LoadCDSFromAce.java File Reference


Functions
Class.	forName ("org.postgresql.Driver")
	LoadCDSFromAce () throws SQLException, ClassNotFoundException
void	connect (String h, int p)
void	connectAce (String dbname)
void	close () throws SQLException
void	closeAce ()
void	updateFrom (String aceQuery, boolean mRNA) throws SQLException, AceException
void	loadFrom (String aceQuery, boolean mRNA) throws SQLException, AceException
void	createFileFrom (String aceQuery, boolean mRNA) throws SQLException, AceException
void	insert () throws SQLException, AceException
void	loadOrganism (String div) throws SQLException, AceException
int	getOrgid (String orgName) throws SQLException
String	getOrgidString (String orgName) throws SQLException
Vector	getUnusedId () throws SQLException
int	nextID ()
static void	main (String[] args)
Variables
	psconn = DriverManager.getConnection(pgDB, usr, pgPassword)
	stmt = psconn.createStatement()
	orgidStmt = psconn.prepareStatement("Select id from species where name=?")
	unusedIds = getUnusedId()

Function Documentation

void close ( ) throws SQLException

References orgidStmt, and psconn.

Referenced by readGFSR(), writeGFSR(), and Socket::~Socket().

void closeAce ( )

void connect	(	String	h,
		int	p
	)

This is to connect to an ACEDB on host h and port p.

References user.

Referenced by cadbc::cadbc().

void connectAce ( String dbname )

void createFileFrom	(	String	aceQuery,
		boolean	mRNA
	)			throws SQLException, AceException

create a file for the postgres command, this can speed up Database loading by 1000x. Duging loading also drop index. This can also greately increase the speed of loading

References aceid, getOrgidString(), length, n_cluster, nextID(), p_cluster, and prtid.

Class. forName ( "org.postgresql.Driver" ) [package]

int getOrgid ( String orgName ) throws SQLException

does a database query from species table to obtain the id of species from name, orgName must be scientific

References orgidStmt.

Referenced by loadFrom(), and updateFrom().

String getOrgidString ( String orgName ) throws SQLException

References orgidStmt.

Referenced by createFileFrom().

Vector getUnusedId ( ) throws SQLException [private]

used to obtain unused cds_id in the cds table, run at

/** used to obtain unused cds_id in the cds table, run at object construction. Called by the constructor.

Referenced by LoadCDSFromAce().

void insert ( ) throws SQLException, AceException

References loadFrom().

LoadCDSFromAce ( ) throws SQLException, ClassNotFoundException

References getUnusedId(), orgidStmt, psconn, stmt, unusedIds, and user.

void loadFrom	(	String	aceQuery,
		boolean	mRNA
	)			throws SQLException, AceException

use this function when the cds table is originally empty. Or all of the entries are mostly new. When called for both CDS and CDS_from_mRNA, usually the second call fails with large databases such as bony, human, ... I have no solutions yet. The failer is from the backend!!!

References aceid, getOrgid(), nextID(), prtid, and psconn.

Referenced by insert().

void loadOrganism ( String div ) throws SQLException, AceException

Load all organisms from this acedb to the species table in the relational database. If organism already exist then just ignore. So this function can update an existing organism table div provides a division such as rod, vrt depends on postgres sequence to keep track of the id

References psconn.

static void main ( String[] args ) [static]