Class SequencePoster
- All Implemented Interfaces:
ImageObserver
,MenuContainer
,Serializable
,SwingConstants
,SequenceRenderContext
,Changeable
A SequencePoster 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 SequencePoster 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 SequencePoster positions them.
- Author:
- Thomas Down, Matthew Pocock
- See Also:
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Nested Class Summary
Nested ClassesNested 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
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Field Summary
FieldsFields 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
Deprecated.void
Deprecated.Add a listener that will be informed of all changes.void
Deprecated.Add a listener that will be informed of changes of a given type.void
Deprecated.void
Deprecated.protected int[]
Deprecated.protected ChangeSupport
Deprecated.int
Deprecated.Retrieve the current rendering direction.Deprecated.The features to render.Deprecated.Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.int
getLines()
Deprecated.Retrieve the number of lines that the sequence will be rendered over.getRange()
Deprecated.The range of the SymbolList to render.Deprecated.double
getScale()
Deprecated.Retrieve the current scale.Deprecated.int
Deprecated.Retrieve the current spacer valueDeprecated.Retrieve the currently rendered SymbolListDeprecated.Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.Deprecated.int
graphicsToSequence
(double gPos) Deprecated.Converts a graphical position into a sequence coordinate.int
graphicsToSequence
(Point2D point) Deprecated.Converts a graphical position into a sequence coordinate.protected boolean
Deprecated.protected boolean
isActive()
Deprecated.boolean
Deprecated.A particular ChangeType can never be raised by this Changeable.void
Deprecated.Paint this component.void
Deprecated.Remove a listener that was interested in all types of changes.void
Deprecated.Remove a listener that was interested in a specific types of changes.void
Deprecated.void
Deprecated.void
Deprecated.double
sequenceToGraphics
(int seqPos) Deprecated.Converts a sequence index into a graphical coordinate.void
setDirection
(int dir) Deprecated.Set the direction that this SequencePoster renders in.void
setLines
(int lines) Deprecated.Set the absolute number of lines that the sequence will be rendered on.void
Deprecated.void
setRenderingHints
(RenderingHints renderingHints) Deprecated.Use this to switch on effects like Anti-aliasing etcvoid
setScale
(double scale) Deprecated.Set the scale.void
Deprecated.Set the SymboList to be rendered.void
setSpacer
(int spacer) Deprecated.Set the number of pixels to leave blank between each block of sequence information.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, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface org.biojava.bio.gui.sequence.SequenceRenderContext
getFont
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Field Details
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RENDERER
Deprecated.
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Constructor Details
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SequencePoster
public SequencePoster()Deprecated.Create a new SeqeuncePanel.
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Method Details
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addSequenceViewerListener
Deprecated. -
removeSequenceViewerListener
Deprecated. -
addSequenceViewerMotionListener
Deprecated. -
removeSequenceViewerMotionListener
Deprecated. -
hasChangeListeners
Deprecated. -
getChangeSupport
Deprecated. -
addChangeListener
Deprecated.Description copied from interface:Changeable
Add a listener that will be informed of all changes.- Specified by:
addChangeListener
in interfaceChangeable
- Parameters:
cl
- the ChangeListener to add
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addChangeListener
Deprecated.Description copied from interface:Changeable
Add a listener that will be informed of changes of a given type.- Specified by:
addChangeListener
in interfaceChangeable
- Parameters:
cl
- the ChangeListenerct
- the ChangeType it is to be informed of
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removeChangeListener
Deprecated.Description copied from interface:Changeable
Remove a listener that was interested in all types of changes.- Specified by:
removeChangeListener
in interfaceChangeable
- Parameters:
cl
- a ChangeListener to remove
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removeChangeListener
Deprecated.Description copied from interface:Changeable
Remove a listener that was interested in a specific types of changes.- Specified by:
removeChangeListener
in interfaceChangeable
- Parameters:
cl
- a ChangeListener to removect
- the ChangeType that it was interested in
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isUnchanging
Deprecated.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 interfaceChangeable
- Parameters:
ct
- the ChangeType to check- Returns:
- true if ChangeEvents of this type are guaranteed to never be fired
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setSequence
Deprecated.Set the SymboList to be rendered. This symbol list will be passed onto the SequenceRenderer instances registered with this SequencePoster.- Parameters:
