org.biomage.DesignElement
Class CompositePosition

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.BioSequence.SequencePosition
          extended by org.biomage.DesignElement.CompositePosition
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasComposite, HasMismatchInformation, HasPropertySets

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/interfaces inherited from interface org.biomage.Interface.HasMismatchInformation
HasMismatchInformation.MismatchInformation_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  CompositeSequence composite
          A source CompositeSequence that is part of a target CompositeSequence
protected  java.util.List mismatchInformation
          Differences in how the contained compositeSequence matches its target compositeSequence's sequence.
 
Fields inherited from class org.biomage.BioSequence.SequencePosition
ojbConcreteClass
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 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
 java.lang.String getModelClassName()
           
 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, 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

composite

protected CompositeSequence composite
A source CompositeSequence that is part of a target CompositeSequence


mismatchInformation

protected java.util.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

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 SequencePosition
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()
Overrides:
emptyMAGEobject in class SequencePosition

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
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 SequencePosition
Throws:
java.io.IOException

getModelClassName

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

setComposite

public void setComposite(CompositeSequence composite)
Set method for composite

Specified by:
setComposite in interface HasComposite
Parameters:
value - to set

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
Parameters:
value - to set

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