de.hu.berlin.wbi.objects

Class UniprotFeature

java.lang.Object

de.hu.berlin.wbi.objects.UniprotFeature

public class UniprotFeature
extends Object

Represents a UniProt entry; loaded from database.

Author:

Philippe Thomas

Constructor Summary

Constructors

Constructor and Description
UniprotFeature(int geneId, String modificationType, int startLoc, int endLoc)

Method Summary

Modifier and Type	Method and Description
int	getEndLoc() Returns end location of the modification on the peptide
static List<UniprotFeature>	getFeatures(int geneID) Returns all UniProt features for one specific Entrez-Gene Identifier
int	getGeneId() Returns associated Enzrez Gene ID
String	getModificationType() Returns modification type (e.g.
int	getStartLoc() Returns start location of the modification on the peptide
static void	init(DatabaseConnection mysql, String uniProt_Table) Initializes prepared statements to retrieve UniProt features, like signaling peptide information
String	toString() (non-Javadoc)

Methods inherited from class java.lang.Object

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

Constructor Detail

UniprotFeature

public UniprotFeature(int geneId,
                      String modificationType,
                      int startLoc,
                      int endLoc)

Method Detail

init

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

Initializes prepared statements to retrieve UniProt features, like signaling peptide information

Parameters:

mysql - mySQL database

uniProt_Table - Table name

Throws:

SQLException

getFeatures

public static List<UniprotFeature> getFeatures(int geneID)

Returns all UniProt features for one specific Entrez-Gene Identifier

Parameters:

geneID - -- Entrez Gene ID

Returns:

List of UniProt features

toString

public String toString()

(non-Javadoc)

Overrides:

toString in class Object

See Also:

MutationMention.toString()

getGeneId

public int getGeneId()

Returns associated Enzrez Gene ID

Returns:

Entrez Gene ID

getModificationType

public String getModificationType()

Returns modification type (e.g. signaling peptide)

Returns:

modification type

getStartLoc

public int getStartLoc()

Returns start location of the modification on the peptide

Returns:

start location

getEndLoc

public int getEndLoc()

Returns end location of the modification on the peptide

Returns:

end location