edu.mssm.crover.mutations.drivers
Class Mutation

java.lang.Object
  |
  +--edu.mssm.crover.mutations.drivers.Mutation

All Implemented Interfaces:

java.lang.Comparable

public final class Mutation

extends java.lang.Object

implements java.lang.Comparable

Field Summary

static short	CHIMERA
static short	DELETION
java.lang.String	descriptionURL
GenericPosition	genericPosition
static short	INSERTION
java.lang.String	mutatedResidues
java.lang.String	mutationID
static short	POINT_MUTATION
int	position
short	type
java.lang.String	wildResidues

Constructor Summary

Mutation()

Mutation(int _ob_a0, java.lang.String _ob_a1, short _ob_a2, java.lang.String _ob_a3, java.lang.String _ob_a4, java.lang.String _ob_a5)

Method Summary

int	compareTo(java.lang.Object o) Natural ordering of Mutation, by absolute position, then wildtype residues, than mutated residues.
boolean	equals(java.lang.Object o)
AccessionCode	getChMTAc()
int	getChMTEnd()
java.lang.String	getChMTEndRes()
java.lang.String	getChMTSeq()
int	getChMTStart()
java.lang.String	getChMTStartRes()
int	getChWTPEnd()
java.lang.String	getChWTPEndRes()
java.lang.String	getChWTPSeq()
int	getChWTPStart()
java.lang.String	getChWTPStartRes()
GenericPosition	getDefaultGenericPosition()
java.lang.String	getDescriptionURL()
GenericPosition	getGenericPosition()
java.lang.String	getMutatedResidues()
java.lang.String	getMutationID()
int	getPosition()
java.lang.String	getStringType()
short	getType()
java.lang.String	getWildTypeResidues()
int	hashCode()
void	setChMTAc(java.lang.String ac, java.lang.String db, java.lang.String organism)
void	setChMTEnd(int end)
void	setChMTEndRes(java.lang.String res)
void	setChMTSeq(java.lang.String seq)
void	setChMTStart(int start)
void	setChMTStartRes(java.lang.String res)
void	setChWTPEnd(int end)
void	setChWTPEndRes(java.lang.String res)
void	setChWTPSeq(java.lang.String seq)
void	setChWTPStart(int start)
void	setChWTPStartRes(java.lang.String res)
void	setGenericPosition(GenericPosition genericPosition)
void	setMutatedResidues(java.lang.String mr)
void	setPosition(int position)
void	setType(short t)
void	setWildTypeResidues(java.lang.String wtr)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

POINT_MUTATION

public static final short POINT_MUTATION

See Also:

Constant Field Values

DELETION

public static final short DELETION

See Also:

Constant Field Values

INSERTION

public static final short INSERTION

See Also:

Constant Field Values

CHIMERA

public static final short CHIMERA

See Also:

Constant Field Values

position

public int position

descriptionURL

public java.lang.String descriptionURL

type

public short type

wildResidues

public java.lang.String wildResidues

mutatedResidues

public java.lang.String mutatedResidues

mutationID

public java.lang.String mutationID

genericPosition

public GenericPosition genericPosition

Constructor Detail

Mutation

public Mutation()

Mutation

public Mutation(int _ob_a0,
                java.lang.String _ob_a1,
                short _ob_a2,
                java.lang.String _ob_a3,
                java.lang.String _ob_a4,
                java.lang.String _ob_a5)

Method Detail

getPosition

public int getPosition()

setPosition

public void setPosition(int position)

getGenericPosition

public GenericPosition getGenericPosition()

getDefaultGenericPosition

public GenericPosition getDefaultGenericPosition()

setGenericPosition

public void setGenericPosition(GenericPosition genericPosition)

setType

public void setType(short t)

getType

public short getType()

getStringType

public java.lang.String getStringType()

setWildTypeResidues

public void setWildTypeResidues(java.lang.String wtr)

getWildTypeResidues

public java.lang.String getWildTypeResidues()

setMutatedResidues

public void setMutatedResidues(java.lang.String mr)

getMutatedResidues

public java.lang.String getMutatedResidues()

setChWTPStart

public void setChWTPStart(int start)

setChWTPEnd

public void setChWTPEnd(int end)

setChMTStart

public void setChMTStart(int start)

setChMTEnd

public void setChMTEnd(int end)

setChMTAc

public void setChMTAc(java.lang.String ac,
                      java.lang.String db,
                      java.lang.String organism)

setChWTPSeq

public void setChWTPSeq(java.lang.String seq)

setChMTSeq

public void setChMTSeq(java.lang.String seq)

setChMTStartRes

public void setChMTStartRes(java.lang.String res)

setChMTEndRes

public void setChMTEndRes(java.lang.String res)

setChWTPStartRes

public void setChWTPStartRes(java.lang.String res)

setChWTPEndRes

public void setChWTPEndRes(java.lang.String res)

getChWTPStart

public int getChWTPStart()

getChWTPEnd

public int getChWTPEnd()

getChMTStart

public int getChMTStart()

getChMTEnd

public int getChMTEnd()

getChMTAc

public AccessionCode getChMTAc()

getChWTPSeq

public java.lang.String getChWTPSeq()

getChWTPStartRes

public java.lang.String getChWTPStartRes()

getChWTPEndRes

public java.lang.String getChWTPEndRes()

getChMTSeq

public java.lang.String getChMTSeq()

getChMTStartRes

public java.lang.String getChMTStartRes()

getChMTEndRes

public java.lang.String getChMTEndRes()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getMutationID

public java.lang.String getMutationID()

getDescriptionURL

public java.lang.String getDescriptionURL()

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

compareTo

public int compareTo(java.lang.Object o)

Natural ordering of Mutation, by absolute position, then wildtype residues, than mutated residues.

Specified by:

compareTo in interface java.lang.Comparable