uk.ac.man.bioinf.gui.viewer
Class JAlignmentViewer
java.lang.Object
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+--java.awt.Component
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+--java.awt.Container
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+--javax.swing.JComponent
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+--uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
- All Implemented Interfaces:
- AlignmentListener, AlignmentSelectionListener, EventListener, ImageObserver, MenuContainer, SequenceListener, Serializable
- Direct Known Subclasses:
- PrintableJAlignmentViewer
- public class JAlignmentViewer
- extends JComponent
- implements AlignmentListener, SequenceListener, AlignmentSelectionListener
JAlignmentViewer.java
Created: Tue Mar 14 16:28:59 2000
- Version:
- $Id: JAlignmentViewer.java,v 1.28 2002/03/08 14:53:57 lord Exp $
- Author:
- Phillip Lord
- See Also:
- Serialized Form
Method Summary |
void |
addCursorChangeListener(ChangeListener listener)
|
void |
changeOccurred(AlignmentEvent event)
method signalled after a change has occured to a multiple alignment |
void |
changeOccurred(SequenceEvent event)
Method called when a change occurs |
void |
clearSelection()
|
void |
deleteGapsAt(int x,
int y,
int sizeOfGap)
|
void |
deleteGapsAt(SequenceAlignmentPoint point,
int sizeOfGap)
|
void |
deleteGapsAtCursor(int sizeOfGap)
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void |
ensureSequencePointIsVisible(SequenceAlignmentPoint point)
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void |
extendSelection(SequenceAlignmentPoint point)
|
AlignmentSelectionRenderer |
getAlignmentSelectionRenderer()
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Rectangle |
getCellBounds(SequenceAlignmentPoint point)
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int |
getCellHeight()
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AlignmentViewerCellRenderer |
getCellRenderer()
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int |
getCellWidth()
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ColorMap |
getColorMap()
Returns the current color map. |
SequenceCursor |
getCursorModel()
|
FastAlignmentViewerCellRenderer |
getFastCellRenderer()
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SequenceAlignmentPoint |
getMark()
|
Dimension |
getMaximumSize()
|
Dimension |
getMinimumSize()
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SequenceAlignmentPoint |
getPoint()
|
Point |
getPointAtSequencePoint(int x,
int y)
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Dimension |
getPreferredScrollableViewportSize()
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Dimension |
getPreferredSize()
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Rectangle |
getRectangleForSequenceRectangle(SequenceAlignmentRectangle seqRect)
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int |
getScrollableBlockIncrement(Rectangle visibleRect,
int orientation,
int direction)
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boolean |
getScrollableTracksViewportHeight()
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boolean |
getScrollableTracksViewportWidth()
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int |
getScrollableUnitIncrement(Rectangle visibleRect,
int orientation,
int direction)
|
AlignmentSelectionModel |
getSelectionModel()
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SequenceAlignment |
getSequenceAlignment()
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SequenceAlignmentPoint |
getSequencePointAtPoint(int x,
int y)
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SequenceAlignmentPoint |
getSequencePointAtPoint(Point point)
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String |
getUIClassID()
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SequenceAlignmentRectangle |
getVisibleSequenceRectangle()
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void |
insertGapsAt(int x,
int y,
int sizeOfGap)
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void |
insertGapsAt(SequenceAlignmentPoint point,
int sizeOfGap)
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void |
insertGapsAtCursor(int sizeOfGap)
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boolean |
isReadonly()
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void |
moveCursor(SequenceAlignmentPoint newPoint)
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void |
moveCursorBeginningOfAlignment()
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void |
moveCursorBeginningOfSequence()
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void |
moveCursorDown(int number)
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void |
moveCursorEndOfAlignment()
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void |
moveCursorEndOfSequence()
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void |
moveCursorLeft(int number)
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void |
moveCursorPageDown()
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void |
moveCursorPageLeft()
