apollo.dataadapter.ensj19
Class EnsJAdapterGUI

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.bdgp.swing.AbstractDataAdapterUI
                      apollo.dataadapter.ensj19.EnsJAdapterGUI

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, org.bdgp.io.DataAdapterUI

Direct Known Subclasses:

AnnotationEnsJAdapterGUI

public abstract class EnsJAdapterGUI
extends org.bdgp.swing.AbstractDataAdapterUI

Configuration GUI for the EnsJAdapter class. It enables the user to specify:

• a region of a chromosome to retrieve data, or a clone fragment (contig accesion/stable ID).
• Ensj-driver settings. Where to get data from.
• Logging configuration for ensj-core.

This class interacts with the Apollo history framework by getting and setting various history parameters.

Usage: the user should add the line DataAdapterInstall "apollo.dataadapter.ensj.EnsJAdapter" to her apollo.cfg file. The Adaptor and this GUI will then be made available from the initial apollo screen.

Originally based on EnsCGIAdaptorGUI.

See Also:

Serialized Form

Nested Class Summary

class	EnsJAdapterGUI.ChromosomeDropdownPopupListener When the user pops up the chromosome dropdown, it is populated - this listener makes the call to the driver, in turn to retrieve the chromsome list.
class	EnsJAdapterGUI.DataSourceChangeListener This class clears out chromosome dd, leaving the initialisation taks to the dd's popup menu listener
class	EnsJAdapterGUI.DataTypeButton

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 static java.lang.String	DEFAULT_CONFIG_FILE
javax.swing.JPanel	locationPanel
protected static org.apache.log4j.Logger	logger

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

EnsJAdapterGUI(org.bdgp.io.IOOperation op)

Method Summary

protected void	buildGUI()
protected javax.swing.JPanel	buildIncludePanel()
protected javax.swing.JPanel	buildLocationPanel()
protected javax.swing.border.TitledBorder	createBorder(java.lang.String label)
abstract java.util.Properties	createStateInformation()
protected java.lang.String	findFile(java.lang.String file) Trys to locate file using apollo's Config class first and by searching the classpath second.
protected java.awt.event.ActionListener	getChrAction()
javax.swing.JRadioButton	getChrButton()
javax.swing.JComboBox	getChrDropdown()
javax.swing.JComboBox	getChrStartEndList()
protected javax.swing.JRadioButton	getCloneFragmentButton()
javax.swing.Box	getCloneFragmentPanel()
org.bdgp.io.DataAdapter	getDataAdapter()
protected EnsJAdapterGUI.DataTypeButton[]	getDataTypeButtons()
javax.swing.JTextField	getEndTextBox()
protected java.util.Properties	getInitialSettings()
javax.swing.JPanel	getLocationPanel()
java.lang.String	getLoggingFile()
org.bdgp.io.IOOperation	getOperation()
protected java.util.Vector	getPrefixedProperties(java.util.Properties settings, java.lang.String prefix, boolean convertValueToFilePath) Construct a vector containing all the values of properties with a key that begins with _prefix_.
java.util.Properties	getProperties() Returns the UI properties for this DataAdapterUI.
java.lang.String	getSelectedChr()
java.lang.String	getSelectedChrStartEnd()
protected java.lang.String	getSelectedCloneFragment()
java.lang.String	getSelectedEnd()
java.lang.String	getSelectedStableID()
java.lang.String	getSelectedStart()
javax.swing.JRadioButton	getStableIdButton()
javax.swing.JTextField	getStartTextBox()
void	initialiseChromosomeDropdown()
protected boolean	isChromosomeListInitialised()
protected void	putPrefixedProperties(java.util.Properties settings, java.util.Vector values, java.lang.String prefix) Puts each element from _values_ into _settings_.
void	setDataAdapter(org.bdgp.io.DataAdapter adapter) Sets the data adapter for this UI.
protected void	setDataTypeButtons(EnsJAdapterGUI.DataTypeButton[] buttons)
void	setLoggingFile(java.lang.String newValue)
void	setProperties(java.util.Properties input) Loads history values into 'drop down' lists and other GUI components.
void	setSelectedStableId(java.lang.String stableId)

Methods inherited from class org.bdgp.swing.AbstractDataAdapterUI

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, getPreferredSize, 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, doLayout, 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

Methods inherited from interface org.bdgp.io.DataAdapterUI

doOperation

Field Detail

logger

protected static final org.apache.log4j.Logger logger

DEFAULT_CONFIG_FILE

protected static final java.lang.String DEFAULT_CONFIG_FILE

See Also:

