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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
apollo.gui.genomemap.ApolloPanel
public class ApolloPanel
This class is a container to hold and manage the various Views which are needed by Apollo. It holds all the views from both strands.
| 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 boolean |
allowsMovement
|
protected java.awt.Image |
backBuffer
|
protected int |
backBufferHeight
|
protected int |
backBufferWidth
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protected Controller |
controller
|
protected TierViewI |
dragTierView
|
protected ViewI |
focus
|
protected boolean |
inDrag
|
protected boolean |
inTierDrag
|
protected boolean |
invalid
|
protected ApolloLayoutManager |
layout_manager
|
protected java.awt.Rectangle |
layoutBounds
|
protected java.util.Vector |
linearViews
|
protected static org.apache.log4j.Logger |
logger
|
protected java.lang.String |
name
|
protected java.util.Vector |
pickViews
|
protected java.awt.event.MouseEvent |
pressEvent
|
protected RubberbandRectangle |
rubberband
|
protected boolean |
showEdgeMatches
|
protected StatusBar |
statusBar
|
protected boolean |
syncLimits
|
| 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 |
| Method Summary | |
|---|---|
void |
add(ViewI view)
|
void |
add(ViewI view,
java.lang.Object constraints)
Add a View to the views. |
void |
changeTierHeights(int change)
|
void |
clearEdges()
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void |
clearSelection()
|
void |
doLayout()
|
protected void |
doMiddleClick(java.awt.event.MouseEvent evt)
|
protected void |
doTierDrag(java.awt.event.MouseEvent evt)
|
protected void |
doViewDrag(java.awt.event.MouseEvent evt)
|
void |
endTierDrag(java.awt.event.MouseEvent evt)
|
void |
endViewDrag(java.awt.event.MouseEvent evt)
|
void |
finalize()
|
java.lang.Object |
getApolloLock()
|
java.awt.Image |
getBackBuffer()
|
Controller |
getController()
Gets the apollo event controller for the panel. |
java.lang.Object |
getControllerWindow()
Shouldnt this return Window - would we ever want a non-window? |
DragViewI |
getDragView()
|
java.util.Vector |
getDragViews()
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ViewI |
getFocus()
|
int |
getLinearCentre()
|
int |
getLinearMaximum()
|
int |
getLinearMinimum()
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java.lang.String |
getName()
Returns the name of the panel. |
PickViewI |
getPickViewFocus()
If focus is a pick focus, returns the PickViewI |
java.util.Vector |
getPickViews(java.awt.Rectangle bounds)
find pick views which are at least partly within a specified rectangle |
java.awt.Dimension |
getPreferredSize()
|
RubberbandRectangle |
getRubberband()
Rubberband related methods |
Selection |
getSelection()
|
StatusBar |
getStatusBar()
|
StrandedZoomableApolloPanel |
getStrandedZoomableApolloPanel()
|
protected ViewI |
getViewAt(java.awt.Point p)
Get the View at a specified location in the Panel |
java.awt.Graphics |
getViewGraphics()
Get the Graphics to draw to. |
java.util.Vector |
getViews()
get the views Vector |
java.util.Vector |
getViews(java.awt.Rectangle bounds)
find non drag views which are at least partly within a specified rectangle |
java.util.Vector |
getViews(java.awt.Rectangle bounds,
java.util.Vector viewVector)
|
int |
getVisibleBasepairWidth()
This returns the width of the panel in base pairs NOT pixels. |
boolean |
handleBaseFocusEvent(BaseFocusEvent evt)
|
boolean |
handleDataLoadEvent(DataLoadEvent evt)
|
boolean |
handleFeatureSelectionEvent(FeatureSelectionEvent evt)
FeatureSelectionListener - should this scroll to the selection? YES This sets Selection selection to the features in the selection event that are found in the views. |
boolean |
handleRubberbandEvent(RubberbandEvent evt)
|
boolean |
handleViewEvent(ViewEvent evt)
|
void |
highlightEdges(Selection sel,
boolean state)
I believe this highlights edges in other views that line up with the edges in the selection |
boolean |
isShowingEdgeMatches()
|
boolean |
isSynced()
Gets flag indicating whether to synchronise the limits on all the LinearViews. |
void |
keyPressed(java.awt.event.KeyEvent evt)
Keyboard event listeners |
void |
keyReleased(java.awt.event.KeyEvent evt)
|
void |
keyTyped(java.awt.event.KeyEvent evt)
|
void |
mouseClicked(java.awt.event.MouseEvent evt)
|
void |
mouseDragged(java.awt.event.MouseEvent evt)
