org.biomage.DesignElement
Class MismatchInformation

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.DesignElement.MismatchInformation
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasPropertySets

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/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
MismatchInformation()
          Default constructor.
MismatchInformation(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 java.lang.String getModelClassName()
           
 java.lang.String getNewSequence()
          Get method for newSequence
 java.lang.Integer getReplacedLength()
          Get method for replacedLength
 java.lang.Integer getStartCoord()
          Get method for startCoord
 void setNewSequence(java.lang.String newSequence)
          Set method for newSequence
 void setReplacedLength(java.lang.Integer replacedLength)
          Set method for replacedLength
 void setStartCoord(java.lang.Integer 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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setAttributes, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, 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

Parameters:
atts: - the attribute list.
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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

setStartCoord

public void setStartCoord(java.lang.Integer startCoord)
Set method for startCoord

Parameters:
value - to set

getStartCoord

public java.lang.Integer getStartCoord()
Get method for startCoord

Returns:
value of the attribute

setNewSequence

public void setNewSequence(java.lang.String newSequence)
Set method for newSequence

Parameters:
value - to set

getNewSequence

public java.lang.String getNewSequence()
Get method for newSequence

Returns:
value of the attribute

setReplacedLength

public void setReplacedLength(java.lang.Integer replacedLength)
Set method for replacedLength

Parameters:
value - to set

getReplacedLength

public java.lang.Integer getReplacedLength()
Get method for replacedLength

Returns:
value of the attribute

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Extendable