de.hu.berlin.wbi.objects

Class dbSNP

java.lang.Object

de.hu.berlin.wbi.objects.dbSNP

Direct Known Subclasses:

dbSNPNormalized

public class dbSNP
extends Object

Represents a dbSNP entry; loaded from a local database.

Author:

Philippe Thomas

Field Summary

Fields

Modifier and Type	Field and Description
protected int	aaPosition location of the mutation in terms of amino acids
protected int	geneID gene associated with this dbSNP entry.
protected Set<HGVS>	hgvs Different Strings describing the variations in nomenclature
protected Set<String>	residues known mutated amino acid residues for this SNP
protected int	rsID dbSNP internal id.
protected String	wildtype Mutation has one wildtype

Constructor Summary

Constructors

Constructor and Description
dbSNP() Simple constructor
dbSNP(int rsID, int geneID, Set<String> residues, int aaPosition, String wildtype) Constructor

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj) (non-Javadoc)
int	getAaPosition()
int	getGeneID() Get the associated entrez gene identifier
Set<HGVS>	getHgvs()
Set<String>	getResidues()
int	getRsID() Get dbSNP identifier (rs-id)
static List<dbSNP>	getSNP(int geneID) Retrieves a list of dbSNP entries associated with a specific entrez-gene ID
String	getWildtype()
int	hashCode() (non-Javadoc)
static void	init(DatabaseConnection mysql, String psmTable, String hgvs_view) Initializes prepared statements for retrieving SNP information
void	setAaPosition(int aaPosition)
void	setGeneID(int geneID) Set the associated entrez gene identifier
void	setHgvs(Set<HGVS> hgvs)
void	setResidues(Set<String> residues)
void	setRsID(int rsID) Set the dbSNP identifier (e.g., rs334)
String	toString() (non-Javadoc)

Methods inherited from class java.lang.Object

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

Field Detail

rsID

protected int rsID

dbSNP internal id.

geneID

protected int geneID

gene associated with this dbSNP entry.

residues

protected Set<String> residues

known mutated amino acid residues for this SNP

wildtype

protected String wildtype

Mutation has one wildtype

aaPosition

protected int aaPosition

location of the mutation in terms of amino acids

hgvs

protected Set<HGVS> hgvs

Different Strings describing the variations in nomenclature

Constructor Detail

dbSNP

public dbSNP()

Simple constructor

dbSNP

public dbSNP(int rsID,
             int geneID,
             Set<String> residues,
             int aaPosition,
             String wildtype)

Constructor

Parameters:

rsID - dbSNP identifier

geneID - Entrez Gene identifier

residues - PSM residues

aaPosition - PSM location

wildtype - PSM wildtype allele

Method Detail

init

public static void init(DatabaseConnection mysql,
                        String psmTable,
                        String hgvs_view)
                 throws SQLException

Initializes prepared statements for retrieving SNP information

Parameters:

mysql - database connection

psmTable - PSM Table name

hgvs_view - HGVS Table name

Throws:

SQLException

getSNP

public static List<dbSNP> getSNP(int geneID)

Retrieves a list of dbSNP entries associated with a specific entrez-gene ID

Parameters:

geneID - Entrez-Gene Identifier

Returns:

list of all snps associated with geneID

getRsID

public int getRsID()

Get dbSNP identifier (rs-id)

Returns:

the unique dbSNP identifier

setRsID

public void setRsID(int rsID)

Set the dbSNP identifier (e.g., rs334)

Parameters:

rsID - dbSNP ID

getGeneID

public int getGeneID()

Get the associated entrez gene identifier

Returns:

the associated entrez gene identifier

setGeneID

public void setGeneID(int geneID)

Set the associated entrez gene identifier

Parameters:

geneID - Entrez Gene ID

getResidues

public Set<String> getResidues()

Returns:

all possible amino-acid mutations

getWildtype

public String getWildtype()

Returns:

wildtype residue

setResidues

public void setResidues(Set<String> residues)

Parameters:

residues - PSM residues

getAaPosition

public int getAaPosition()

Returns:

location of the mutation wrt. the amino acid

setAaPosition

public void setAaPosition(int aaPosition)

Parameters:

aaPosition - Amino acid location

getHgvs

public Set<HGVS> getHgvs()

Returns:

list of associated HGVS mutations

setHgvs

public void setHgvs(Set<HGVS> hgvs)

Parameters:

hgvs - HGVS entries associated with this SNP

hashCode

public int hashCode()

(non-Javadoc)

Overrides:

hashCode in class Object

See Also:

Object.hashCode()

equals

public boolean equals(Object obj)

(non-Javadoc)

Overrides:

equals in class Object

See Also:

Object.equals(java.lang.Object)

toString

public String toString()

(non-Javadoc)

Overrides:

toString in class Object

See Also:

Object.toString()