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org.biomage.DesignElement
Class ReporterPosition  

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

All Implemented Interfaces:

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

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public class ReporterPosition

extends org.biomage.BioSequence.SequencePosition

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

The location in the composite target's sequence to which a source reporter 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  org.biomage.Interface.HasMismatchInformation.MismatchInformation_list	mismatchInformation           Differences in how the reporter matches its compositeSequence's sequence.
private  Reporter	reporter           A reporter that comprises part of a CompositeSequence.

 

Fields inherited from class org.biomage.BioSequence.SequencePosition

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

ReporterPosition()           Default constructor.

ReporterPosition(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
MismatchInformation	getFromMismatchInformation(int position)           Method to get MismatchInformation from MismatchInformation_list
org.biomage.Interface.HasMismatchInformation.MismatchInformation_list	getMismatchInformation()           Get method for mismatchInformation
Reporter	getReporter()           Get method for reporter
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	setMismatchInformation(org.biomage.Interface.HasMismatchInformation.MismatchInformation_list mismatchInformation)           Set method for mismatchInformation
void	setReporter(Reporter reporter)           Set method for reporter
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

reporter

private Reporter reporter

A reporter that comprises part of a CompositeSequence.

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mismatchInformation

private org.biomage.Interface.HasMismatchInformation.MismatchInformation_list mismatchInformation

Differences in how the reporter matches its compositeSequence's sequence.

Constructor Detail

ReporterPosition

public ReporterPosition()

Default constructor.

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ReporterPosition

public ReporterPosition(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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setReporter

public void setReporter(Reporter reporter)

Set method for reporter

Specified by:

setReporter in interface org.biomage.Interface.HasReporter

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getReporter

public Reporter getReporter()

Get method for reporter

Specified by:

getReporter in interface org.biomage.Interface.HasReporter

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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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