java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - javax.swing.JComponent
    - - org.biojava.bio.gui.sequence.SequencePanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, SwingConstants, SequenceRenderContext, Changeable
```
public class SequencePanel
extends JComponent
implements 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 Description

class SequencePanel.Border
- 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

Field Summary

Fields
Modifier and Type Field 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 java.awt.image.ImageObserver
  ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
- 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

Constructor Summary

Constructors
Constructor Description

SequencePanel()
Create a new SequencePanel.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`_setRenderer(SequenceRenderer r)`
`void`	`addChangeListener(ChangeListener cl)`	Add a listener that will be informed of all changes.
`void`	`addChangeListener(ChangeListener cl, ChangeType ct)`	Add a listener that will be informed of changes of a given type.
`void`	`addSequenceViewerListener(SequenceViewerListener svl)`
`void`	`addSequenceViewerMotionListener(SequenceViewerMotionListener svml)`
`protected int[]`	`calcDist()`
`boolean`	`equals(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.
`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(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)`	A particular ChangeType can never be raised by this Changeable.
`void`	`paintComponent(Graphics g)`	Paint this component.
`void`	`removeChangeListener(ChangeListener cl)`	Remove a listener that was interested in all types of changes.
`void`	`removeChangeListener(ChangeListener cl, ChangeType ct)`	Remove a listener that was interested in a specific types of changes.
`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(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, getUI, 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, 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, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, 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(RenderingHints hints)
```
    Use this to switch on effects like Anti-aliasing etc
    
    Parameters:
    
    hints - the desired rendering properties
  - getRenderingHints
```
public 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)
```
    Description copied from interface: Changeable
    
    Add a listener that will be informed of all changes.
    
    Specified by:
    
    addChangeListener in interface Changeable
    
    Parameters:
    
    cl - the ChangeListener to add
  - addChangeListener
```
public void addChangeListener(ChangeListener cl,
                              ChangeType ct)
```
    Description copied from interface: Changeable
    
    Add a listener that will be informed of changes of a given type.
    
    Specified by:
    
    addChangeListener in interface Changeable
    
    Parameters:
    
    cl - the ChangeListener
    
    ct - the ChangeType it is to be informed of
  - removeChangeListener
```
public void removeChangeListener(ChangeListener cl)
```
    Description copied from interface: Changeable
    
    Remove a listener that was interested in all types of changes.
    
    Specified by:
    
    removeChangeListener in interface Changeable
    
    Parameters:
    
    cl - a ChangeListener to remove
  - removeChangeListener
```
public void removeChangeListener(ChangeListener cl,
                                 ChangeType ct)
```
    Description copied from interface: Changeable
    
    Remove a listener that was interested in a specific types of changes.
    
    Specified by:
    
    removeChangeListener in interface Changeable
    
    Parameters:
    
    cl - a ChangeListener to remove
    
    ct - the ChangeType that it was interested in
  - 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
  - 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 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:
    
    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(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 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(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(Object o)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object

Class SequencePanel

Nested Class Summary

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

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

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

Field Summary

Fields inherited from class javax.swing.JComponent

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

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

Fields inherited from interface javax.swing.SwingConstants

Constructor Summary

Method Summary

Methods inherited from class javax.swing.JComponent

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

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

Field Detail

RENDERER

Constructor Detail

SequencePanel

Method Detail

setRenderingHints

getRenderingHints

addSequenceViewerListener

removeSequenceViewerListener

addSequenceViewerMotionListener

removeSequenceViewerMotionListener

hasChangeListeners

getChangeSupport

hasListeners

addChangeListener

addChangeListener

removeChangeListener

removeChangeListener

isUnchanging

setSequence

getSequence

getSymbols

getFeatures

setRange

getRange

setDirection

getDirection

setScale

getScale

getLeadingBorder

getTrailingBorder

paintComponent

setRenderer

_setRenderer

sequenceToGraphics

graphicsToSequence

graphicsToSequence

resizeAndValidate

calcDist

isActive

equals

hashCode