edu.mssm.crover.webapps.dimlib.datamodel
Class SNP

java.lang.Object
  |
  +--edu.mssm.crover.webapps.dimlib.datamodel.SNP

All Implemented Interfaces:

java.lang.Comparable

public class SNP

extends java.lang.Object

implements java.lang.Comparable

Stores all relevant information associated with SNPs.

Author:

luce

Constructor Summary

SNP(WildTypeProtein wtp)

Method Summary

int	compareTo(java.lang.Object o) Natural ordering of SNP - by ID.
void	confirm()
boolean	equals(java.lang.Object o)
int	getAAFrame()
int	getAAPosition()
int	getAffectedResidue()
char[]	getAllowedBases()
Sequence	getAnnotatedWTPSeq()
java.lang.String	getForwardPCRPrimer()
java.lang.String	getID()
int	getProductLength()
java.lang.String	getReversePCRPrimer()
java.lang.String	getSeqAfter()
java.lang.String	getSeqBefore()
SubmitterInfo	getSubmitter()
WildTypeProtein	getWTP()
int	hashCode()
boolean	isConfirmed()
boolean	isMatched()
void	match()
int	numAllowedBases()
void	setAAFrame(int frame)
void	setAAPosition(int position)
void	setAffectedResidue(int res)
void	setAllowedBases(char[] bases)
void	setAnnotatedWTPSeq(Sequence seq)
void	setConfirmationLevel(int level)
void	setForwardPCRPrimer(java.lang.String primer)
void	setID(java.lang.String id)
void	setProductLength(int len)
void	setReversePCRPrimer(java.lang.String primer)
void	setSeqAfter(java.lang.String seq)
void	setSeqBefore(java.lang.String seq)
void	setSubmitter(java.lang.String name, java.lang.String email)
void	setSubmitter(SubmitterInfo submitter)

Methods inherited from class java.lang.Object

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

Constructor Detail

SNP

public SNP(WildTypeProtein wtp)

Method Detail

getWTP

public WildTypeProtein getWTP()

setSeqBefore

public void setSeqBefore(java.lang.String seq)

getSeqBefore

public java.lang.String getSeqBefore()

setSeqAfter

public void setSeqAfter(java.lang.String seq)

getSeqAfter

public java.lang.String getSeqAfter()

setAllowedBases

public void setAllowedBases(char[] bases)

getAllowedBases

public char[] getAllowedBases()

numAllowedBases

public int numAllowedBases()

setForwardPCRPrimer

public void setForwardPCRPrimer(java.lang.String primer)

getForwardPCRPrimer

public java.lang.String getForwardPCRPrimer()

setReversePCRPrimer

public void setReversePCRPrimer(java.lang.String primer)

getReversePCRPrimer

public java.lang.String getReversePCRPrimer()

setProductLength

public void setProductLength(int len)

getProductLength

public int getProductLength()

match

public void match()

isMatched

public boolean isMatched()

confirm

public void confirm()

isConfirmed

public boolean isConfirmed()

setConfirmationLevel

public void setConfirmationLevel(int level)

setAAPosition

public void setAAPosition(int position)

getAAPosition

public int getAAPosition()

setAAFrame

public void setAAFrame(int frame)

getAAFrame

public int getAAFrame()

setAffectedResidue

public void setAffectedResidue(int res)

getAffectedResidue

public int getAffectedResidue()

setSubmitter

public void setSubmitter(java.lang.String name,
                         java.lang.String email)

setSubmitter

public void setSubmitter(SubmitterInfo submitter)

getSubmitter

public SubmitterInfo getSubmitter()

setAnnotatedWTPSeq

public void setAnnotatedWTPSeq(Sequence seq)

getAnnotatedWTPSeq

public Sequence getAnnotatedWTPSeq()

setID

public void setID(java.lang.String id)

getID

public java.lang.String getID()

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 SNP - by ID.

Specified by:

compareTo in interface java.lang.Comparable