org.biojava.bio.gui.sequence

Class SequencePanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

org.biojava.bio.gui.sequence.SequencePanel

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.swing.SwingConstants, SequenceRenderContext, Changeable

public class SequencePanel
extends javax.swing.JComponent
implements javax.swing.SwingConstants, SequenceRenderContext, Changeable

A panel that displays a Sequence.

A SequencePanel 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. It also has a lines property that controls how to wrap the sequence off one end and onto the other.

Each line in the SequencePanel is broken down into a list of strips, each rendered by an individual SequenceRenderer object. You could add a SequenceRenderer that draws on genes, another that draws repeats and another that prints out the DNA sequence. They are responsible for rendering their view of the sequence in the place that the SequencePanel positions them.

Author:

Thomas Down, Matthew Pocock, David Huen

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	SequencePanel.Border

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.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	RENDERER

Fields inherited from class javax.swing.JComponent

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

accessibleContext, 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
SequencePanel() Create a new SequencePanel.

Method Summary

Modifier and Type	Method and Description
protected void	_setRenderer(SequenceRenderer r)
void	addChangeListener(ChangeListener cl)
void	addChangeListener(ChangeListener cl, ChangeType ct)
void	addSequenceViewerListener(SequenceViewerListener svl)
void	addSequenceViewerMotionListener(SequenceViewerMotionListener svml)
protected int[]	calcDist()
boolean	equals(java.lang.Object o)
protected ChangeSupport	getChangeSupport(ChangeType ct)
int	getDirection() Retrieve the current rendering direction.
FeatureHolder	getFeatures() The features to render.
SequenceRenderContext.Border	getLeadingBorder() Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.
RangeLocation	getRange() The range of the SymbolList to render.
java.awt.RenderingHints	getRenderingHints()
double	getScale() Retrieve the current scale.
SymbolList	getSequence()
SymbolList	getSymbols() Retrieve the currently rendered SymbolList
SequenceRenderContext.Border	getTrailingBorder() Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.
int	graphicsToSequence(double gPos) Converts a graphical position into a sequence coordinate.
int	graphicsToSequence(java.awt.geom.Point2D point) Converts a graphical position into a sequence coordinate.
protected boolean	hasChangeListeners()
int	hashCode()
protected boolean	hasListeners()
protected boolean	isActive()
boolean	isUnchanging(ChangeType ct)
void	paintComponent(java.awt.Graphics g) Paint this component.
void	removeChangeListener(ChangeListener cl)
void	removeChangeListener(ChangeListener cl, ChangeType ct)
void	removeSequenceViewerListener(SequenceViewerListener svl)
void	removeSequenceViewerMotionListener(SequenceViewerMotionListener svml)
void	resizeAndValidate()
double	sequenceToGraphics(int seqPos) Converts a sequence index into a graphical coordinate.
void	setDirection(int dir) Set the direction that this SequencePanel renders in.
void	setRange(RangeLocation range)
void	setRenderer(SequenceRenderer r)
void	setRenderingHints(java.awt.RenderingHints hints) Use this to switch on effects like Anti-aliasing etc
void	setScale(double scale) Set the scale.
void	setSequence(SymbolList s) Set the SymboList to be rendered.

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, 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, getAccessibleContext, 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, finalize, getClass, notify, notifyAll, wait, wait, wait

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

getFont

Field Detail

RENDERER

public static final ChangeType RENDERER

Constructor Detail

SequencePanel

public SequencePanel()

Create a new SequencePanel.

Method Detail

setRenderingHints

public void setRenderingHints(java.awt.RenderingHints hints)

Use this to switch on effects like Anti-aliasing etc

Parameters:

hints - the desired rendering properties

getRenderingHints

public java.awt.RenderingHints getRenderingHints()

Returns:

the current rendering properties

addSequenceViewerListener

public void addSequenceViewerListener(SequenceViewerListener svl)

removeSequenceViewerListener

public void removeSequenceViewerListener(SequenceViewerListener svl)

addSequenceViewerMotionListener

public void addSequenceViewerMotionListener(SequenceViewerMotionListener svml)

removeSequenceViewerMotionListener

public void removeSequenceViewerMotionListener(SequenceViewerMotionListener svml)

hasChangeListeners

protected boolean hasChangeListeners()

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

hasListeners

protected boolean hasListeners()

addChangeListener

public void addChangeListener(ChangeListener cl)

Specified by:

addChangeListener in interface Changeable

addChangeListener

public void addChangeListener(ChangeListener cl,
                              ChangeType ct)

Specified by:

addChangeListener in interface Changeable

removeChangeListener

public void removeChangeListener(ChangeListener cl)

Specified by:

removeChangeListener in interface Changeable

removeChangeListener

public void removeChangeListener(ChangeListener cl,
                                 ChangeType ct)

Specified by:

removeChangeListener in interface Changeable

isUnchanging

public boolean isUnchanging(ChangeType ct)

Specified by:

isUnchanging in interface Changeable

setSequence

public void setSequence(SymbolList s)

Set the SymboList to be rendered. This symbol list will be passed onto the SequenceRenderer instances registered with this SequencePanel.

