apollo.dataadapter.chado
Class ChadoDatabase

java.lang.Object
  apollo.dataadapter.chado.ChadoDatabase

public class ChadoDatabase
extends java.lang.Object

Connection and configuration information for a Chado database.

Version:

$Revision: 1.24 $ $Date: 2008-08-26 19:42:31 $ $Author: gk_fan $

Author:

Jonathan Crabtree

Field Summary

protected java.lang.String	adapterClassName Fully-qualified name of a Java class that extends apollo.dataadapter.chado.jdbc.JdbcChadoAdapter; used to implement DBMS-specific features or optimizations.
protected java.lang.String	chadoDb Name of the specific Chado database instance/schema on the database server.
protected java.lang.String	jdbcUrl JDBC connection URL
protected static org.apache.log4j.Logger	logger
protected java.lang.String	name Short (and preferably unique) user-readable identifier for the database.
protected java.lang.String	organismLike String used to limit the sequences listed in the pull-down menu presented by the data adapter.

Constructor Summary

ChadoDatabase()
Default constructor.

ChadoDatabase(java.lang.String name, java.lang.String adapterClassName, java.lang.String jdbcUrl, java.lang.String chadoDb, java.lang.String login, java.lang.String organismLike)

Method Summary

java.lang.String	getAdapterClassName()
boolean	getAllowLoginInput()
boolean	getAllowPasswordInput()
java.lang.String	getChadoDb()
ChadoInstance	getChadoInstance()
java.lang.String	getJdbcUrl()
java.lang.String	getLogin()
java.lang.String	getName()
java.lang.String	getOrganismLike()
java.lang.String	getPassword()
java.lang.String	getStyleFileName()
void	setAdapterClassName(java.lang.String clsName)
void	setAllowLoginInput(boolean b)
void	setAllowPasswordInput(boolean b)
void	setChadoDb(java.lang.String dbName)
void	setChadoInstance(ChadoInstance chadoInstance)
void	setJdbcUrl(java.lang.String url)
void	setLogin(java.lang.String dbUser)
void	setName(java.lang.String name) Set the name that will be displayed in the chado connection pane.
void	setOrganismLike(java.lang.String like)
void	setStyleFileName(java.lang.String fileName)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

name

protected java.lang.String name

Short (and preferably unique) user-readable identifier for the database.

adapterClassName

protected java.lang.String adapterClassName

Fully-qualified name of a Java class that extends apollo.dataadapter.chado.jdbc.JdbcChadoAdapter; used to implement DBMS-specific features or optimizations.

jdbcUrl

protected java.lang.String jdbcUrl

JDBC connection URL

chadoDb

protected java.lang.String chadoDb

Name of the specific Chado database instance/schema on the database server. The interpretation of this value may vary slightly depending on the DBMS. In Oracle, for example, this will most likely be a "schema" (i.e., username), whereas in Sybase or MySQL it will more likely be a database name.

organismLike

protected java.lang.String organismLike

String used to limit the sequences listed in the pull-down menu presented by the data adapter. Implemented via a 'like' query on organism.common_name using this string.

Constructor Detail

ChadoDatabase

public ChadoDatabase()

Default constructor.

ChadoDatabase

public ChadoDatabase(java.lang.String name,
                     java.lang.String adapterClassName,
                     java.lang.String jdbcUrl,
                     java.lang.String chadoDb,
                     java.lang.String login,
                     java.lang.String organismLike)

Parameters:

name - Short (and preferably unique) user-readable identifier for the database.

adapterClassName - Name of a Java class that extends apollo.dataadapter.chado.jdbc.JdbcChadoAdapter.

jdbcUrl - JDBC connection URL.

chadoDb - Name of the specific Chado database instance/schema on the database server.

login - Database login

organismLike - String used to limit the sequences listed in the pull-down menu, via a 'like' query on organism.common_name.

Method Detail

getName

public java.lang.String getName()

setName

public void setName(java.lang.String name)

Set the name that will be displayed in the chado connection pane.

getAdapterClassName

public java.lang.String getAdapterClassName()

Returns:

The name of a Java class that extends apollo.dataadapter.chado.jdbc.JdbcChadoAdapter.

setAdapterClassName

public void setAdapterClassName(java.lang.String clsName)

getJdbcUrl

public java.lang.String getJdbcUrl()

Returns:

The JDBC URL used to connect to the database

setJdbcUrl

public void setJdbcUrl(java.lang.String url)

getChadoDb

public java.lang.String getChadoDb()

Returns:

The database/schema name.

setChadoDb

public void setChadoDb(java.lang.String dbName)

getLogin

public java.lang.String getLogin()

Returns:

Database username/login.

setLogin

public void setLogin(java.lang.String dbUser)

getPassword

public java.lang.String getPassword()

getOrganismLike

public java.lang.String getOrganismLike()

setOrganismLike

public void setOrganismLike(java.lang.String like)

getChadoInstance

public ChadoInstance getChadoInstance()

setChadoInstance

public void setChadoInstance(ChadoInstance chadoInstance)

getStyleFileName

public java.lang.String getStyleFileName()

setStyleFileName

public void setStyleFileName(java.lang.String fileName)

getAllowLoginInput

public boolean getAllowLoginInput()

setAllowLoginInput

public void setAllowLoginInput(boolean b)

getAllowPasswordInput

public boolean getAllowPasswordInput()

setAllowPasswordInput

public void setAllowPasswordInput(boolean b)