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


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.