apollo.dataadapter.chado
Class ChadoAdapterGUI

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.bdgp.swing.AbstractDataAdapterUI
                      apollo.dataadapter.chado.ChadoAdapterGUI

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, org.bdgp.io.DataAdapterUI

public class ChadoAdapterGUI
extends org.bdgp.swing.AbstractDataAdapterUI
implements java.awt.event.ActionListener, java.awt.event.ItemListener

In the Apollo data adapter specification each data adapter has two parts: a class that implements the graphical user interface, and a class that interacts with the data source (as directed by the user via the GUI). This is an implementation of the graphical user interface for the corresponding adapter class apollo.dataadapter.chado.ChadoAdapter.

Version:

$Revision: 1.42 $ $Date: 2008-03-05 18:51:44 $ $Author: gk_fan $

Author:

Jonathan Crabtree

See Also:

ChadoAdapter, Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

javax.swing.JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

protected ChadoDatabase[]	chado_dbs List of Chado databases read by the ChadoAdapter from its configuration file.
protected javax.swing.JLabel	chadoDbPrompt
protected javax.swing.JTextField	chadoDbTextField
protected static java.lang.String	CUSTOM_DB_PROMPT Prompt for the pull-down menu that allows the user to select a Chado database from among those read from the Chado adapter's configuration file.
protected static java.lang.String	CUSTOM_SEQ_PROMPT Prompt for the area in which the user can enter the ID of the sequence he/she wishes to load.
protected javax.swing.JLabel	databaseChoicePrompt
protected javax.swing.JComboBox	databaseComboBox
protected static java.lang.String[]	DRIVER_CLASSES NOTE - subclasses of JdbcChadoAdapter must be explicitly added to this list in order to be usable in the Chado adapter.
protected javax.swing.JComboBox	driverClassComboBox
protected javax.swing.JLabel	driverClassPrompt
protected javax.swing.JLabel	jdbcUrlPrompt
protected javax.swing.JTextField	jdbcUrlTextField
protected static org.apache.log4j.Logger	logger
protected org.bdgp.io.IOOperation	operation The IOOperation (e.g.
protected javax.swing.JLabel	passwordPrompt
protected javax.swing.JPasswordField	passwordTextField
protected javax.swing.JButton	seqChoiceButton
protected javax.swing.JComboBox	seqChoiceComboBox
protected javax.swing.JLabel	seqChoicePrompt
protected javax.swing.JLabel	seqIdPrompt
protected javax.swing.JTextField	seqIdTextField Where seq ids are entered - this should be changed to a drop down list of history
protected javax.swing.JComboBox	seqTypeComboBox
protected javax.swing.JLabel	seqTypePrompt
protected java.lang.String[]	seqTypes
protected javax.swing.JLabel	usernamePrompt
protected javax.swing.JTextField	usernameTextField Where logins are entered - make this a dropdown history list

Fields inherited from class org.bdgp.swing.AbstractDataAdapterUI

driver

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

ChadoAdapterGUI(org.bdgp.io.IOOperation operation, ChadoDatabase[] chado_dbs)

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e)
protected void	clearSeqChoiceComboBox() Reset the seqChoiceComboBox to its original state; called when the current database changes.
void	doLayout() If this JPanel is not displayed in the parent component, setVisible(boolean) will not have any effect.
java.lang.Object	doOperation(java.lang.Object values) The method that actually performs the data adapter operation (presumably by delegating to a data adapter).
protected ChadoDatabase	getChadoDatabaseByName(java.lang.String name) Retrieve one of the objects in this.chado_dbs by name.
protected java.lang.String	getComboBoxValue(javax.swing.JComboBox cb) Method that extracts the currently-selected value of a JComboBox.
protected java.lang.String	getDriverClass()
protected java.lang.String	getJdbcUrl()
protected org.bdgp.io.IOOperation	getOperation()
protected java.lang.String	getPassword()
java.awt.Dimension	getPreferredSize() Need a height of 200 to accomodate different UI's for each db.
java.util.Properties	getProperties() Returns the UI properties for this DataAdapterUI.
protected java.lang.String	getSelectedSeqType()
protected java.lang.String	getSequenceId()
protected java.lang.String	getUsername()
void	itemStateChanged(java.awt.event.ItemEvent e)
protected void	makeReadDataUI() Creates the user interface for OP_READ_DATA.
protected void	makeUI() Create the UI appropriate for this.op.
void	setProperties(java.util.Properties props) Sets UI properties for this DataAdapterUI.

Methods inherited from class org.bdgp.swing.AbstractDataAdapterUI

setDataAdapter, setInput

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

DRIVER_CLASSES

protected static java.lang.String[] DRIVER_CLASSES

NOTE - subclasses of JdbcChadoAdapter must be explicitly added to this list in order to be usable in the Chado adapter. This is a limitation that could be removed if necessary. Yes - this should come from config.

CUSTOM_DB_PROMPT

protected static java.lang.String CUSTOM_DB_PROMPT

Prompt for the pull-down menu that allows the user to select a Chado database from among those read from the Chado adapter's configuration file.

CUSTOM_SEQ_PROMPT

protected static java.lang.String CUSTOM_SEQ_PROMPT

Prompt for the area in which the user can enter the ID of the sequence he/she wishes to load.

operation

protected org.bdgp.io.IOOperation operation

The IOOperation (e.g. reading/writing) that this object was created to support.

chado_dbs

protected ChadoDatabase[] chado_dbs

List of Chado databases read by the ChadoAdapter from its configuration file.

