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org.biomage.DesignElement
Class CompositeSequence  view CompositeSequence download CompositeSequence.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.DesignElement.DesignElement
                  extended byorg.biomage.DesignElement.CompositeSequence
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBiologicalCharacteristics, org.biomage.Interface.HasCompositeCompositeMaps, org.biomage.Interface.HasControlType, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasReporterCompositeMaps, org.biomage.Interface.HasSecurity, java.io.Serializable

public class CompositeSequence
extends DesignElement
implements java.io.Serializable, org.biomage.Interface.HasBiologicalCharacteristics, org.biomage.Interface.HasReporterCompositeMaps, org.biomage.Interface.HasCompositeCompositeMaps

A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasBiologicalCharacteristics
org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list
 
Nested classes inherited from class org.biomage.Interface.HasReporterCompositeMaps
org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list
 
Nested classes inherited from class org.biomage.Interface.HasCompositeCompositeMaps
org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_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.HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics
          The annotation on the BioSequence this CompositeSequence represents.
private  org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps
          A map to the compositeSequences that compose this CompositeSequence.
private  org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps
          A map to the reporters that compose this CompositeSequence.
 
Fields inherited from class org.biomage.DesignElement.DesignElement
 
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
CompositeSequence()
          Default constructor.
CompositeSequence(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBiologicalCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)
          Method to add BioSequence to BiologicalCharacteristics_list
 void addToBiologicalCharacteristics(int position, org.biomage.BioSequence.BioSequence bioSequence)
          Method to add BioSequence at position to BiologicalCharacteristics_list
 void addToCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
          Method to add CompositeCompositeMap to CompositeCompositeMaps_list
 void addToCompositeCompositeMaps(int position, CompositeCompositeMap compositeCompositeMap)
          Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list
 void addToReporterCompositeMaps(int position, ReporterCompositeMap reporterCompositeMap)
          Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list
 void addToReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
          Method to add ReporterCompositeMap to ReporterCompositeMaps_list
 org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list getBiologicalCharacteristics()
          Get method for biologicalCharacteristics
 org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list getCompositeCompositeMaps()
          Get method for compositeCompositeMaps
 org.biomage.BioSequence.BioSequence getFromBiologicalCharacteristics(int position)
          Method to get BioSequence from BiologicalCharacteristics_list
 CompositeCompositeMap getFromCompositeCompositeMaps(int position)
          Method to get CompositeCompositeMap from CompositeCompositeMaps_list
 ReporterCompositeMap getFromReporterCompositeMaps(int position)
          Method to get ReporterCompositeMap from ReporterCompositeMaps_list
 org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list getReporterCompositeMaps()
          Get method for reporterCompositeMaps
 void removeElementAtFromBiologicalCharacteristics(int position)
          Method to remove by position from BiologicalCharacteristics_list
 void removeElementAtFromCompositeCompositeMaps(int position)
          Method to remove by position from CompositeCompositeMaps_list
 void removeElementAtFromReporterCompositeMaps(int position)
          Method to remove by position from ReporterCompositeMaps_list
 void removeFromBiologicalCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)
          Method to remove first BioSequence from BiologicalCharacteristics_list
 void removeFromCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
          Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list
 void removeFromReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
          Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list
 void setBiologicalCharacteristics(org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics)
          Set method for biologicalCharacteristics
 void setCompositeCompositeMaps(org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps)
          Set method for compositeCompositeMaps
 void setReporterCompositeMaps(org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps)
          Set method for reporterCompositeMaps
 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.DesignElement.DesignElement
getControlType, setControlType
 
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

biologicalCharacteristics

private org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics
The annotation on the BioSequence this CompositeSequence represents. Typically the sequences will be a Genes, Exons, or SpliceVariants.


reporterCompositeMaps

private org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps
A map to the reporters that compose this CompositeSequence.


compositeCompositeMaps

private org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps
A map to the compositeSequences that compose this CompositeSequence.

Constructor Detail

CompositeSequence

public CompositeSequence()
Default constructor.


CompositeSequence

public CompositeSequence(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 DesignElement

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 DesignElement

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 DesignElement

setBiologicalCharacteristics

public void setBiologicalCharacteristics(org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics)
Set method for biologicalCharacteristics

Specified by:
setBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

getBiologicalCharacteristics

public org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list getBiologicalCharacteristics()
Get method for biologicalCharacteristics

Specified by:
getBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

addToBiologicalCharacteristics

public void addToBiologicalCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)
Method to add BioSequence to BiologicalCharacteristics_list

Specified by:
addToBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

addToBiologicalCharacteristics

public void addToBiologicalCharacteristics(int position,
                                           org.biomage.BioSequence.BioSequence bioSequence)
Method to add BioSequence at position to BiologicalCharacteristics_list

Specified by:
addToBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

getFromBiologicalCharacteristics

public org.biomage.BioSequence.BioSequence getFromBiologicalCharacteristics(int position)
Method to get BioSequence from BiologicalCharacteristics_list

Specified by:
getFromBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

removeElementAtFromBiologicalCharacteristics

public void removeElementAtFromBiologicalCharacteristics(int position)
Method to remove by position from BiologicalCharacteristics_list

Specified by:
removeElementAtFromBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

removeFromBiologicalCharacteristics

public void removeFromBiologicalCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)
Method to remove first BioSequence from BiologicalCharacteristics_list

Specified by:
removeFromBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

setReporterCompositeMaps

public void setReporterCompositeMaps(org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps)
Set method for reporterCompositeMaps

Specified by:
setReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

getReporterCompositeMaps

public org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list getReporterCompositeMaps()
Get method for reporterCompositeMaps

Specified by:
getReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

addToReporterCompositeMaps

public void addToReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
Method to add ReporterCompositeMap to ReporterCompositeMaps_list

Specified by:
addToReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

addToReporterCompositeMaps

public void addToReporterCompositeMaps(int position,
                                       ReporterCompositeMap reporterCompositeMap)
Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list

Specified by:
addToReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

getFromReporterCompositeMaps

public ReporterCompositeMap getFromReporterCompositeMaps(int position)
Method to get ReporterCompositeMap from ReporterCompositeMaps_list

Specified by:
getFromReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

removeElementAtFromReporterCompositeMaps

public void removeElementAtFromReporterCompositeMaps(int position)
Method to remove by position from ReporterCompositeMaps_list

Specified by:
removeElementAtFromReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

removeFromReporterCompositeMaps

public void removeFromReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list

Specified by:
removeFromReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

setCompositeCompositeMaps

public void setCompositeCompositeMaps(org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps)
Set method for compositeCompositeMaps

Specified by:
setCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

getCompositeCompositeMaps

public org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list getCompositeCompositeMaps()
Get method for compositeCompositeMaps

Specified by:
getCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

addToCompositeCompositeMaps

public void addToCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
Method to add CompositeCompositeMap to CompositeCompositeMaps_list

Specified by:
addToCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

addToCompositeCompositeMaps

public void addToCompositeCompositeMaps(int position,
                                        CompositeCompositeMap compositeCompositeMap)
Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list

Specified by:
addToCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

getFromCompositeCompositeMaps

public CompositeCompositeMap getFromCompositeCompositeMaps(int position)
Method to get CompositeCompositeMap from CompositeCompositeMaps_list

Specified by:
getFromCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

removeElementAtFromCompositeCompositeMaps

public void removeElementAtFromCompositeCompositeMaps(int position)
Method to remove by position from CompositeCompositeMaps_list

Specified by:
removeElementAtFromCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

removeFromCompositeCompositeMaps

public void removeFromCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list

Specified by:
removeFromCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps