PairwiseSequencePanel (biojava-legacy 1.9.1 API)

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

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, SwingConstants, PairwiseRenderContext, SequenceRenderContext, Changeable
```
public class PairwiseSequencePanel
extends JComponent
implements PairwiseRenderContext, Changeable, Serializable
```
A PairwiseSequencePanel is a panel that displays a pair of sequences; one sequence (the primary) may be either left-to-right (HORIZONTAL) or from top-to-bottom (VERTICAL). The other sequence (secondary) will then occupy the remaining direction. It has an associated scale which is the number of pixels per symbol and applies to both sequences. The leading and trailing borders apply to the primary sequence only.

The primary purpose of this component is to provide a means for representing graphically comparisons between two sequences. This could be anything from traditional dotplots (or variants created with lines) to a more complex layered plot involving superimposed renderers.

Each sequence has a translation which is the number of Symbols to skip before rendering starts. In order to produce a scrolling effect, the setSymbolTranslation or setSecondarySymbolTranslation method may be hooked up to an Adjustable such as JScrollBar or to an event listener.

The exact number of Symbols rendered in each sequence depends on the dimensions of the panel and the scale. Resizing the panel will cause the number of Symbols rendered to change accordingly.

The panel will fill its background to the Color defined by the setBackground() method provided that it has been defined as opaque using setOpaque().

The change event handling code is based on the original panel and other BioJava components by Matthew and Thomas.

Since:

1.2

Author:

Keith James, Matthew Pocock

See Also:
Serialized Form

Nested Class Summary
- 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
- Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderContext
  SequenceRenderContext.Border

Field Summary

Fields
Modifier and Type	Field and Description
`static ChangeType`	`RENDERER` Constant `RENDERER` is a `ChangeType` which indicates a change to the renderer, requiring a layout update.
`static ChangeType`	`TRANSLATION` Constant `TRANSLATION` is a `ChangeType` which indicates a change to the translation, requiring a paint update.

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 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
`PairwiseSequencePanel()` Creates a new `PairwiseSequencePanel` with the default settings (primary sequence direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, secondary symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font).

