edu.iastate.anthill.indus.iterator.go
Class GOIterator

java.lang.Object
  edu.iastate.utils.sql.LocalDBConnection
      edu.iastate.anthill.indus.IndusDB
          edu.iastate.anthill.indus.iterator.go.GOIterator

public class GOIterator

extends IndusDB

Since:

1.0 2005-02-18

Author:

Jie Bao

Nested Class Summary

(package private) class

GOIterator.TagValuePair

Field Summary

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

db, driver, password, url, user

Constructor Summary

GOIterator()

Method Summary

(package private) void	addGoRoot() Gene Ontology has no single root, but three nodes for biological_process, cellular_component, molecular_function .
(package private) void	addHeadEntry(java.lang.String tag, java.lang.String details)
(package private) void	addRelationship(java.lang.String go_id, java.util.Vector source)
(package private) void	addSynonym(java.lang.String go_id, java.lang.String type, java.util.Vector source)
(package private) boolean	addTermEntry(java.util.Vector strings, java.lang.String default_namespace)
(package private) boolean	addTypedefEntry(java.util.Vector strings) Add a typdef item eg: [Typedef] id: part_of name: part of is_transitive: true
(package private) void	clearAllData()
(package private) java.lang.String	filterGO_ID(java.lang.String id)
void	loadToDB()
(package private) GOIterator.TagValuePair	parseTagValuePair(java.lang.String str)
(package private) GOIterator.TagValuePair	parseXref(java.lang.String xref)
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

GOIterator

public GOIterator()

Method Detail

loadToDB

public void loadToDB()

addTypedefEntry

boolean addTypedefEntry(java.util.Vector strings)

Add a typdef item eg: [Typedef] id: part_of name: part of is_transitive: true

Parameters:

strings - Vector

Returns:

boolean

Since:

2005-02-20

addTermEntry

boolean addTermEntry(java.util.Vector strings,
                     java.lang.String default_namespace)

Parameters:

strings - Vector

Since:

2005-02-18

addRelationship

void addRelationship(java.lang.String go_id,
                     java.util.Vector source)

Parameters:

go_id - String

source - Vector

addSynonym

void addSynonym(java.lang.String go_id,
                java.lang.String type,
                java.util.Vector source)

Parameters:

go_id - String

type - String "general", "related", "exact","broad", "narrow"

source - Vector

parseXref

GOIterator.TagValuePair parseXref(java.lang.String xref)

filterGO_ID

java.lang.String filterGO_ID(java.lang.String id)

Parameters:

id - String eg: GO:0012509

Returns:

String eg: 0012509

addHeadEntry

void addHeadEntry(java.lang.String tag,
                  java.lang.String details)

test

public static void test()

parseTagValuePair

GOIterator.TagValuePair parseTagValuePair(java.lang.String str)

clearAllData

void clearAllData()

addGoRoot

void addGoRoot()

Gene Ontology has no single root, but three nodes for biological_process, cellular_component, molecular_function . We add a new node 0000000 as the root for all of them

Since:

2005-03-31