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void |
moveCursorPageRight()
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void |
moveCursorPageUp()
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void |
moveCursorRight(int number)
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void |
moveCursorToSequencePoint(int x,
int y)
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void |
moveCursorToSequencePoint(SequenceAlignmentPoint point)
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void |
moveCursorUp(int number)
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void |
removeCursorChangeListener(ChangeListener listener)
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void |
setAlignmentSelectionRenderer(AlignmentSelectionRenderer selectionRenderer)
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void |
setCellHeight(int height)
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void |
setCellRenderer(AlignmentViewerCellRenderer renderer)
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void |
setCellWidth(int width)
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void |
setColorMap(ColorMap colorMap)
Changes the color map and notifies of change. |
void |
setCursorModel(SequenceCursor cursor)
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void |
setFastCellRenderer(FastAlignmentViewerCellRenderer renderer)
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void |
setMark()
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void |
setPoint(SequenceAlignmentPoint point)
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void |
setReadonly(boolean readonly)
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void |
setSelectionModel(AlignmentSelectionModel selectionModel)
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void |
setSequenceAlignment(SequenceAlignment msa)
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void |
setUI(AlignmentViewerUI ui)
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void |
stopSelection(SequenceAlignmentPoint point)
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void |
updateUI()
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void |
valueChanged(AlignmentSelectionEvent event)
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Methods inherited from class javax.swing.JComponent |
addAncestorListener, addNotify, addPropertyChangeListener, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getAccessibleContext, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getGraphics, getHeight, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getNextFocusableComponent, getPropertyChangeListeners, getPropertyChangeListeners, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, paramString, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFont, setForeground, 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, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, 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, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, 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, processMouseEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, 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 |
uiClassID
public static final String uiClassID
- See Also:
- Constant Field Values
readonly
protected boolean readonly
JAlignmentViewer
public JAlignmentViewer()
JAlignmentViewer
public JAlignmentViewer(SequenceAlignment alignment)
setCellRenderer
public void setCellRenderer(AlignmentViewerCellRenderer renderer)
getCellRenderer
public AlignmentViewerCellRenderer getCellRenderer()
setFastCellRenderer
public void setFastCellRenderer(FastAlignmentViewerCellRenderer renderer)
getFastCellRenderer
public FastAlignmentViewerCellRenderer getFastCellRenderer()
setAlignmentSelectionRenderer
public void setAlignmentSelectionRenderer(AlignmentSelectionRenderer selectionRenderer)
getAlignmentSelectionRenderer
public AlignmentSelectionRenderer getAlignmentSelectionRenderer()
setCellHeight
public void setCellHeight(int height)
getCellHeight
public int getCellHeight()
setCellWidth
public void setCellWidth(int width)
getCellWidth
public int getCellWidth()
getPreferredSize
public Dimension getPreferredSize()
- Overrides:
getPreferredSize
in class JComponent
getMinimumSize
public Dimension getMinimumSize()
- Overrides:
getMinimumSize
in class JComponent
getMaximumSize
public Dimension getMaximumSize()
- Overrides:
getMaximumSize
in class JComponent
setColorMap
public void setColorMap(ColorMap colorMap)
- Changes the color map and notifies of change.
- Parameters:
colorMap
- the new color map
getColorMap
public ColorMap getColorMap()
- Returns the current color map.
- Returns:
- the color map
setCursorModel
public void setCursorModel(SequenceCursor cursor)
getCursorModel
public SequenceCursor getCursorModel()
addCursorChangeListener
public void addCursorChangeListener(ChangeListener listener)
removeCursorChangeListener
public void removeCursorChangeListener(ChangeListener listener)
setPoint
public void setPoint(SequenceAlignmentPoint point)
