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org.biomage.DesignElement
Class CompositePosition  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.BioSequence.SequencePosition
          org.biomage.DesignElement.CompositePosition

All Implemented Interfaces:

org.biomage.Interface.HasComposite, org.biomage.Interface.HasMismatchInformation, org.biomage.Interface.HasPropertySets, java.io.Serializable

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public class CompositePosition

extends org.biomage.BioSequence.SequencePosition

implements java.io.Serializable, org.biomage.Interface.HasComposite, org.biomage.Interface.HasMismatchInformation

The location in the compositeSequence target's sequence to which a source compositeSequence maps. The association to MismatchInformation allows the specification, usually for control purposes, of deviations from the CompositeSequence's BioMaterial.

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Nested Class Summary

 

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

org.biomage.Interface.HasMismatchInformation.MismatchInformation_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  CompositeSequence	composite           A source CompositeSequence that is part of a target CompositeSequence
private  org.biomage.Interface.HasMismatchInformation.MismatchInformation_list	mismatchInformation           Differences in how the contained compositeSequence matches its target compositeSequence's sequence.

 

Fields inherited from class org.biomage.BioSequence.SequencePosition

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

CompositePosition()           Default constructor.

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

 

Method Summary
void	addToMismatchInformation(int position, MismatchInformation mismatchInformation)           Method to add MismatchInformation at position to MismatchInformation_list
void	addToMismatchInformation(MismatchInformation mismatchInformation)           Method to add MismatchInformation to MismatchInformation_list
CompositeSequence	getComposite()           Get method for composite
MismatchInformation	getFromMismatchInformation(int position)           Method to get MismatchInformation from MismatchInformation_list
org.biomage.Interface.HasMismatchInformation.MismatchInformation_list	getMismatchInformation()           Get method for mismatchInformation
void	removeElementAtFromMismatchInformation(int position)           Method to remove by position from MismatchInformation_list
void	removeFromMismatchInformation(MismatchInformation mismatchInformation)           Method to remove first MismatchInformation from MismatchInformation_list
void	setComposite(CompositeSequence composite)           Set method for composite
void	setMismatchInformation(org.biomage.Interface.HasMismatchInformation.MismatchInformation_list mismatchInformation)           Set method for mismatchInformation
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.BioSequence.SequencePosition

getEnd, getStart, setEnd, setStart

 

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

composite

private CompositeSequence composite

A source CompositeSequence that is part of a target CompositeSequence

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mismatchInformation

private org.biomage.Interface.HasMismatchInformation.MismatchInformation_list mismatchInformation

Differences in how the contained compositeSequence matches its target compositeSequence's sequence.

Constructor Detail

CompositePosition

public CompositePosition()

Default constructor.

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CompositePosition

public CompositePosition(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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setComposite

public void setComposite(CompositeSequence composite)

Set method for composite

Specified by:

setComposite in interface org.biomage.Interface.HasComposite

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getComposite

public CompositeSequence getComposite()

Get method for composite

Specified by:

getComposite in interface org.biomage.Interface.HasComposite

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setMismatchInformation

public void setMismatchInformation(org.biomage.Interface.HasMismatchInformation.MismatchInformation_list mismatchInformation)

Set method for mismatchInformation

Specified by:

setMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

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getMismatchInformation

public org.biomage.Interface.HasMismatchInformation.MismatchInformation_list getMismatchInformation()

Get method for mismatchInformation

Specified by:

getMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

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addToMismatchInformation

public void addToMismatchInformation(MismatchInformation mismatchInformation)

Method to add MismatchInformation to MismatchInformation_list

Specified by:

addToMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

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addToMismatchInformation

public void addToMismatchInformation(int position,
                                     MismatchInformation mismatchInformation)

Method to add MismatchInformation at position to MismatchInformation_list

Specified by:

addToMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

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getFromMismatchInformation

public MismatchInformation getFromMismatchInformation(int position)

Method to get MismatchInformation from MismatchInformation_list

Specified by:

getFromMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

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removeElementAtFromMismatchInformation

public void removeElementAtFromMismatchInformation(int position)

Method to remove by position from MismatchInformation_list

Specified by:

removeElementAtFromMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

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removeFromMismatchInformation

public void removeFromMismatchInformation(MismatchInformation mismatchInformation)

Method to remove first MismatchInformation from MismatchInformation_list

Specified by:

removeFromMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

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