org.biomage.DesignElement
Class MismatchInformation

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.DesignElement.MismatchInformation

All Implemented Interfaces:

HasPropertySets, java.io.Serializable

public class MismatchInformation

extends Extendable

implements java.io.Serializable

Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.

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

MismatchInformation()
Default constructor.

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

Method Summary

java.lang.String	getNewSequence() Get method for newSequence
int	getReplacedLength() Get method for replacedLength
int	getStartCoord() Get method for startCoord
void	setNewSequence(java.lang.String newSequence) Set method for newSequence
void	setReplacedLength(int replacedLength) Set method for replacedLength
void	setStartCoord(int startCoord) Set method for startCoord
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

MismatchInformation

public MismatchInformation()

Default constructor.

MismatchInformation

public MismatchInformation(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

setStartCoord

public void setStartCoord(int startCoord)

Set method for startCoord

getStartCoord

public int getStartCoord()

Get method for startCoord

Returns:

value of the attribute

setNewSequence

public void setNewSequence(java.lang.String newSequence)

Set method for newSequence

getNewSequence

public java.lang.String getNewSequence()

Get method for newSequence

Returns:

value of the attribute

setReplacedLength

public void setReplacedLength(int replacedLength)

Set method for replacedLength

getReplacedLength

public int getReplacedLength()

Get method for replacedLength

Returns:

value of the attribute