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org.biomage.BioSequence
Class SequencePosition  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.BioSequence.SequencePosition

All Implemented Interfaces:

org.biomage.Interface.HasPropertySets, java.io.Serializable

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public class SequencePosition

extends org.biomage.Common.Extendable

implements java.io.Serializable

Designates the position of the Feature in its BioSequence.

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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.

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end

int end

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

Constructor Detail

SequencePosition

public SequencePosition()

Default constructor.

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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.

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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.

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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.

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setStart

public void setStart(int start)

Set method for start

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getStart

public int getStart()

Get method for start

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setEnd

public void setEnd(int end)

Set method for end

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getEnd

public int getEnd()

Get method for end

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioSequence overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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