,
                                    org.biomage.DesignElement.CompositeSequence compositeSequence)

Method to add CompositeSequence at position to CompositeSequences_list

Specified by:

addToCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

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getFromCompositeSequences

public org.biomage.DesignElement.CompositeSequence getFromCompositeSequences(int position)

Method to get CompositeSequence from CompositeSequences_list

Specified by:

getFromCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

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removeElementAtFromCompositeSequences

public void removeElementAtFromCompositeSequences(int position)

Method to remove by position from CompositeSequences_list

Specified by:

removeElementAtFromCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

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removeFromCompositeSequences

public void removeFromCompositeSequences(org.biomage.DesignElement.CompositeSequence compositeSequence)

Method to remove first CompositeSequence from CompositeSequences_list

Specified by:

removeFromCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

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

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