setMark
public void setMark()
moveCursor
public void moveCursor(SequenceAlignmentPoint newPoint)
moveCursorUp
public void moveCursorUp(int number)
moveCursorDown
public void moveCursorDown(int number)
moveCursorPageUp
public void moveCursorPageUp()
moveCursorPageDown
public void moveCursorPageDown()
moveCursorBeginningOfAlignment
public void moveCursorBeginningOfAlignment()
moveCursorEndOfAlignment
public void moveCursorEndOfAlignment()
moveCursorRight
public void moveCursorRight(int number)
moveCursorLeft
public void moveCursorLeft(int number)
moveCursorPageRight
public void moveCursorPageRight()
moveCursorPageLeft
public void moveCursorPageLeft()
moveCursorBeginningOfSequence
public void moveCursorBeginningOfSequence()
moveCursorEndOfSequence
public void moveCursorEndOfSequence()
moveCursorToSequencePoint
public void moveCursorToSequencePoint(int x,
int y)
moveCursorToSequencePoint
public void moveCursorToSequencePoint(SequenceAlignmentPoint point)
getPoint
public SequenceAlignmentPoint getPoint()
getMark
public SequenceAlignmentPoint getMark()
getSequencePointAtPoint
public SequenceAlignmentPoint getSequencePointAtPoint(int x,
int y)
getSequencePointAtPoint
public SequenceAlignmentPoint getSequencePointAtPoint(Point point)
getPointAtSequencePoint
public Point getPointAtSequencePoint(int x,
int y)
getRectangleForSequenceRectangle
public Rectangle getRectangleForSequenceRectangle(SequenceAlignmentRectangle seqRect)
getCellBounds
public Rectangle getCellBounds(SequenceAlignmentPoint point)
ensureSequencePointIsVisible
public void ensureSequencePointIsVisible(SequenceAlignmentPoint point)
setReadonly
public void setReadonly(boolean readonly)
isReadonly
public boolean isReadonly()
insertGapsAt
public void insertGapsAt(SequenceAlignmentPoint point,
int sizeOfGap)
throws SequenceVetoException,
AlignmentVetoException,
ReadonlyException
SequenceVetoException
AlignmentVetoException
ReadonlyException
insertGapsAt
public void insertGapsAt(int x,
int y,
int sizeOfGap)
throws SequenceVetoException,
AlignmentVetoException,
ReadonlyException
SequenceVetoException
AlignmentVetoException
ReadonlyException
deleteGapsAt
public void deleteGapsAt(SequenceAlignmentPoint point,
int sizeOfGap)
throws NoGapAtThisPositionException,
SequenceVetoException,
AlignmentVetoException,
ReadonlyException
NoGapAtThisPositionException
SequenceVetoException
AlignmentVetoException
ReadonlyException
deleteGapsAt
public void deleteGapsAt(int x,
int y,
int sizeOfGap)
throws NoGapAtThisPositionException,
SequenceVetoException,
AlignmentVetoException,
ReadonlyException
NoGapAtThisPositionException
SequenceVetoException
AlignmentVetoException
ReadonlyException
insertGapsAtCursor
public void insertGapsAtCursor(int sizeOfGap)
throws SequenceVetoException,
AlignmentVetoException,
ReadonlyException
SequenceVetoException
AlignmentVetoException
ReadonlyException
deleteGapsAtCursor
public void deleteGapsAtCursor(int sizeOfGap)
throws NoGapAtThisPositionException,
SequenceVetoException,
AlignmentVetoException,
ReadonlyException
NoGapAtThisPositionException
SequenceVetoException
AlignmentVetoException
ReadonlyException
getVisibleSequenceRectangle
public SequenceAlignmentRectangle getVisibleSequenceRectangle()
getSelectionModel
public AlignmentSelectionModel getSelectionModel()
setSelectionModel
public void setSelectionModel(AlignmentSelectionModel selectionModel)
extendSelection
public void extendSelection(SequenceAlignmentPoint point)
stopSelection
public void stopSelection(SequenceAlignmentPoint point)
clearSelection
public void clearSelection()
setSequenceAlignment
public void setSequenceAlignment(SequenceAlignment msa)
getSequenceAlignment
public SequenceAlignment getSequenceAlignment()
changeOccurred
public void changeOccurred(AlignmentEvent event)
- Description copied from interface:
AlignmentListener
- method signalled after a change has occured to a multiple alignment
- Specified by:
changeOccurred
in interface AlignmentListener
- Parameters:
event
- the event type
changeOccurred
public void changeOccurred(SequenceEvent event)
- Description copied from interface:
SequenceListener
- Method called when a change occurs
- Specified by:
changeOccurred
in interface SequenceListener
- Parameters:
event
-
valueChanged
public void valueChanged(AlignmentSelectionEvent event)
- Specified by:
valueChanged
in interface AlignmentSelectionListener
getPreferredScrollableViewportSize
public Dimension getPreferredScrollableViewportSize()
getScrollableUnitIncrement
public int getScrollableUnitIncrement(Rectangle visibleRect,
int orientation,
int direction)
getScrollableBlockIncrement
public int getScrollableBlockIncrement(Rectangle visibleRect,
int orientation,
int direction)
getScrollableTracksViewportWidth
public boolean getScrollableTracksViewportWidth()
getScrollableTracksViewportHeight
public boolean getScrollableTracksViewportHeight()
getUIClassID
public String getUIClassID()
- Overrides:
getUIClassID
in class JComponent
setUI
public void setUI(AlignmentViewerUI ui)
updateUI
public void updateUI()
- Overrides:
updateUI
in class JComponent