s
- the SymboList to render
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getSequence
Deprecated. -
getSymbols
Deprecated.Retrieve the currently rendered SymbolList- Specified by:
getSymbols
in interfaceSequenceRenderContext
- Returns:
- the current SymbolList
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getFeatures
Deprecated.Description copied from interface:SequenceRenderContext
The features to render.- Specified by:
getFeatures
in interfaceSequenceRenderContext
- Returns:
- a FeatureHolder with the Features to render
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getRange
Deprecated.Description copied from interface:SequenceRenderContext
The range of the SymbolList to render.- Specified by:
getRange
in interfaceSequenceRenderContext
- Returns:
- the RangeLocation specifying which indices (inclusive) to render
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getVisibleRange
Deprecated. -
setDirection
Deprecated.Set the direction that this SequencePoster 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
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getDirection
Deprecated.Retrieve the current rendering direction.- Specified by:
getDirection
in interfaceSequenceRenderContext
- Returns:
- the rendering direction (one of HORIZONTAL and VERTICAL)
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setSpacer
Deprecated.Set the number of pixels to leave blank between each block of sequence information.If the SeqeuncePanel chooses to display the sequence information split across multiple lines, then the spacer parameter indicates how many pixles will seperate each line.
- Parameters:
spacer
- the number of pixels seperating each line of sequence information
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getSpacer
Deprecated.Retrieve the current spacer value- Returns:
- the number of pixels between each line of sequence information
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setScale
Deprecated.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 pixles-per-symbol ratio
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getScale
Deprecated.Retrieve the current scale.- Specified by:
getScale
in interfaceSequenceRenderContext
- Returns:
- the number of pixles used to render one symbol
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setLines
Deprecated.Set the absolute number of lines that the sequence will be rendered on. If this is set to 0, then the number of lines will be calculated according to how many lines will be needed to render the sequence in the currently available space. If it is set to any positive non-zero value, the sequence will be rendered using that many lines, and the SequencePoster will request enough space to accomplish this.- Parameters:
lines
- the number of lines to split the sequence information over
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getLines
Deprecated.Retrieve the number of lines that the sequence will be rendered over.- Returns:
- the current number of lines (0 if autocalculated)
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getLeadingBorder
Deprecated.Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.- Specified by:
getLeadingBorder
in interfaceSequenceRenderContext
- Returns:
- a SequenceRenderContext.Border instance
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getTrailingBorder
Deprecated.Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.- Specified by:
getTrailingBorder
in interfaceSequenceRenderContext
- Returns:
- a SequenceRenderContext.Border instance
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paintComponent
Deprecated.Paint this component.This calls the paint method of the currently registered SequenceRenderer after setting up the graphics appropriately.
- Overrides:
paintComponent
in classJComponent
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setRenderer
Deprecated.- Throws:
ChangeVetoException
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_setRenderer
Deprecated. -
sequenceToGraphics
Deprecated.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 interfaceSequenceRenderContext
- Parameters:
seqPos
- Index within the sequence- Returns:
- Equivalent graphical position in pixels
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graphicsToSequence
Deprecated.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 interfaceSequenceRenderContext
- Parameters:
gPos
- A pixel position- Returns:
- The corresponding sequence index
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graphicsToSequence
Deprecated.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 interfaceSequenceRenderContext
- Parameters:
point
- a point representing the position- Returns:
- the corresponding sequence index
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resizeAndValidate
Deprecated. -
calcLineExtent
Deprecated. -
isActive
Deprecated. -
getRenderingHints
Deprecated.- Returns:
- the current rendering properties
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setRenderingHints
Deprecated.Use this to switch on effects like Anti-aliasing etc- Parameters:
renderingHints
- the desired rendering properties
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