There are 2 types of dragging - tierDrag and viewDrag. |
void |
mouseEntered(java.awt.event.MouseEvent evt)
MouseInputListener routines |
void |
mouseExited(java.awt.event.MouseEvent evt)
|
void |
mouseMoved(java.awt.event.MouseEvent evt)
Gets features under mouse and puts name and position in status bar |
void |
mousePressed(java.awt.event.MouseEvent evt)
When the mouse button comes down (but is not released) it may be either the right mouse button or the left. |
void |
mouseReleased(java.awt.event.MouseEvent evt)
|
void |
mouseWheelMoved(java.awt.event.MouseWheelEvent 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 |
paintComponent(java.awt.Graphics g)
Overidden paintComponent to draw any views requiring a repaint |
void |
print(java.io.File file,
java.lang.String orientation,
java.lang.String scale)
|
void |
putVerticalScrollbarsAtStart()
|
void |
remove(ViewI view)
Remove a View from the views |
void |
setController(Controller controller)
Sets the event controller for the panel. |
void |
setEdgeMatching(boolean state)
|
protected void |
setFocusView(ViewI focus)
Sets the view which has 'focus' |
void |
setInvalidity(boolean state)
Causes views to layout if this.doLayout is called |
void |
setLayout(ApolloLayoutManager manager)
Set the Apollo specific layout manager for this Panel |
void |
setLinearCentre(int Position)
Sets the linear centre for the focused view, or all LinearViews depending on syncLimits flag |
void |
setMovementAllowed(boolean state)
|
void |
setName(java.lang.String name)
Sets the name of the panel - is this used at all? |
void |
setScaleView(ScaleView scale)
|
void |
setStatusBar(StatusBar sb)
|
void |
setSyncLimits(boolean state)
Sets flag indicating whether to synchronise the limits on all the LinearViews. |
void |
setSyncLimits(boolean state,
int reglow,
int reghigh)
|
void |
setViewGraphics(java.awt.Graphics g)
Set the Graphics to draw to. |
void |
setVisible(boolean state)
|
void |
setZoomFactor(double xFactor,
double yFactor)
Set zoom factor on all views |
void |
setZoomFactorX(double xFactor)
Set X zoom factor on all views |
void |
setZoomFactorY(double yFactor)
Set Y zoom factor on all views |
protected void |
syncViewLimits(int reglow,
int reghigh)
Actually do the view limit synchronisation This actually adds a 1/100 of seq length as padding to each end, and updates all the views with these limits. |
| 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, 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, 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, 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, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle |
| Methods inherited from class java.lang.Object |
|---|
clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
| Field Detail |
|---|
protected static final org.apache.log4j.Logger logger
protected java.awt.Image backBuffer
protected int backBufferWidth
protected int backBufferHeight
protected java.util.Vector linearViews
protected java.util.Vector pickViews
protected ApolloLayoutManager layout_manager
protected Controller controller
protected ViewI focus
protected java.lang.String name
protected boolean syncLimits
protected RubberbandRectangle rubberband
protected boolean inDrag
protected java.awt.event.MouseEvent pressEvent
protected boolean inTierDrag
protected TierViewI dragTierView
protected StatusBar statusBar
protected java.awt.Rectangle layoutBounds
protected boolean invalid
protected boolean allowsMovement
protected boolean showEdgeMatches
| Method Detail |
|---|
public final java.lang.Object getApolloLock()
public void add(ViewI view,
java.lang.Object constraints)
public void add(ViewI view)
public void setScaleView(ScaleView scale)
public void setLayout(ApolloLayoutManager manager)
public void remove(ViewI view)
public void putVerticalScrollbarsAtStart()
public void setSyncLimits(boolean state)
public void setSyncLimits(boolean state,
int reglow,
int reghigh)
public boolean isSynced()
protected void syncViewLimits(int reglow,
int reghigh)
public void setLinearCentre(int Position)
public void setMovementAllowed(boolean state)
public int getLinearCentre()
public int getLinearMinimum()
public int getLinearMaximum()
public void setVisible(boolean state)
setVisible in class javax.swing.JComponentpublic int getVisibleBasepairWidth()
public void setZoomFactor(double xFactor,
double yFactor)
public void setZoomFactorX(double xFactor)
public void setZoomFactorY(double yFactor)
