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org.biomage.BioSequence
Class SequencePosition  view SequencePosition download SequencePosition.java

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

public class SequencePosition
extends org.biomage.Common.Extendable
implements java.io.Serializable

Designates the position of the Feature in its BioSequence.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
(package private)  int end
          The location of the base, for nucleotides, that the SeqFeature ends.
(package private)  int start
          The location of the base, for nucleotides, that the SeqFeature starts.
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
SequencePosition()
          Default constructor.
SequencePosition(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 int getEnd()
          Get method for end
 int getStart()
          Get method for start
 void setEnd(int end)
          Set method for end
 void setStart(int start)
          Set method for start
 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.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

start

int start
The location of the base, for nucleotides, that the SeqFeature starts.


end

int end
The location of the base, for nucleotides, that the SeqFeature ends.

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

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.


setStart

public void setStart(int start)
Set method for start


getStart

public int getStart()
Get method for start


setEnd

public void setEnd(int end)
Set method for end


getEnd

public int getEnd()
Get method for end