See Also:

ChadoAdapter.readConfigFile

databaseChoicePrompt

protected javax.swing.JLabel databaseChoicePrompt

databaseComboBox

protected javax.swing.JComboBox databaseComboBox

driverClassPrompt

protected javax.swing.JLabel driverClassPrompt

driverClassComboBox

protected javax.swing.JComboBox driverClassComboBox

jdbcUrlPrompt

protected javax.swing.JLabel jdbcUrlPrompt

jdbcUrlTextField

protected javax.swing.JTextField jdbcUrlTextField

chadoDbPrompt

protected javax.swing.JLabel chadoDbPrompt

chadoDbTextField

protected javax.swing.JTextField chadoDbTextField

usernamePrompt

protected javax.swing.JLabel usernamePrompt

usernameTextField

protected javax.swing.JTextField usernameTextField

Where logins are entered - make this a dropdown history list

passwordPrompt

protected javax.swing.JLabel passwordPrompt

passwordTextField

protected javax.swing.JPasswordField passwordTextField

seqTypes

protected java.lang.String[] seqTypes

seqTypePrompt

protected javax.swing.JLabel seqTypePrompt

seqTypeComboBox

protected javax.swing.JComboBox seqTypeComboBox

seqChoicePrompt

protected javax.swing.JLabel seqChoicePrompt

seqChoiceComboBox

protected javax.swing.JComboBox seqChoiceComboBox

seqChoiceButton

protected javax.swing.JButton seqChoiceButton

seqIdPrompt

protected javax.swing.JLabel seqIdPrompt

seqIdTextField

protected javax.swing.JTextField seqIdTextField

Where seq ids are entered - this should be changed to a drop down list of history

Constructor Detail

ChadoAdapterGUI

public ChadoAdapterGUI(org.bdgp.io.IOOperation operation,
                       ChadoDatabase[] chado_dbs)

Parameters:

operation - The IOOperation that this GUI was invoked to perform.

chado_dbs - A list of Chado database descriptors from which the user may choose.

Method Detail

doLayout

public void doLayout()

If this JPanel is not displayed in the parent component, setVisible(boolean) will not have any effect. So seqQueryPanel will be displayed if it is never displayed for writing operation.

Overrides:

doLayout in class java.awt.Container

getPreferredSize

public java.awt.Dimension getPreferredSize()

Need a height of 200 to accomodate different UI's for each db. May or may not have login. If switch from not having to having a login panel, if the height is not explicitly set the newly added login panel will get squeezed out(as window size is not changing on db change). Is there a better way to do this? Will need to make height larger for databases that provide all the fields (tigr) - for release fixing at 200.

Overrides:

getPreferredSize in class javax.swing.JComponent

setProperties

public void setProperties(java.util.Properties props)

Description copied from interface: org.bdgp.io.DataAdapterUI

Sets UI properties for this DataAdapterUI. The source of these properties is up to the widget that displays the DataAdapterUI. Most of the time these properties will contain some sort of history information and will be loaded from a file. The Properties object may be null if there are no properties to set.

Specified by:

setProperties in interface org.bdgp.io.DataAdapterUI

getProperties

public java.util.Properties getProperties()

Description copied from interface: org.bdgp.io.DataAdapterUI

Returns the UI properties for this DataAdapterUI. These properties may be recorded by the widget that displays the DataAdapterUI and provided to the setDataAdapter method of later instances of the DataAdapterUI. This method may return null if there are no properties to record.

Specified by:

getProperties in interface org.bdgp.io.DataAdapterUI

doOperation

public java.lang.Object doOperation(java.lang.Object values)
                             throws ApolloAdapterException

Description copied from interface: org.bdgp.io.DataAdapterUI

The method that actually performs the data adapter operation (presumably by delegating to a data adapter). The input and outputs to this method are entirely dependant on the operation the data adapter is supposed to perform. The input or output of this method may be null.

Specified by:

doOperation in interface org.bdgp.io.DataAdapterUI

Throws:

ApolloAdapterException

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

itemStateChanged

public void itemStateChanged(java.awt.event.ItemEvent e)

Specified by:

itemStateChanged in interface java.awt.event.ItemListener

getChadoDatabaseByName

protected ChadoDatabase getChadoDatabaseByName(java.lang.String name)

Retrieve one of the objects in this.chado_dbs by name.

Parameters:

name - The human-readable name of one of the databases in chado_dbs

Returns:

The named Chado database descriptor.

makeUI

protected void makeUI()

Create the UI appropriate for this.op.

makeReadDataUI

protected void makeReadDataUI()

Creates the user interface for OP_READ_DATA.

getOperation

protected org.bdgp.io.IOOperation getOperation()

Returns:

The IOOperation this UI was instantiated to perform.

getComboBoxValue

protected java.lang.String getComboBoxValue(javax.swing.JComboBox cb)

Method that extracts the currently-selected value of a JComboBox.

Parameters:

cb - The aforementioned JComboBox

Returns:

The currently-selected String, or null if there is not a unique String-valued current selection.

clearSeqChoiceComboBox

protected void clearSeqChoiceComboBox()

Reset the seqChoiceComboBox to its original state; called when the current database changes.

getDriverClass

protected java.lang.String getDriverClass()

getJdbcUrl

protected java.lang.String getJdbcUrl()

getUsername

protected java.lang.String getUsername()

getPassword

protected java.lang.String getPassword()

getSelectedSeqType

protected java.lang.String getSelectedSeqType()

getSequenceId

protected java.lang.String getSequenceId()