org.biojava.bio.gui.sequence

Class TranslatedSequencePanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

org.biojava.bio.gui.sequence.TranslatedSequencePanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, SwingConstants, SequenceRenderContext, Changeable

public class TranslatedSequencePanel
extends JComponent
implements SequenceRenderContext, Changeable

TranslatedSequencePanel is a panel that displays a Sequence. Its features are that it will always draw at low pixel coordinates when using Java2D to render very long sequences and it is quite fast (approximately 8x faster than SequencePanel

.

A TranslatedSequencePanel can either display the sequence from left-to-right (HORIZONTAL) or from top-to-bottom (VERTICAL). It has an associated scale which is the number of pixels per symbol and a translation which is the number of Symbols to skip before rendering starts. In order to produce a scrolling effect, the setSymbolTranslation method may be hooked up to an Adjustable such as JScrollBar or to an event listener.

The exact number of Symbols rendered depends on the width of the panel and the scale. Resizing the panel will cause the number of Symbols rendered to change accordingly.

The panel will fill its background to the Color defined by the setBackground() method provided that it has been defined as opaque using setOpaque().

The change event handling code is based on the original panel and other BioJava components by Matthew and Thomas.

Since:

1.2

Author:

Keith James, Matthew Pocock, Thomas Down, Jolyon Holdstock

See Also:

Serialized Form

Nested Class Summary

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

JComponent.AccessibleJComponent

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

Container.AccessibleAWTContainer

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

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderContext

SequenceRenderContext.Border

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	RENDERER Constant RENDERER is a ChangeType which indicates a change to the renderer, requiring a layout update.
static ChangeType	TRANSLATION Constant TRANSLATION is a ChangeType which indicates a change to the translation, requiring a paint update.

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 org.biojava.bio.gui.sequence.SequenceRenderContext

LAYOUT, REPAINT

Fields inherited from interface javax.swing.SwingConstants

BOTTOM, CENTER, EAST, HORIZONTAL, LEADING, LEFT, NEXT, NORTH, NORTH_EAST, NORTH_WEST, PREVIOUS, RIGHT, SOUTH, SOUTH_EAST, SOUTH_WEST, TOP, TRAILING, VERTICAL, WEST

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

Constructors

Constructor and Description
TranslatedSequencePanel() Creates a new TranslatedSequencePanel with the default settings (direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font).

Method Summary

Methods

Modifier and Type	Method and Description
void	addChangeListener(ChangeListener cl) addChangeListener adds a listener for all types of change.
void	addChangeListener(ChangeListener cl, ChangeType ct) addChangeListener adds a listener for specific types of change.
void	addSequenceViewerListener(SequenceViewerListener svl) addSequenceViewerListener adds a listener for mouse click SequenceViewerEvents.
void	addSequenceViewerMotionListener(SequenceViewerMotionListener svml) addSequenceViewerMotionListener adds a listener for mouse motion SequenceViewerEvents.
protected ChangeSupport	getChangeSupport(ChangeType ct) getChangeSupport lazily instantiates a helper for change listeners.
int	getDirection() getDirection returns the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.
FeatureHolder	getFeatures() getFeatures returns all of the Features belonging to the currently rendered Sequence.
SequenceRenderContext.Border	getLeadingBorder() getLeadingBorder returns the leading border.
RangeLocation	getRange() getRange returns a RangeLocation representing the region of the sequence currently being rendered.
SequenceRenderer	getRenderer() getRenderer returns the current SequenceRenderer.
RenderingHints	getRenderingHints() getRenderingHints returns the RenderingHints currently being used by the Graphics2D instances of delegate renderers.
double	getScale() getScale returns the scale in pixels per Symbol.
SymbolList	getSequence() getSequence returns the entire Sequence currently being rendered.
SymbolList	getSymbols() getSymbols returns all of the Symbols belonging to the currently rendered Sequence.
int	getSymbolTranslation() getSymbolTranslation returns the current translation in Symbols which will be applied when rendering.
SequenceRenderContext.Border	getTrailingBorder() getTrailingBorder returns the trailing border.
int	getVisibleSymbolCount() getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the TranslatedSequencePanel at the current scale.
int	graphicsToSequence(double graphicsPos) graphicsToSequence converts a graphical position to a sequence index.
int	graphicsToSequence(Point2D point) graphicsToSequence converts a graphical position to a sequence index.
protected boolean	hasListeners() hasListeners returns true if there are active listeners for BioJava events.
protected boolean	isActive() isActive returns true if both the Sequence to be rendered and the SequenceRenderer are not null.
boolean	isUnchanging(ChangeType ct) A particular ChangeType can never be raised by this Changeable.
void	paintComponent(Graphics g) paintComponent paints this component.
void	removeChangeListener(ChangeListener cl) removeChangeListener removes a listener.
void	removeChangeListener(ChangeListener cl, ChangeType ct) removeChangeListener removes a listener.
void	removeSequenceViewerListener(SequenceViewerListener svl) removeSequenceViewerListener removes a listener for mouse click SequenceViewerEvents.
void	removeSequenceViewerMotionListener(SequenceViewerMotionListener svml) addSequenceViewerMotionListener removes a listener for mouse motion SequenceViewerEvents.
void	resizeAndValidate() resizeAndValidate sets the minimum, preferred and maximum sizes of the component according to the current leading and trailing borders, renderer depth and visible symbol count.
double	sequenceToGraphics(int sequencePos) sequenceToGraphics converts a sequence index to a graphical position.
void	setDirection(int direction) setDirection sets the direction in which this context will render sequences - HORIZONTAL or VERTICAL.
void	setRenderer(SequenceRenderer renderer) setRenderer sets the current SequenceRenderer.
void	setRenderingHints(RenderingHints hints) setRenderingHints sets the RenderingHints which will be used by the Graphics2D instances of delegate renderers.
void	setScale(double scale) setScale sets the scale in pixels per Symbol.
void	setSequence(SymbolList sequence) setSequence sets the Sequence to be rendered.
void	setSymbolTranslation(int translation) setSymbolTranslation sets the translation in Symbols which will be applied when rendering.

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getAccessibleContext, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, 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, getUIClassID, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, paramString, 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, updateUI

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, 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, 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, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.bio.gui.sequence.SequenceRenderContext

getFont

Field Detail

RENDERER

public static final ChangeType RENDERER

Constant RENDERER is a ChangeType which indicates a change to the renderer, requiring a layout update.

TRANSLATION

public static final ChangeType TRANSLATION

Constant TRANSLATION is a ChangeType which indicates a change to the translation, requiring a paint update.

Constructor Detail

TranslatedSequencePanel

public TranslatedSequencePanel()

Creates a new TranslatedSequencePanel with the default settings (direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font).

Method Detail

getSequence

public SymbolList getSequence()

getSequence returns the entire Sequence currently being rendered.

Returns:

a Sequence.

setSequence

public void setSequence(SymbolList sequence)

setSequence sets the Sequence to be rendered.

Parameters:

sequence - a Sequence.

getSymbols

public SymbolList getSymbols()

getSymbols returns all of the Symbols belonging to the currently rendered Sequence.

Specified by:

getSymbols in interface SequenceRenderContext

Returns:

a SymbolList.

getFeatures

public FeatureHolder getFeatures()

getFeatures returns all of the Features belonging to the currently rendered Sequence.

Specified by:

getFeatures in interface SequenceRenderContext

Returns:

a FeatureHolder.

getRange

public RangeLocation getRange()

getRange returns a RangeLocation representing the region of the sequence currently being rendered. This is calculated from the size of the TranslatedSequencePanel, minus its SequenceRenderContext.Borders and its delegate renderer borders (if any), the current rendering translation and the current scale. The value will therefore change when the TranslatedSequencePanel is resized or "scrolled" by changing the translation.

Specified by:

getRange in interface SequenceRenderContext

Returns:

a RangeLocation.

getDirection

public int getDirection()

getDirection returns the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.

Specified by:

getDirection in interface SequenceRenderContext

Returns:

an int.

setDirection

public void setDirection(int direction)
                  throws IllegalArgumentException

setDirection sets the direction in which this context will render sequences - HORIZONTAL or VERTICAL.

Parameters:

direction - an int.

Throws:

IllegalArgumentException - if an error occurs.

getScale

public double getScale()

getScale returns the scale in pixels per Symbol.

Specified by:

getScale in interface SequenceRenderContext

Returns:

a double.

setScale

public void setScale(double scale)

setScale sets the scale in pixels per Symbol.

Parameters:

scale - a double.

getSymbolTranslation

public int getSymbolTranslation()

getSymbolTranslation returns the current translation in Symbols which will be applied when rendering. The sequence will be rendered, immediately after any borders, starting at this translation. Values may be from 0 to the length of the rendered sequence.

Returns:

an int.

setSymbolTranslation

public void setSymbolTranslation(int translation)
                          throws IndexOutOfBoundsException

setSymbolTranslation sets the translation in Symbols which will be applied when rendering. The sequence will be rendered, immediately after any borders, starting at that translation. Values may be from 0 to the length of the rendered sequence.

Parameters:

translation - an int.

Throws:

IndexOutOfBoundsException - if the translation is greater than the sequence length.

getLeadingBorder

public SequenceRenderContext.Border getLeadingBorder()

getLeadingBorder returns the leading border.

Specified by:

getLeadingBorder in interface SequenceRenderContext

Returns:

a SequenceRenderContext.Border.

getTrailingBorder

public SequenceRenderContext.Border getTrailingBorder()

getTrailingBorder returns the trailing border.

Specified by:

getTrailingBorder in interface SequenceRenderContext

Returns:

a SequenceRenderContext.Border.

getRenderer

public SequenceRenderer getRenderer()

getRenderer returns the current SequenceRenderer.

