edu.iastate.anthill.indus.iterator.ec
Class ECIterator

java.lang.Object
  edu.iastate.utils.sql.LocalDBConnection
      edu.iastate.anthill.indus.IndusDB
          edu.iastate.anthill.indus.iterator.ec.ECIterator

public class ECIterator

extends IndusDB

Since:

2005-03-31 CREATE TABLE ec ( id char(20) NOT NULL, name varchar(256), parent varchar, CONSTRAINT "EC_pkey" PRIMARY KEY (id) ) WITHOUT OIDS; ALTER TABLE ec OWNER TO indus; EC file format ftp://ftp.expasy.org/databases/enzyme/release/enzuser.txt

Author:

Jie Bao , baojie@cs.iastate.edu

Field Summary

Fields inherited from class edu.iastate.utils.sql.LocalDBConnection

db, driver, password, url, user

Constructor Summary

ECIterator()

Method Summary

private void	clearAllData() clearAllData
(package private) java.lang.String	getParentId(java.lang.String id)
private void	loadLeaves() We just parse ID and DE line in this version Example ID 1.1.1.2 DE Alcohol dehydrogenase (NADP+).
private void	loadToDB() loadToDB Note: a Unix host can only accept passive ftp visit
private void	loadTop3Level()
static void	main(java.lang.String[] args)
static void	test()

Methods inherited from class edu.iastate.anthill.indus.IndusDB

connect

Methods inherited from class edu.iastate.utils.sql.LocalDBConnection

connect, connect, disconnect, finalize, getDriver, getPassword, getUrl, getUser, setDriver, setPassword, setUrl, setUser

Methods inherited from class java.lang.Object

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

Constructor Detail

ECIterator

public ECIterator()

Method Detail

test

public static void test()

loadToDB

private void loadToDB()

loadToDB Note: a Unix host can only accept passive ftp visit

loadLeaves

private void loadLeaves()

We just parse ID and DE line in this version Example ID 1.1.1.2 DE Alcohol dehydrogenase (NADP+). AN Aldehyde reductase (NADPH). CA An alcohol + NADP(+) = an aldehyde + NADPH. CF Zinc. CC -!- Some members of this group oxidize only primary alcohols; others act CC also on secondary alcohols. CC -!- May be identical with EC 1.1.1.19, EC 1.1.1.33 and EC 1.1.1.55. CC -!- A-specific with respect to NADPH. PR PROSITE; PDOC00061; DR P35630, ADH1_ENTHI ; Q24857, ADH3_ENTHI ; Q04894, ADH6_YEAST ; DR P25377, ADH7_YEAST ; O57380, ADH8_RANPE ; P0A4X1, ADHC_MYCBO ; DR P0A4X0, ADHC_MYCTU ; P25984, ADH_CLOBE ; P75214, ADH_MYCPN ; DR P14941, ADH_THEBR ; O70473, AK1A1_CRIGR; P14550, AK1A1_HUMAN; DR Q9JII6, AK1A1_MOUSE; P50578, AK1A1_PIG ; P51635, AK1A1_RAT ; DR Q9UUN9, ALD2_SPOSA ; P27800, ALDX_SPOSA ; // The currently used line types, along with their respective line codes, are listed below: ID Identification (Begins each entry; 1 per entry) DE Description (official name) (>=1 per entry) AN Alternate name(s) (>=0 per entry) CA Catalytic activity (>=0 per entry) CF Cofactor(s) (>=0 per entry) CC Comments (>=0 per entry) DI Disease(s) associated with the enzyme (>=0 per entry) PR Cross-references to PROSITE (>=0 per entry) DR Cross-references to SWISS-PROT (>=0 per entry) // Termination line (Ends each entry; 1 per entry) Some entries do not contain all of the line types, and some line types occur many times in a single entry. Each entry must begin with an identification line (ID) and end with a terminator line (//). A detailed description of each line type is given in the next section of this document.

Since:

2005-03-31

getParentId

java.lang.String getParentId(java.lang.String id)

loadTop3Level

private void loadTop3Level()

clearAllData

private void clearAllData()

clearAllData

main

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