apollo.gui.synteny
Class CompositeApolloFrame

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      apollo.gui.ApolloFrame
                          apollo.gui.synteny.CompositeApolloFrame

All Implemented Interfaces:

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

public class CompositeApolloFrame
extends ApolloFrame

The synteny panels need to display many stranded-zoomable-apollo-panels at once, (unlike the standard apollo frame). However apollo's menus are very aware of apollo frames...this subclass is an attempt to circumvent these issues without having to rewrite lots of the apollo menu-handling code to support synteny viewing.

The idea is: to hold many copies of the instance variables that an Apollo frame usually holds (one for each browsed species). When the user their switches between different species, each copy of these instance variables is, in turn, switched over to the set specific to that species. Menu items (and anything else which explicitly needs to see the frame) should be oblivious to the change.

Of course, we override the drawing/initialisation code to set up multiple stranded-zoomable-apollo-panels, controllers etc.

Warning this code is scary

1. It is obscure

2. It relies upon the hash keys to be exact string matches to the names of variables in ApolloFrame makes this extremely vulnerable to bugs cropping up because of name changes to the variables or other changes in initialization. It completely depends upon the exposure of the object internals. It strikes me that this is really not an object that extends the basic ApolloFrame, but really one that manages ApolloFrames.

NEEDS TO BE REFACTORED!

Should CompositeApolloFrame be merged with ApolloFrame now that CAF is used for single and multi species?

See Also:

Serialized Form

Nested Class Summary

static class

CompositeApolloFrame.MacApplicationSupport

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

Fields inherited from class apollo.gui.ApolloFrame

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

static CompositeApolloFrame	getApolloFrame()
void	loadData(ApolloDataAdapterI dataAdapter, CompositeDataHolder cdh) loadData gets called with every data load(see LoadUtil).
void	loadSyntenyLink(SeqFeatureI link) Load new species and links for the link passed in This needs to be moved to LoadUtil/DataLoader
void	setLockScrolling(boolean value)
void	setShadeByPercId(boolean value)
void	setShiftZoomLock(boolean state)
void	setUseOpaqueLinks(boolean value) We have to clear data from each one of the child curation sets owned by the composite.
void	setVisible(boolean state) Propagate the setVisible call to all stranded-zoomable panels: their setVisible call is quite involved...

Methods inherited from class apollo.gui.ApolloFrame

applyLayout, centerOnScreen, completeGUIInitialization, getCompositeDataHolder, getController, getControllerWindow, getCurationManager, getCurationState, getFrame, getPreferredFrameHeight, getSplitPane, getSyntenyPanel, handleDataLoadEvent, handleLazyLoadEvent, needsAutoRemoval, saveLayout, setController, setSyntenyPanel

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

addNotify, 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, dispose, 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, 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

Method Detail

getApolloFrame

public static CompositeApolloFrame getApolloFrame()

loadData

public void loadData(ApolloDataAdapterI dataAdapter,
                     CompositeDataHolder cdh)

loadData gets called with every data load(see LoadUtil). This is where the data gets loaded (previously called init())

setVisible

public void setVisible(boolean state)

Propagate the setVisible call to all stranded-zoomable panels: their setVisible call is quite involved...

Overrides:

setVisible in class ApolloFrame

setUseOpaqueLinks

public void setUseOpaqueLinks(boolean value)

We have to clear data from each one of the child curation sets owned by the composite.

setShadeByPercId

public void setShadeByPercId(boolean value)

loadSyntenyLink

public void loadSyntenyLink(SeqFeatureI link)

Load new species and links for the link passed in This needs to be moved to LoadUtil/DataLoader

Overrides:

loadSyntenyLink in class ApolloFrame

setLockScrolling

public void setLockScrolling(boolean value)

setShiftZoomLock

public void setShiftZoomLock(boolean state)