edu.iastate.metnet.birdseyeview.db
Class Database

java.lang.Object
  edu.iastate.metnet.birdseyeview.db.Database

public class Database
extends java.lang.Object

The Database Class encapsulates the functionality that interacts with the Metnet MySQL database.

Author:

Matt Studham Created Mar 19, 2005

Field Summary

(package private) java.sql.Connection

connection

Constructor Summary

Database()
Constructor.

Method Summary

java.util.HashMap	getAllLocationInfo() This method retrieves all of the cellular location information from the database.
java.util.ArrayList	getGoBioProcesses(java.lang.Integer goID) This method returns a list of GO biological process term IDs in which the given entity participates.
java.util.ArrayList	getGoChildren(java.lang.Integer goNodeID) This method retrieves a list of the child nodes for the given node.
java.util.ArrayList	getGoFunctions(java.lang.Integer goID) This method returns a list of GO molecular function term IDs in which the given entity is involved.
java.lang.Integer	getGoGeneProductID(java.lang.String locusID) This method converts the given locus ID into a GO gene product ID querying the GO database in the Metnet DB.
java.lang.String	getGoNodeName(java.lang.Integer goNodeID) This method retrieves the name of the GO node with the given ID.
java.util.ArrayList	getGoNodesWithinDistance(java.lang.Integer rootNodeID, int distance) This method retrieves a unique list of the nodes of the hierarchy for the given root within the given distance from the root.
java.util.ArrayList	getGoTermAncestors(java.lang.Integer goTermID) This method returns a list of terms which are the ancestors (parents, itself, etc.) for the given term.
java.util.ArrayList	getLocations(java.lang.Integer entityID) This method returns a list of cellular locations for the given entity.
java.util.ArrayList	getLocusIDs(java.lang.String affyID) This method converts the given affymetrix ID (..._at) into Locus IDs (AT-G----...) by querying a cross-ref table in the Metnet DB.
java.lang.Integer	getMetnetEntityID(java.lang.String locusID) This method converts the given locus ID into a Metnet Entity ID by querying the Metnet DB.
java.util.ArrayList	getPathways(java.lang.Integer entityID) This method returns a list of pathways in which the given entity participates.
java.util.ArrayList	getPolypeptides(java.lang.Integer entityID) This method returns a list of polypeptides for the given entity (gene).
java.util.ArrayList	getProteinComplexes(java.lang.Integer entityID) This method returns a list of protein complexes of which the given entity (polypeptide) is a component.
void	initialize() This method makes the connection to the Metnet DB.
static void	main(java.lang.String[] args) This method tests the Database class.

Methods inherited from class java.lang.Object

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

Field Detail

connection

java.sql.Connection connection

Constructor Detail

Database

public Database()

Constructor.

Method Detail

initialize

public void initialize()
                throws BirdsEyeViewException

This method makes the connection to the Metnet DB.

Throws:

BirdsEyeViewException - SQL error

getMetnetEntityID

public java.lang.Integer getMetnetEntityID(java.lang.String locusID)
                                    throws BirdsEyeViewException

This method converts the given locus ID into a Metnet Entity ID by querying the Metnet DB. The locus ID is the Entity Name in Metnet. If there given ID is null or there is no such entity in Metnet, null is returned.

Parameters:

locusID - Locus ID

Returns:

Integer - may be null

Throws:

BirdsEyeViewException - SQL error

getLocusIDs

public java.util.ArrayList getLocusIDs(java.lang.String affyID)
                                throws BirdsEyeViewException

This method converts the given affymetrix ID (..._at) into Locus IDs (AT-G----...) by querying a cross-ref table in the Metnet DB. If there is no such entity in Metnet, the returned list is empty.

Parameters:

affyID - Affymatrix ID

Returns:

ArrayList - may be empty

Throws:

BirdsEyeViewException - SQL error

getPolypeptides

public java.util.ArrayList getPolypeptides(java.lang.Integer entityID)
                                    throws BirdsEyeViewException

This method returns a list of polypeptides for the given entity (gene). The list may be empty. This query first gets a list of RNA's (as block ID's) and then uses that list to get the list of polypeptides for each RNA. We don't differentiate the different polypeptides from the different RNAs.