Parameters:

s - the SymboList to render

getSequence

public SymbolList getSequence()

getSymbols

public SymbolList getSymbols()

Retrieve the currently rendered SymbolList

Specified by:

getSymbols in interface SequenceRenderContext

Returns:

the current SymbolList

getFeatures

public FeatureHolder getFeatures()

Description copied from interface: SequenceRenderContext

The features to render.

Specified by:

getFeatures in interface SequenceRenderContext

Returns:

a FeatureHolder with the Features to render

setRange

public void setRange(RangeLocation range)

getRange

public RangeLocation getRange()

Description copied from interface: SequenceRenderContext

The range of the SymbolList to render.

Specified by:

getRange in interface SequenceRenderContext

Returns:

the RangeLocation specifying which indices (inclusive) to render

setDirection

public void setDirection(int dir)
                  throws java.lang.IllegalArgumentException

Set the direction that this SequencePanel renders in. The direction can be one of HORIZONTAL or VERTICAL. Once the direction is set, the display will redraw. HORIZONTAL represents left-to-right rendering. VERTICAL represents AceDB-style vertical rendering.

Parameters:

dir - the new rendering direction

Throws:

java.lang.IllegalArgumentException

getDirection

public int getDirection()

Retrieve the current rendering direction.

Specified by:

getDirection in interface SequenceRenderContext

Returns:

the rendering direction (one of HORIZONTAL and VERTICAL)

setScale

public void setScale(double scale)

Set the scale.

The scale parameter is interpreted as the number of pixels per symbol. This may take on a wide range of values - for example, to render the symbols as text, you will need a scale of > 8, where as to render chromosome 1 you will want a scale < 0.00000001

Parameters:

scale - the new pixels-per-symbol ratio

getScale

public double getScale()

Retrieve the current scale.

Specified by:

getScale in interface SequenceRenderContext

Returns:

the number of pixels used to render one symbol

getLeadingBorder

public SequenceRenderContext.Border getLeadingBorder()

Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.

Specified by:

getLeadingBorder in interface SequenceRenderContext

Returns:

a SequenceRenderContext.Border instance

getTrailingBorder

public SequenceRenderContext.Border getTrailingBorder()

Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.

Specified by:

getTrailingBorder in interface SequenceRenderContext

Returns:

a SequenceRenderContext.Border instance

paintComponent

public void paintComponent(java.awt.Graphics g)

Paint this component.

This calls the paint method of the currently registered SequenceRenderer after setting up the graphics appropriately.

Overrides:

paintComponent in class javax.swing.JComponent

setRenderer

public void setRenderer(SequenceRenderer r)
                 throws ChangeVetoException

Throws:

ChangeVetoException

_setRenderer

protected void _setRenderer(SequenceRenderer r)

sequenceToGraphics

public double sequenceToGraphics(int seqPos)

Description copied from interface: SequenceRenderContext

Converts a sequence index into a graphical coordinate. You will need to use this in conjunction with getDirection to correctly lay graphics out.

Specified by:

sequenceToGraphics in interface SequenceRenderContext

Parameters:

seqPos - Index within the sequence

Returns:

Equivalent graphical position in pixels

graphicsToSequence

public int graphicsToSequence(double gPos)

Description copied from interface: SequenceRenderContext

Converts a graphical position into a sequence coordinate. You will need to have used getDirection to decide whether to use the x or y coordinate.

Specified by:

graphicsToSequence in interface SequenceRenderContext

Parameters:

gPos - A pixel position

Returns:

The corresponding sequence index

graphicsToSequence

public int graphicsToSequence(java.awt.geom.Point2D point)

Description copied from interface: SequenceRenderContext

Converts a graphical position into a sequence coordinate. This will use getDirection to decide whether to use the x or y coordinate.

Specified by:

graphicsToSequence in interface SequenceRenderContext

Parameters:

point - a point representing the position

Returns:

the corresponding sequence index

resizeAndValidate

public void resizeAndValidate()

calcDist

protected int[] calcDist()

isActive

protected boolean isActive()

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object