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org.biomage.DesignElement
Class MismatchInformation  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.DesignElement.MismatchInformation

All Implemented Interfaces:

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

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public class MismatchInformation

extends org.biomage.Common.Extendable

implements java.io.Serializable

Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.

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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)  java.lang.String	newSequence           The sequence that replaces the specified sequence starting at start_coord.
(package private)  int	replacedLength           Length of the original sequence that is replaced.
(package private)  int	startCoord           Offset into the sequence that the mismatch occurs.

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

MismatchInformation()           Default constructor.

MismatchInformation(org.xml.sax.Attributes atts)           Attribute constructor.

 

Method Summary
java.lang.String	getNewSequence()           Get method for newSequence
int	getReplacedLength()           Get method for replacedLength
int	getStartCoord()           Get method for startCoord
void	setNewSequence(java.lang.String newSequence)           Set method for newSequence
void	setReplacedLength(int replacedLength)           Set method for replacedLength
void	setStartCoord(int startCoord)           Set method for startCoord
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

startCoord

int startCoord

Offset into the sequence that the mismatch occurs.

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newSequence

java.lang.String newSequence

The sequence that replaces the specified sequence starting at start_coord.

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replacedLength

int replacedLength

Length of the original sequence that is replaced. A deletion is specified when the length of the newSequence is less than the replacedLength.

Constructor Detail

MismatchInformation

public MismatchInformation()

Default constructor.

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MismatchInformation

public MismatchInformation(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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setStartCoord

public void setStartCoord(int startCoord)

Set method for startCoord

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getStartCoord

public int getStartCoord()

Get method for startCoord

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setNewSequence

public void setNewSequence(java.lang.String newSequence)

Set method for newSequence

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getNewSequence

public java.lang.String getNewSequence()

Get method for newSequence

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setReplacedLength

public void setReplacedLength(int replacedLength)

Set method for replacedLength

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getReplacedLength

public int getReplacedLength()

Get method for replacedLength

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

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