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java.lang.Object | +--java.awt.Component | +--java.awt.Container | +--javax.swing.JComponent | +--org.biojava.bio.gui.SequencePanel
A panel that visualy 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.
Inner Class Summary | |
class |
SequencePanel.Border
|
Inner classes inherited from class javax.swing.JComponent |
javax.swing.JComponent.AccessibleJComponent |
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 javax.swing.SwingConstants |
BOTTOM,
CENTER,
EAST,
HORIZONTAL,
LEADING,
LEFT,
NORTH,
NORTH_EAST,
NORTH_WEST,
RIGHT,
SOUTH,
SOUTH_EAST,
SOUTH_WEST,
TOP,
TRAILING,
VERTICAL,
WEST |
Constructor Summary | |
SequencePanel()
|
Method Summary | |
void |
addRenderer(SequenceRenderer r)
|
int |
getDirection()
|
SequencePanel.Border |
getLeadingBorder()
|
int |
getLines()
|
double |
getScale()
|
Sequence |
getSequence()
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int |
getSpacer()
|
SequencePanel.Border |
getTrailingBorder()
|
int |
graphicsToSequence(double gPos)
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void |
paintComponent(java.awt.Graphics g)
|
void |
resizeAndValidate()
|
double |
sequenceToGraphics(int seqPos)
|
void |
setDirection(int dir)
|
void |
setLines(int lines)
|
void |
setScale(double scale)
|
void |
setSequence(Sequence s)
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void |
setSpacer(int spacer)
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Methods inherited from class javax.swing.JComponent |
addAncestorListener,
addNotify,
addPropertyChangeListener,
addPropertyChangeListener,
addVetoableChangeListener,
computeVisibleRect,
contains,
createToolTip,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
fireVetoableChange,
getAccessibleContext,
getActionForKeyStroke,
getAlignmentX,
getAlignmentY,
getAutoscrolls,
getBorder,
getBounds,
getClientProperty,
getComponentGraphics,
getConditionForKeyStroke,
getDebugGraphicsOptions,
getGraphics,
getHeight,
getInsets,
getInsets,
getLocation,
getMaximumSize,
getMinimumSize,
getNextFocusableComponent,
getPreferredSize,
getRegisteredKeyStrokes,
getRootPane,
getSize,
getToolTipLocation,
getToolTipText,
getToolTipText,
getTopLevelAncestor,
getUIClassID,
getVisibleRect,
getWidth,
getX,
getY,
grabFocus,
hasFocus,
isDoubleBuffered,
isFocusCycleRoot,
isFocusTraversable,
isLightweightComponent,
isManagingFocus,
isOpaque,
isOptimizedDrawingEnabled,
isPaintingTile,
isRequestFocusEnabled,
isValidateRoot,
paint,
paintBorder,
paintChildren,
paintImmediately,
paintImmediately,
paramString,
print,
printAll,
processComponentKeyEvent,
processFocusEvent,
processKeyEvent,
processMouseMotionEvent,
putClientProperty,
registerKeyboardAction,
registerKeyboardAction,
removeAncestorListener,
removeNotify,
removePropertyChangeListener,
removePropertyChangeListener,
removeVetoableChangeListener,
repaint,
repaint,
requestDefaultFocus,
requestFocus,
resetKeyboardActions,
reshape,
revalidate,
scrollRectToVisible,
setAlignmentX,
setAlignmentY,
setAutoscrolls,
setBackground,
setBorder,
setDebugGraphicsOptions,
setDoubleBuffered,
setEnabled,
setFont,
setForeground,
setMaximumSize,
setMinimumSize,
setNextFocusableComponent,
setOpaque,
setPreferredSize,
setRequestFocusEnabled,
setToolTipText,
setUI,
setVisible,
unregisterKeyboardAction,
update,
updateUI |
Methods inherited from class java.awt.Container |
add,
add,
add,
add,
add,
addContainerListener,
addImpl,
countComponents,
deliverEvent,
doLayout,
findComponentAt,
findComponentAt,
getComponent,
getComponentAt,
getComponentAt,
getComponentCount,
getComponents,
getLayout,
insets,
invalidate,
isAncestorOf,
layout,
list,
list,
locate,
minimumSize,
paintComponents,
preferredSize,
printComponents,
processContainerEvent,
processEvent,
remove,
remove,
removeAll,
removeContainerListener,
setCursor,
setLayout,
validate,
validateTree |
Methods inherited from class java.awt.Component |
action,
add,
addComponentListener,
addFocusListener,
addInputMethodListener,
addKeyListener,
addMouseListener,
addMouseMotionListener,
bounds,
checkImage,
checkImage,
coalesceEvents,
contains,
createImage,
createImage,
disable,
disableEvents,
dispatchEvent,
enable,
enable,
enableEvents,
enableInputMethods,
getBackground,
getBounds,
getColorModel,
getComponentOrientation,
getCursor,
getDropTarget,
getFont,
getFontMetrics,
getForeground,
getInputContext,
getInputMethodRequests,
getLocale,
getLocation,
getLocationOnScreen,
getName,
getParent,
getPeer,
getSize,
getToolkit,
getTreeLock,
gotFocus,
handleEvent,
hide,
imageUpdate,
inside,
isDisplayable,
isEnabled,
isLightweight,
isShowing,
isValid,
isVisible,
keyDown,
keyUp,
list,
list,
list,
location,
lostFocus,
mouseDown,
mouseDrag,
mouseEnter,
mouseExit,
mouseMove,
mouseUp,
move,
nextFocus,
paintAll,
postEvent,
prepareImage,
prepareImage,
processComponentEvent,
processInputMethodEvent,
processMouseEvent,
remove,
removeComponentListener,
removeFocusListener,
removeInputMethodListener,
removeKeyListener,
removeMouseListener,
removeMouseMotionListener,
repaint,
repaint,
repaint,
resize,
resize,
setBounds,
setBounds,
setComponentOrientation,
setDropTarget,
setLocale,
setLocation,
setLocation,
setName,
setSize,
setSize,
show,
show,
size,
toString,
transferFocus |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
wait,
wait,
wait |
Constructor Detail |
public SequencePanel()
Method Detail |
public void setSequence(Sequence s)
public Sequence getSequence()
public void setDirection(int dir) throws java.lang.IllegalArgumentException
public int getDirection()
public void setSpacer(int spacer)
public int getSpacer()
public void setScale(double scale)
public double getScale()
public void setLines(int lines)
public int getLines()
public SequencePanel.Border getLeadingBorder()
public SequencePanel.Border getTrailingBorder()
public void paintComponent(java.awt.Graphics g)
public void addRenderer(SequenceRenderer r)
public double sequenceToGraphics(int seqPos)
public int graphicsToSequence(double gPos)
public void resizeAndValidate()
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