org.biomage.BioSequence
Class SequencePosition

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.BioSequence.SequencePosition
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasPropertySets
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/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.lang.String ojbConcreteClass
           
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
SequencePosition()
          Default constructor.
SequencePosition(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 java.lang.Integer getEnd()
          Get method for end
 java.lang.String getModelClassName()
           
 java.lang.Integer getStart()
          Get method for start
 void setEnd(java.lang.Integer end)
          Set method for end
 void setStart(java.lang.Integer 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, 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
 

Field Detail

ojbConcreteClass

protected java.lang.String ojbConcreteClass
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

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

setStart

public void setStart(java.lang.Integer start)
Set method for start

Parameters:
value - to set

getStart

public java.lang.Integer getStart()
Get method for start

Returns:
value of the attribute

setEnd

public void setEnd(java.lang.Integer end)
Set method for end

Parameters:
value - to set

getEnd

public java.lang.Integer getEnd()
Get method for end

Returns:
value of the attribute

getModelClassName

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