org.biomage.DesignElement
Class ReporterPosition

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

All Implemented Interfaces:

HasMismatchInformation, HasPropertySets, HasReporter, java.io.Serializable

public class ReporterPosition

extends SequencePosition

implements java.io.Serializable, HasReporter, 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.

See Also:

Serialized Form

Nested Class Summary

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

HasMismatchInformation.MismatchInformation_list

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

HasPropertySets.PropertySets_list

Field Summary

protected HasMismatchInformation.MismatchInformation_list	mismatchInformation Differences in how the reporter matches its compositeSequence's sequence.
protected Reporter	reporter A reporter that comprises part of a CompositeSequence.

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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(HasMismatchInformation.MismatchInformation_list mismatchInformation) Set method for mismatchInformation
void	setReporter(Reporter reporter) Set method for reporter
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.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

protected Reporter reporter

A reporter that comprises part of a CompositeSequence.

mismatchInformation

protected HasMismatchInformation.MismatchInformation_list mismatchInformation

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

Constructor Detail

ReporterPosition

public ReporterPosition()

Default constructor.

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.

Overrides:

writeMAGEML in class SequencePosition

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 SequencePosition

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 SequencePosition

java.io.IOException

setReporter

public void setReporter(Reporter reporter)

Set method for reporter

Specified by:

setReporter in interface HasReporter

getReporter

public Reporter getReporter()

Get method for reporter

Specified by:

getReporter in interface HasReporter

Returns:

value of the attribute

setMismatchInformation

public void setMismatchInformation(HasMismatchInformation.MismatchInformation_list mismatchInformation)

Set method for mismatchInformation

Specified by:

setMismatchInformation in interface HasMismatchInformation

getMismatchInformation

public HasMismatchInformation.MismatchInformation_list getMismatchInformation()

Get method for mismatchInformation

Specified by:

getMismatchInformation in interface HasMismatchInformation

Returns:

value of the attribute

addToMismatchInformation

public void addToMismatchInformation(MismatchInformation mismatchInformation)

Method to add MismatchInformation to MismatchInformation_list

Specified by:

addToMismatchInformation in interface HasMismatchInformation

addToMismatchInformation

public void addToMismatchInformation(int position,
                                     MismatchInformation mismatchInformation)

Method to add MismatchInformation at position to MismatchInformation_list

Specified by:

addToMismatchInformation in interface HasMismatchInformation

getFromMismatchInformation

public MismatchInformation getFromMismatchInformation(int position)

Method to get MismatchInformation from MismatchInformation_list

Specified by:

getFromMismatchInformation in interface HasMismatchInformation

removeElementAtFromMismatchInformation

public void removeElementAtFromMismatchInformation(int position)

Method to remove by position from MismatchInformation_list

Specified by:

removeElementAtFromMismatchInformation in interface HasMismatchInformation

removeFromMismatchInformation

public void removeFromMismatchInformation(MismatchInformation mismatchInformation)

Method to remove first MismatchInformation from MismatchInformation_list

Specified by:

removeFromMismatchInformation in interface HasMismatchInformation