org.biomage.BioSequence
Class SequencePosition

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

All Implemented Interfaces:

HasPropertySets, java.io.Serializable

Direct Known Subclasses:

CompositePosition, ReporterPosition

public class SequencePosition

extends Extendable

implements java.io.Serializable

Designates the position of the Feature in its BioSequence.

See Also:

Serialized Form

Nested Class Summary

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

HasPropertySets.PropertySets_list

Field Summary

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

SequencePosition()
Default constructor.

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

Method Summary

int	getEnd() Get method for end
int	getStart() Get method for start
void	setEnd(int end) Set method for end
void	setStart(int start) Set method for start
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.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

Constructor Detail

SequencePosition

public SequencePosition()

Default constructor.

SequencePosition

public SequencePosition(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 Extendable

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 Extendable

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 Extendable

java.io.IOException

setStart

public void setStart(int start)

Set method for start

getStart

public int getStart()

Get method for start

Returns:

value of the attribute

setEnd

public void setEnd(int end)

Set method for end

getEnd

public int getEnd()

Get method for end

Returns:

value of the attribute