org.biomage.DesignElement
Class CompositePosition

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

All Implemented Interfaces:

HasComposite, HasMismatchInformation, HasPropertySets, java.io.Serializable

public class CompositePosition

extends SequencePosition

implements java.io.Serializable, HasComposite, 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.

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 CompositeSequence	composite A source CompositeSequence that is part of a target CompositeSequence
protected HasMismatchInformation.MismatchInformation_list	mismatchInformation Differences in how the contained compositeSequence matches its target compositeSequence's sequence.

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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(HasMismatchInformation.MismatchInformation_list mismatchInformation) Set method for mismatchInformation
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

composite

protected CompositeSequence composite

A source CompositeSequence that is part of a target CompositeSequence

mismatchInformation

protected HasMismatchInformation.MismatchInformation_list mismatchInformation

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

Constructor Detail

CompositePosition

public CompositePosition()

Default constructor.

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.

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

setComposite

public void setComposite(CompositeSequence composite)

Set method for composite

Specified by:

setComposite in interface HasComposite

getComposite

public CompositeSequence getComposite()

Get method for composite

Specified by:

getComposite in interface HasComposite

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