apollo.gui.annotinfo
Class FeatureEditorDialog

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      apollo.gui.annotinfo.FeatureEditorDialog

All Implemented Interfaces:

DataLoadListener, AnnotationChangeListener, ControlledObjectI, FeatureSelectionListener, FeatureNavigationI, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class FeatureEditorDialog
extends javax.swing.JFrame
implements ControlledObjectI, AnnotationChangeListener, FeatureSelectionListener, DataLoadListener, FeatureNavigationI

FeatureEditorDialog Editor for comments, gene and transcript names, etc Editing is disabled in browser mode. In browser mode just used to view the comments. FeatureNavigationI interface is for internal FeatureTreePanel to call featureSelected on FeatureEditorDialog.

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JFrame.AccessibleJFrame

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

java.awt.Frame.AccessibleAWTFrame

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

java.awt.Window.AccessibleAWTWindow

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.awt.Color	bgColor
protected static org.apache.log4j.Logger	logger

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

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

Method Summary

void	addNotify()
void	dispose() disposes commentator, then calls super.dispose (Window)
static void	disposeAllEditors() Dispose all FeatureEditorDialogs currently in existence.
void	featureSelected(SeqFeatureI sf) Listen to selections from the tree view and respond to FeatureSelection events.
protected void	fireAnnotEvent(AnnotationChangeEvent ace)
protected AnnotatedFeatureI	getAnnot(SeqFeatureI sf)
Controller	getController() Gets the Controller for the object
java.lang.Object	getControllerWindow() Shouldnt this return Window - would we ever want a non-window?
protected ApolloNameAdapterI	getNameAdapter(AnnotatedFeatureI annot)
protected Transcript	getTranscript()
boolean	handleAnnotationChangeEvent(AnnotationChangeEvent evt) Calls setFeature with new annotation.
boolean	handleDataLoadEvent(DataLoadEvent e)
boolean	handleFeatureSelectionEvent(FeatureSelectionEvent evt)
boolean	needsAutoRemoval() If getControllerWindow is non null, and needsAutoRemoval is true then Controller will automatically remove the ControlledObjectI as a listener when its ControllerWindow is closing.
void	setController(Controller c) Sets the Controller for the object
void	setSelectionManager(SelectionManager sm) Set selection manager, controller for selection.
static void	showTextEditor(SeqFeatureI sf, GuiCurationState s)
static void	testNameUndo(junit.framework.TestCase testCase)
void	windowClosed(java.awt.event.WindowEvent e)

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.awt.Frame

finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, show, toBack, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

logger

protected static final org.apache.log4j.Logger logger

bgColor

protected static java.awt.Color bgColor

Method Detail

showTextEditor

public static void showTextEditor(SeqFeatureI sf,
                                  GuiCurationState s)

featureSelected

public void featureSelected(SeqFeatureI sf)

Listen to selections from the tree view and respond to FeatureSelection events. This is the method from the interface FeatureNavigationI that allows FeatureTreePanel to set the selection of FeatureEditorDialog. This is solely used by FeatureTreePanel

Specified by:

featureSelected in interface FeatureNavigationI

getTranscript

protected Transcript getTranscript()

dispose

public void dispose()

disposes commentator, then calls super.dispose (Window)

Overrides:

dispose in class java.awt.Window

windowClosed

public void windowClosed(java.awt.event.WindowEvent e)

disposeAllEditors

public static void disposeAllEditors()

Dispose all FeatureEditorDialogs currently in existence. Keeps track of all instances for this purpose

getAnnot

protected AnnotatedFeatureI getAnnot(SeqFeatureI sf)

setController

public void setController(Controller c)

Description copied from interface: ControlledObjectI

Sets the Controller for the object

Specified by:

setController in interface ControlledObjectI

getController

public Controller getController()

Description copied from interface: ControlledObjectI

Gets the Controller for the object

Specified by:

getController in interface ControlledObjectI

setSelectionManager

public void setSelectionManager(SelectionManager sm)

Set selection manager, controller for selection. Set up listener to transcript panel feature list selection. Selecting a a gene in genePanel causes a transcript to get selected which then causes this inner listener to be called. oldAnnot has to get set to new gene here i believe

addNotify

public void addNotify()

Overrides:

addNotify in class java.awt.Frame

getControllerWindow

public java.lang.Object getControllerWindow()

Description copied from interface: ControlledObjectI

Shouldnt this return Window - would we ever want a non-window?

Specified by:

getControllerWindow in interface ControlledObjectI

needsAutoRemoval

public boolean needsAutoRemoval()

Description copied from interface: ControlledObjectI

If getControllerWindow is non null, and needsAutoRemoval is true then Controller will automatically remove the ControlledObjectI as a listener when its ControllerWindow is closing. If getControllerWindow is null needsAutoRemoval is meaningless. Rename this removeAsListenerOnWindowClose?

Specified by:

needsAutoRemoval in interface ControlledObjectI

handleAnnotationChangeEvent

public boolean handleAnnotationChangeEvent(AnnotationChangeEvent evt)

Calls setFeature with new annotation. This triggers a recloning of the gene (via GeneEditPanel.loadSelectedFeature), which wipes out any uncommitted edits to the old clone. This is erroneous. The old clone needs to be preserved or copied.

Specified by:

handleAnnotationChangeEvent in interface AnnotationChangeListener

handleFeatureSelectionEvent

public boolean handleFeatureSelectionEvent(FeatureSelectionEvent evt)

Specified by:

handleFeatureSelectionEvent in interface FeatureSelectionListener

handleDataLoadEvent

public boolean handleDataLoadEvent(DataLoadEvent e)

Specified by:

handleDataLoadEvent in interface DataLoadListener

fireAnnotEvent

protected void fireAnnotEvent(AnnotationChangeEvent ace)

getNameAdapter

protected ApolloNameAdapterI getNameAdapter(AnnotatedFeatureI annot)

testNameUndo

public static void testNameUndo(junit.framework.TestCase testCase)