Constant Field Values

locationPanel

public javax.swing.JPanel locationPanel

Constructor Detail

EnsJAdapterGUI

public EnsJAdapterGUI(org.bdgp.io.IOOperation op)

Method Detail

getPrefixedProperties

protected java.util.Vector getPrefixedProperties(java.util.Properties settings,
                                                 java.lang.String prefix,
                                                 boolean convertValueToFilePath)

Construct a vector containing all the values of properties with a key that begins with _prefix_. The indexes should begin at 0 and be consecutive. Example key/value format expected:

 cloneFragmentItem0=3333
 cloneFragmentItem1=55
 

putPrefixedProperties

protected void putPrefixedProperties(java.util.Properties settings,
                                     java.util.Vector values,
                                     java.lang.String prefix)

Puts each element from _values_ into _settings_. Each element is given a unique name beginning with _prefix_. An additional element is added to the vector containing the number of elements. This is the inverse of "getPrefixedProperties()"

setProperties

public void setProperties(java.util.Properties input)

Loads history values into 'drop down' lists and other GUI components. Uses defaults where necessary.

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.

Returns:

all of the history information for the drop-down lists.

createBorder

protected javax.swing.border.TitledBorder createBorder(java.lang.String label)

buildLocationPanel

protected javax.swing.JPanel buildLocationPanel()

buildIncludePanel

protected javax.swing.JPanel buildIncludePanel()

buildGUI

protected void buildGUI()

setDataAdapter

public void setDataAdapter(org.bdgp.io.DataAdapter adapter)

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

Sets the data adapter for this UI. Since the UI provides it's own implementation of the IOOperation via the {link #doOperation(Object)}, the DataAdapterUI can decide whether or not to actually use the DataAdapter to perform the operation. However, a correct implementation of this interface will use the DataAdapter given in setDataAdapter.

Specified by:

setDataAdapter in interface org.bdgp.io.DataAdapterUI

Overrides:

setDataAdapter in class org.bdgp.swing.AbstractDataAdapterUI

getDataAdapter

public org.bdgp.io.DataAdapter getDataAdapter()

getSelectedStableID

public java.lang.String getSelectedStableID()

getSelectedCloneFragment

protected java.lang.String getSelectedCloneFragment()

getSelectedChrStartEnd

public java.lang.String getSelectedChrStartEnd()

getSelectedChr

public java.lang.String getSelectedChr()

getSelectedStart

public java.lang.String getSelectedStart()

getSelectedEnd

public java.lang.String getSelectedEnd()

getChrDropdown

public javax.swing.JComboBox getChrDropdown()

getStartTextBox

public javax.swing.JTextField getStartTextBox()

getEndTextBox

public javax.swing.JTextField getEndTextBox()

findFile

protected java.lang.String findFile(java.lang.String file)

Trys to locate file using apollo's Config class first and by searching the classpath second.

Returns:

filpath to file IF found, otherwise null.

getChrAction

protected java.awt.event.ActionListener getChrAction()

getChrStartEndList

public javax.swing.JComboBox getChrStartEndList()

getChrButton

public javax.swing.JRadioButton getChrButton()

getCloneFragmentButton

protected javax.swing.JRadioButton getCloneFragmentButton()

getStableIdButton

public javax.swing.JRadioButton getStableIdButton()

getDataTypeButtons

protected EnsJAdapterGUI.DataTypeButton[] getDataTypeButtons()

setDataTypeButtons

protected void setDataTypeButtons(EnsJAdapterGUI.DataTypeButton[] buttons)

getInitialSettings

protected java.util.Properties getInitialSettings()

getCloneFragmentPanel

public javax.swing.Box getCloneFragmentPanel()

getLocationPanel

public javax.swing.JPanel getLocationPanel()

setSelectedStableId

public void setSelectedStableId(java.lang.String stableId)

getOperation

public org.bdgp.io.IOOperation getOperation()

setLoggingFile

public void setLoggingFile(java.lang.String newValue)

getLoggingFile

public java.lang.String getLoggingFile()

initialiseChromosomeDropdown

public void initialiseChromosomeDropdown()

isChromosomeListInitialised

protected boolean isChromosomeListInitialised()

createStateInformation

public abstract java.util.Properties createStateInformation()
                                                     throws ApolloAdapterException

Throws:

ApolloAdapterException