apollo.gui.detailviewers.sequencealigner
Class TierPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  apollo.gui.detailviewers.sequencealigner.AbstractTierPanel
                      apollo.gui.detailviewers.sequencealigner.TierPanel

All Implemented Interfaces:

AnnotationChangeListener, BaseScrollable, TierPanelI, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.Scrollable

public class TierPanel
extends AbstractTierPanel

A Tier Panel is a JPanel which is used to render a TierI. The Orientation of the tier panel determines what direction the tier should be rendered while the BaseRendererI determines how each individual base is rendered.

See Also:

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

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

TierPanel(TierI tier)
Constructor.

TierPanel(TierI tier, Orientation orientation, BaseRendererI renderer)
Constructor.

Method Summary

SeqFeatureI	featureAt(int p, TierI.Level level) Given a pixel position return the feature at that position
int	getBaseHeight() pixel size
int	getBaseWidth() pixel size
int	getHigh() the highest pixel position on the tier
int	getHigh(SeqFeatureI f) the highest pixel position on a feature
int	getLow() the lowest pixel position on the tier
int	getLow(SeqFeatureI f) the lowest pixel position on a feature
SeqFeatureI	getNextFeature(int p, TierI.Level level) Given a pixel position return the next feature on the tier
Orientation	getOrientation()
java.awt.Point	getPixelForPosition(int p) Gets a pixel in the tier panel for a given (pixel) position in the tier panel
int	getPositionForPixel(java.awt.Point p) Gets the (pixel) position in the tierPanel for a given pixel
java.awt.Dimension	getPreferredScrollableViewportSize() These Are the methods needed to implement the Scrollable interface.
SeqFeatureI	getPrevFeature(int p, TierI.Level level) Given a pixel position return the previous feature on the tier
BaseRendererI	getRenderer()
int	getScrollableBlockIncrement(java.awt.Rectangle visibleRect, int orientation, int direction)
boolean	getScrollableTracksViewportHeight()
boolean	getScrollableTracksViewportWidth()
int	getScrollableUnitIncrement(java.awt.Rectangle visibleRect, int orientation, int direction)
TierI	getTier()
int	getVisibleBase()
int	getVisibleBaseCount()
boolean	handleAnnotationChangeEvent(AnnotationChangeEvent evt)
void	paint(java.awt.Graphics g) Paints this tier within the clipping bounds of the graphic.
int	pixelPositionToTierPosition(int p)
void	reformat(boolean isRecursive) Set the preferred size for this panel
void	scrollToBase(int pos)
void	setOrientation(Orientation orientation)
void	setRenderer(BaseRendererI r)
int	tierPositionToPixelPosition(int p)

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, 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

Constructor Detail

TierPanel

public TierPanel(TierI tier)

Constructor. The default orientation is FIVE_TO_THREE.

Parameters:

tier - the tier to be rendered

TierPanel

public TierPanel(TierI tier,
                 Orientation orientation,
                 BaseRendererI renderer)

Constructor.

Parameters:

tier -

orientation -

renderer -

Method Detail

paint

public void paint(java.awt.Graphics g)

Paints this tier within the clipping bounds of the graphic.

Specified by:

paint in interface TierPanelI

Overrides:

paint in class javax.swing.JComponent

Parameters:

g - the graphic in which the tier will be painted

reformat

public void reformat(boolean isRecursive)

Set the preferred size for this panel

getBaseWidth

public int getBaseWidth()

pixel size

getBaseHeight

public int getBaseHeight()

pixel size

getPositionForPixel

public int getPositionForPixel(java.awt.Point p)

Gets the (pixel) position in the tierPanel for a given pixel

getPixelForPosition

public java.awt.Point getPixelForPosition(int p)

Gets a pixel in the tier panel for a given (pixel) position in the tier panel

pixelPositionToTierPosition

public int pixelPositionToTierPosition(int p)

tierPositionToPixelPosition

public int tierPositionToPixelPosition(int p)

getHigh

public int getHigh()

the highest pixel position on the tier

getLow

public int getLow()

the lowest pixel position on the tier

getHigh

public int getHigh(SeqFeatureI f)

the highest pixel position on a feature

getLow

public int getLow(SeqFeatureI f)

the lowest pixel position on a feature

getNextFeature

public SeqFeatureI getNextFeature(int p,
                                  TierI.Level level)

Given a pixel position return the next feature on the tier

featureAt

public SeqFeatureI featureAt(int p,
                             TierI.Level level)

Given a pixel position return the feature at that position

getPrevFeature

public SeqFeatureI getPrevFeature(int p,
                                  TierI.Level level)

Given a pixel position return the previous feature on the tier

getRenderer

public BaseRendererI getRenderer()

setRenderer

public void setRenderer(BaseRendererI r)

getTier

public TierI getTier()

getOrientation

public Orientation getOrientation()

setOrientation

public void setOrientation(Orientation orientation)

getPreferredScrollableViewportSize

public java.awt.Dimension getPreferredScrollableViewportSize()

These Are the methods needed to implement the Scrollable interface.

See Also:

Scrollable

getScrollableBlockIncrement

public int getScrollableBlockIncrement(java.awt.Rectangle visibleRect,
                                       int orientation,
                                       int direction)

getScrollableTracksViewportHeight

public boolean getScrollableTracksViewportHeight()

getScrollableTracksViewportWidth

public boolean getScrollableTracksViewportWidth()

getScrollableUnitIncrement

public int getScrollableUnitIncrement(java.awt.Rectangle visibleRect,
                                      int orientation,
                                      int direction)

getVisibleBase

public int getVisibleBase()

getVisibleBaseCount

public int getVisibleBaseCount()

scrollToBase

public void scrollToBase(int pos)

handleAnnotationChangeEvent

public boolean handleAnnotationChangeEvent(AnnotationChangeEvent evt)