Returns:

a SequenceRenderer.

setRenderer

public void setRenderer(SequenceRenderer renderer)
                 throws ChangeVetoException

setRenderer sets the current SequenceRenderer.

Parameters:

renderer - set the SequenceRenderer used

Throws:

ChangeVetoException

getRenderingHints

public RenderingHints getRenderingHints()

getRenderingHints returns the RenderingHints currently being used by the Graphics2D instances of delegate renderers. If none is set, the constructor creates one with a null Map.

Returns:

a RenderingHints.

setRenderingHints

public void setRenderingHints(RenderingHints hints)

setRenderingHints sets the RenderingHints which will be used by the Graphics2D instances of delegate renderers.

Parameters:

hints - a RenderingHints.

sequenceToGraphics

public double sequenceToGraphics(int sequencePos)

sequenceToGraphics converts a sequence index to a graphical position.

Specified by:

sequenceToGraphics in interface SequenceRenderContext

Parameters:

sequencePos - an int.

Returns:

a double.

graphicsToSequence

public int graphicsToSequence(double graphicsPos)

graphicsToSequence converts a graphical position to a sequence index.

Specified by:

graphicsToSequence in interface SequenceRenderContext

Parameters:

graphicsPos - a double.

Returns:

an int.

graphicsToSequence

public int graphicsToSequence(Point2D point)

graphicsToSequence converts a graphical position to a sequence index.

Specified by:

graphicsToSequence in interface SequenceRenderContext

Parameters:

point - the Point2D to transform

Returns:

an int.

getVisibleSymbolCount

public int getVisibleSymbolCount()

getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the TranslatedSequencePanel at the current scale. Note that if the translation is greater than 0, the actual number of Symbols rendered will be less.

Returns:

an int.

paintComponent

public void paintComponent(Graphics g)

paintComponent paints this component.

Overrides:

paintComponent in class JComponent

Parameters:

g - a Graphics object.

resizeAndValidate

public void resizeAndValidate()

resizeAndValidate sets the minimum, preferred and maximum sizes of the component according to the current leading and trailing borders, renderer depth and visible symbol count.

addChangeListener

public void addChangeListener(ChangeListener cl)

addChangeListener adds a listener for all types of change.

Specified by:

addChangeListener in interface Changeable

Parameters:

cl - a ChangeListener.

addChangeListener

public void addChangeListener(ChangeListener cl,
                     ChangeType ct)

addChangeListener adds a listener for specific types of change.

Specified by:

addChangeListener in interface Changeable

Parameters:

cl - a ChangeListener.

ct - a ChangeType.

removeChangeListener

public void removeChangeListener(ChangeListener cl)

removeChangeListener removes a listener.

Specified by:

removeChangeListener in interface Changeable

Parameters:

cl - a ChangeListener.

removeChangeListener

public void removeChangeListener(ChangeListener cl,
                        ChangeType ct)

removeChangeListener removes a listener.

Specified by:

removeChangeListener in interface Changeable

Parameters:

cl - a ChangeListener.

ct - a ChangeType.

isUnchanging

public boolean isUnchanging(ChangeType ct)

Description copied from interface: Changeable

A particular ChangeType can never be raised by this Changeable.

If this returns true, then it is guaranteed that change events of this type (and all child types) can never under any circumstances be fired by this Changeable instance. If it returns false, that does not mean that this type of event will or even can be raised, but that it is worth registering listeners incase.

Specified by:

isUnchanging in interface Changeable

Parameters:

ct - the ChangeType to check

Returns:

true if ChangeEvents of this type are guaranteed to never be fired

addSequenceViewerListener

public void addSequenceViewerListener(SequenceViewerListener svl)

addSequenceViewerListener adds a listener for mouse click SequenceViewerEvents.

Parameters:

svl - a SequenceViewerListener.

removeSequenceViewerListener

public void removeSequenceViewerListener(SequenceViewerListener svl)

removeSequenceViewerListener removes a listener for mouse click SequenceViewerEvents.

Parameters:

svl - a SequenceViewerListener.

addSequenceViewerMotionListener

public void addSequenceViewerMotionListener(SequenceViewerMotionListener svml)

addSequenceViewerMotionListener adds a listener for mouse motion SequenceViewerEvents.

Parameters:

svml - a SequenceViewerMotionListener.

removeSequenceViewerMotionListener

public void removeSequenceViewerMotionListener(SequenceViewerMotionListener svml)

addSequenceViewerMotionListener removes a listener for mouse motion SequenceViewerEvents.

Parameters:

svml - a SequenceViewerMotionListener.

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

getChangeSupport lazily instantiates a helper for change listeners.

Parameters:

ct - a ChangeType.

Returns:

a ChangeSupport object.

hasListeners

protected boolean hasListeners()

hasListeners returns true if there are active listeners for BioJava events.

Returns:

a boolean value.

isActive

protected boolean isActive()

isActive returns true if both the Sequence to be rendered and the SequenceRenderer are not null.

Returns:

a boolean value.