public void setController(Controller controller)
setController in interface ControlledObjectIpublic Selection getSelection()
getSelection in interface ApolloPanelIpublic Controller getController()
getController in interface ControlledObjectIgetController in interface ApolloPanelIpublic java.lang.Object getControllerWindow()
ControlledObjectI
getControllerWindow in interface ControlledObjectIpublic boolean needsAutoRemoval()
ControlledObjectI
needsAutoRemoval in interface ControlledObjectI
public void print(java.io.File file,
java.lang.String orientation,
java.lang.String scale)
public void paintComponent(java.awt.Graphics g)
paintComponent in class javax.swing.JComponentpublic void doLayout()
doLayout in class java.awt.Containerpublic void setViewGraphics(java.awt.Graphics g)
g - The new graphics to draw to.public void setInvalidity(boolean state)
public java.awt.Graphics getViewGraphics()
g - The new graphics to draw to.public java.awt.Image getBackBuffer()
getBackBuffer in interface ApolloPanelIpublic java.lang.String getName()
getName in class java.awt.Componentpublic void setName(java.lang.String name)
setName in class java.awt.Componentname - The name of the panel.protected ViewI getViewAt(java.awt.Point p)
protected void setFocusView(ViewI focus)
public ViewI getFocus()
getFocus in interface ApolloPanelIpublic boolean handleDataLoadEvent(DataLoadEvent evt)
handleDataLoadEvent in interface DataLoadListenerpublic boolean handleViewEvent(ViewEvent evt)
handleViewEvent in interface ViewListenerpublic boolean handleBaseFocusEvent(BaseFocusEvent evt)
handleBaseFocusEvent in interface BaseFocusListenerpublic boolean handleFeatureSelectionEvent(FeatureSelectionEvent evt)
handleFeatureSelectionEvent in interface FeatureSelectionListener
public void highlightEdges(Selection sel,
boolean state)
public void setEdgeMatching(boolean state)
public boolean isShowingEdgeMatches()
public void clearEdges()
public void mouseWheelMoved(java.awt.event.MouseWheelEvent evt)
mouseWheelMoved in interface java.awt.event.MouseWheelListenerpublic void mouseEntered(java.awt.event.MouseEvent evt)
mouseEntered in interface java.awt.event.MouseListenerpublic void mouseExited(java.awt.event.MouseEvent evt)
mouseExited in interface java.awt.event.MouseListenerpublic void mouseClicked(java.awt.event.MouseEvent evt)
mouseClicked in interface java.awt.event.MouseListenerpublic PickViewI getPickViewFocus()
protected void doMiddleClick(java.awt.event.MouseEvent evt)
public void mousePressed(java.awt.event.MouseEvent evt)
mousePressed in interface java.awt.event.MouseListenerevt - public void mouseReleased(java.awt.event.MouseEvent evt)
mouseReleased in interface java.awt.event.MouseListenerpublic void endViewDrag(java.awt.event.MouseEvent evt)
public void endTierDrag(java.awt.event.MouseEvent evt)
public void mouseDragged(java.awt.event.MouseEvent evt)
mouseDragged in interface java.awt.event.MouseMotionListenerprotected void doTierDrag(java.awt.event.MouseEvent evt)
protected void doViewDrag(java.awt.event.MouseEvent evt)
public void mouseMoved(java.awt.event.MouseEvent evt)
mouseMoved in interface java.awt.event.MouseMotionListenerpublic void changeTierHeights(int change)
public void keyPressed(java.awt.event.KeyEvent evt)
keyPressed in interface java.awt.event.KeyListenerpublic void keyReleased(java.awt.event.KeyEvent evt)
keyReleased in interface java.awt.event.KeyListenerpublic void keyTyped(java.awt.event.KeyEvent evt)
keyTyped in interface java.awt.event.KeyListenerpublic RubberbandRectangle getRubberband()
public boolean handleRubberbandEvent(RubberbandEvent evt)
handleRubberbandEvent in interface RubberbandListenerpublic java.util.Vector getViews()
public java.util.Vector getPickViews(java.awt.Rectangle bounds)
public java.util.Vector getViews(java.awt.Rectangle bounds)
public java.util.Vector getViews(java.awt.Rectangle bounds,
java.util.Vector viewVector)
public java.util.Vector getDragViews()
public DragViewI getDragView()
public java.awt.Dimension getPreferredSize()
getPreferredSize in class javax.swing.JComponentpublic void clearSelection()
clearSelection in interface ApolloPanelIpublic void setStatusBar(StatusBar sb)
public StatusBar getStatusBar()
public void finalize()
finalize in class java.lang.Objectpublic StrandedZoomableApolloPanel getStrandedZoomableApolloPanel()
getStrandedZoomableApolloPanel in interface ApolloPanelI
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