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org.biomage.DesignElement
Class CompositePosition  view CompositePosition download CompositePosition.java

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

public class CompositePosition
extends org.biomage.BioSequence.SequencePosition
implements java.io.Serializable, org.biomage.Interface.HasComposite, org.biomage.Interface.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.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasMismatchInformation
org.biomage.Interface.HasMismatchInformation.MismatchInformation_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  CompositeSequence composite
          A source CompositeSequence that is part of a target CompositeSequence
private  org.biomage.Interface.HasMismatchInformation.MismatchInformation_list mismatchInformation
          Differences in how the contained compositeSequence matches its target compositeSequence's sequence.
 
Fields inherited from class org.biomage.BioSequence.SequencePosition
 
Fields inherited from class org.biomage.Common.Extendable
 
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
 CompositeSequence getComposite()
          Get method for composite
 MismatchInformation getFromMismatchInformation(int position)
          Method to get MismatchInformation from MismatchInformation_list
 org.biomage.Interface.HasMismatchInformation.MismatchInformation_list getMismatchInformation()
          Get method for mismatchInformation
 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(org.biomage.Interface.HasMismatchInformation.MismatchInformation_list mismatchInformation)
          Set method for mismatchInformation
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
Methods inherited from class org.biomage.BioSequence.SequencePosition
getEnd, getStart, setEnd, setStart
 
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
 

Field Detail

composite

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


mismatchInformation

private org.biomage.Interface.HasMismatchInformation.MismatchInformation_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

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.


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.


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.


setComposite

public void setComposite(CompositeSequence composite)
Set method for composite

Specified by:
setComposite in interface org.biomage.Interface.HasComposite

getComposite

public CompositeSequence getComposite()
Get method for composite

Specified by:
getComposite in interface org.biomage.Interface.HasComposite

setMismatchInformation

public void setMismatchInformation(org.biomage.Interface.HasMismatchInformation.MismatchInformation_list mismatchInformation)
Set method for mismatchInformation

Specified by:
setMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

getMismatchInformation

public org.biomage.Interface.HasMismatchInformation.MismatchInformation_list getMismatchInformation()
Get method for mismatchInformation

Specified by:
getMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

addToMismatchInformation

public void addToMismatchInformation(MismatchInformation mismatchInformation)
Method to add MismatchInformation to MismatchInformation_list

Specified by:
addToMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

addToMismatchInformation

public void addToMismatchInformation(int position,
                                     MismatchInformation mismatchInformation)
Method to add MismatchInformation at position to MismatchInformation_list

Specified by:
addToMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

getFromMismatchInformation

public MismatchInformation getFromMismatchInformation(int position)
Method to get MismatchInformation from MismatchInformation_list

Specified by:
getFromMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

removeElementAtFromMismatchInformation

public void removeElementAtFromMismatchInformation(int position)
Method to remove by position from MismatchInformation_list

Specified by:
removeElementAtFromMismatchInformation in interface org.biomage.Interface.HasMismatchInformation

removeFromMismatchInformation

public void removeFromMismatchInformation(MismatchInformation mismatchInformation)
Method to remove first MismatchInformation from MismatchInformation_list

Specified by:
removeFromMismatchInformation in interface org.biomage.Interface.HasMismatchInformation