de.hu.berlin.wbi.stuff.xml

Class PSM

java.lang.Object

de.hu.berlin.wbi.stuff.xml.PSM

public class PSM
extends Object

Class represents a protein sequence mutation

Author:

Philippe Thomas

Constructor Summary

Constructors

Constructor and Description
PSM(int entrez, int aaLoc, String reference, String mutations)

Method Summary

Modifier and Type	Method and Description
void	addMutation(String mutation)
void	addMutations(Set<String> mutations)
int	getAaLoc()
int	getEntrez()
String	getMutations()
String	getWildtype()
boolean	isValid() Checks if the PSM object is valid.
void	setAaLoc(int aaLoc)
void	setEntrez(int entrez)
void	setWildtype(String wildtype)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

PSM

public PSM(int entrez,
           int aaLoc,
           String reference,
           String mutations)

Method Detail

isValid

public boolean isValid()

Checks if the PSM object is valid. It has to contain a entrez-gene Id, location, and a wildtype, and a mutation Not given for SPNs like rs9341281

Returns:

true if SNP is valid

getEntrez

public int getEntrez()

setEntrez

public void setEntrez(int entrez)

getAaLoc

public int getAaLoc()

setAaLoc

public void setAaLoc(int aaLoc)

getWildtype

public String getWildtype()

setWildtype

public void setWildtype(String wildtype)

getMutations

public String getMutations()

addMutation

public void addMutation(String mutation)

addMutations

public void addMutations(Set<String> mutations)

toString

public String toString()

Overrides:

toString in class Object