Parameters:

entityID -

Returns:

ArrayList Polypeptide objects

Throws:

BirdsEyeViewException - SQL error

getProteinComplexes

public java.util.ArrayList getProteinComplexes(java.lang.Integer entityID)
                                        throws BirdsEyeViewException

This method returns a list of protein complexes of which the given entity (polypeptide) is a component. The list may be empty.

Parameters:

entityID -

Returns:

ArrayList Protein Complex objects

Throws:

BirdsEyeViewException - SQL error

getLocations

public java.util.ArrayList getLocations(java.lang.Integer entityID)
                                 throws BirdsEyeViewException

This method returns a list of cellular locations for the given entity. The list may be empty.

Parameters:

entityID -

Returns:

ArrayList String objects

Throws:

BirdsEyeViewException - SQL error

getPathways

public java.util.ArrayList getPathways(java.lang.Integer entityID)
                                throws BirdsEyeViewException

This method returns a list of pathways in which the given entity participates. The list may be empty.

Parameters:

entityID -

Returns:

ArrayList String objects

Throws:

BirdsEyeViewException - SQL error

getGoGeneProductID

public java.lang.Integer getGoGeneProductID(java.lang.String locusID)
                                     throws BirdsEyeViewException

This method converts the given locus ID into a GO gene product ID querying the GO database in the Metnet DB. If there given ID is null or there is no such entity in Metnet, null is returned.

Parameters:

locusID - Locus ID

Returns:

Integer - may be null

Throws:

BirdsEyeViewException - SQL error

getGoBioProcesses

public java.util.ArrayList getGoBioProcesses(java.lang.Integer goID)
                                      throws BirdsEyeViewException

This method returns a list of GO biological process term IDs in which the given entity participates. The list may be empty.

Parameters:

goID -

Returns:

ArrayList Integer objects

Throws:

BirdsEyeViewException - SQL error

getGoFunctions

public java.util.ArrayList getGoFunctions(java.lang.Integer goID)
                                   throws BirdsEyeViewException

This method returns a list of GO molecular function term IDs in which the given entity is involved. The list may be empty.

Parameters:

goID -

Returns:

ArrayList Integer objects

Throws:

BirdsEyeViewException - SQL error

getGoChildren

public java.util.ArrayList getGoChildren(java.lang.Integer goNodeID)
                                  throws BirdsEyeViewException

This method retrieves a list of the child nodes for the given node.

Parameters:

goNodeID -

Returns:

ArrayList List of Integer objects; ID's of child nodes

Throws:

BirdsEyeViewException

getGoTermAncestors

public java.util.ArrayList getGoTermAncestors(java.lang.Integer goTermID)
                                       throws BirdsEyeViewException

This method returns a list of terms which are the ancestors (parents, itself, etc.) for the given term. The returned list will include the given term!

Parameters:

goTermID - GO term ID

Returns:

ArrayList List of GO term IDs (Integers)

Throws:

BirdsEyeViewException

getGoNodesWithinDistance

public java.util.ArrayList getGoNodesWithinDistance(java.lang.Integer rootNodeID,
                                                    int distance)
                                             throws BirdsEyeViewException

This method retrieves a unique list of the nodes of the hierarchy for the given root within the given distance from the root.

Parameters:

rootNodeID -

distance - Distance from the root (inclusive)

Returns:

ArrayList Unique list of Integer objects; ID's of nodes

Throws:

BirdsEyeViewException

getGoNodeName

public java.lang.String getGoNodeName(java.lang.Integer goNodeID)
                               throws BirdsEyeViewException

This method retrieves the name of the GO node with the given ID.

Parameters:

goNodeID -

Returns:

String Node name (Term name)

Throws:

BirdsEyeViewException - Database error

getAllLocationInfo

public java.util.HashMap getAllLocationInfo()
                                     throws BirdsEyeViewException

This method retrieves all of the cellular location information from the database.

Returns:

HashMap Key=Integer code, Value=String name

Throws:

BirdsEyeViewException - Database error

main

public static void main(java.lang.String[] args)

This method tests the Database class.

Parameters:

args -