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addChangeListener(ChangeListener cl)` `addChangeListener` adds a listener for all types of change.
`void`	`addChangeListener(ChangeListener cl, ChangeType ct)` `addChangeListener` adds a listener for specific types of change.
`void`	`addSequenceViewerListener(SequenceViewerListener svl)` `addSequenceViewerListener` adds a listener for mouse click `SequenceViewerEvent`s.
`void`	`addSequenceViewerMotionListener(SequenceViewerMotionListener svml)` `addSequenceViewerMotionListener` adds a listener for mouse motion `SequenceViewerEvent`s.
`protected ChangeSupport`	`getChangeSupport(ChangeType ct)` `getChangeSupport` lazily instantiates a helper for change listeners.
`int`	`getDirection()` `getDirection` returns the direction in which this context expects the sequence to be rendered - HORIZONTAL or VERTICAL.
`FeatureHolder`	`getFeatures()` `getFeatures` returns all of the `Feature`s belonging to the currently rendered `Sequence`.
`SequenceRenderContext.Border`	`getLeadingBorder()` `getLeadingBorder` returns the leading border of the primary sequence.
`RangeLocation`	`getRange()` `getRange` returns a `RangeLocation` representing the region of the sequence currently being rendered.
`PairwiseSequenceRenderer`	`getRenderer()` `getRenderer` returns the current `PairwiseSequenceRenderer`.
`RenderingHints`	`getRenderingHints()` `getRenderingHints` returns the `RenderingHints` currently being used by the `Graphics2D` instances of delegate renderers.
`double`	`getScale()` `getScale` returns the scale in pixels per `Symbol`.
`int`	`getSecondaryDirection()` `getSecondaryDirection` returns the direction in which this context expects the secondary sequence to be rendered - HORIZONTAL or VERTICAL.
`FeatureHolder`	`getSecondaryFeatures()` `getSecondaryFeatures` returns all of the `Feature`s belonging to the currently rendered secondary `Sequence`.
`RangeLocation`	`getSecondaryRange()` `getSecondaryRange` returns a `RangeLocation` representing the region of the secondary sequence currently being rendered.
`Sequence`	`getSecondarySequence()` `getSecondarySequence` returns the entire secondary `Sequence` currently being rendered.
`SymbolList`	`getSecondarySymbols()` `getSecondarySymbols` returns all of the `Symbol`s belonging to the currently rendered secondary `Sequence`.
`int`	`getSecondarySymbolTranslation()` `getSecondarySymbolTranslation` returns the current translation in `Symbol`s which will be applied when rendering.
`Sequence`	`getSequence()` `getSequence` returns the entire `Sequence` currently being rendered.
`SymbolList`	`getSymbols()` `getSymbols` returns all of the `Symbol`s belonging to the currently rendered `Sequence`.
`int`	`getSymbolTranslation()` `getSymbolTranslation` returns the current translation in `Symbol`s which will be applied when rendering.
`SequenceRenderContext.Border`	`getTrailingBorder()` `getTrailingBorder` returns the trailing border of the primary sequence.
`int`	`getVisibleSecondarySymbolCount()` `getVisibleSecondarySymbolCount` returns the maximum number of secondary `Symbol`s which can be rendered in the visible area (excluding all borders) of the `PairwiseSequencePanel` at the current scale.
`int`	`getVisibleSymbolCount()` `getVisibleSymbolCount` returns the maximum number of `Symbol`s which can be rendered in the visible area (excluding all borders) of the `PairwiseSequencePanel` at the current scale.
`int`	`graphicsToSecondarySequence(double graphicsPos)` `graphicsToSecondarySequence` converts a graphical position to a secondary sequence index.
`int`	`graphicsToSecondarySequence(Point point)` `graphicsToSecondarySequence` converts a graphical position to a secondary sequence index.
`int`	`graphicsToSequence(double graphicsPos)` `graphicsToSequence` converts a graphical position to a sequence index.
`int`	`graphicsToSequence(Point2D point)` `graphicsToSequence` converts a graphical position to a sequence index.
`protected boolean`	`hasListeners()` `hasListeners` returns true if there are active listeners for BioJava events.
`protected boolean`	`isActive()` `isActive` returns true if both the `Sequence`s to be rendered and the `PairwiseHomologyRenderer` are not null.
`boolean`	`isUnchanging(ChangeType ct)` A particular ChangeType can never be raised by this Changeable.
`void`	`paintComponent(Graphics g)`
`void`	`removeChangeListener(ChangeListener cl)` `removeChangeListener` removes a listener.
`void`	`removeChangeListener(ChangeListener cl, ChangeType ct)` `removeChangeListener` removes a listener.
`void`	`removeSequenceViewerListener(SequenceViewerListener svl)` `removeSequenceViewerListener` removes a listener for mouse click `SequenceViewerEvent`s.
`void`	`removeSequenceViewerMotionListener(SequenceViewerMotionListener svml)` `addSequenceViewerMotionListener` removes a listener for mouse motion `SequenceViewerEvent`s.
`void`	`resizeAndValidate()` `resizeAndValidate` sets the minimum, preferred and maximum sizes of the component according to the current visible symbol count.
`double`	`secondarySequenceToGraphics(int sequencePos)` `secondarySequenceToGraphics` converts a sequence index to a graphical position.
`double`	`sequenceToGraphics(int sequencePos)` `sequenceToGraphics` converts a sequence index to a graphical position.
`void`	`setDirection(int direction)` `setDirection` sets the direction in which this context will render the sequence - HORIZONTAL or VERTICAL.
`void`	`setRenderer(PairwiseSequenceRenderer renderer)` `setRenderer` sets the current `PairwiseSequenceRenderer`.
`void`	`setRenderingHints(RenderingHints hints)` `setRenderingHints` sets the `RenderingHints` which will be used by the `Graphics2D` instances of delegate renderers.
`void`	`setScale(double scale)` `setScale` sets the scale in pixels per `Symbol`.
`void`	`setSecondarySequence(Sequence sequence)` `setSecondarySequence` sets the secondary `Sequence` to be rendered.
`void`	`setSecondarySymbolTranslation(int translation)` `setSecondarySymbolTranslation` sets the translation in `Symbol`s which will be applied when rendering.
`void`	`setSequence(Sequence sequence)` `setSequence` sets the `Sequence` to be rendered.
`void`	`setSymbolTranslation(int translation)` `setSymbolTranslation` sets the translation in `Symbol`s which will be applied when rendering.

Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getAccessibleContext, 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, 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, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

- Field Detail
  - RENDERER
```
public static final ChangeType RENDERER
```
    Constant RENDERER is a ChangeType which indicates a change to the renderer, requiring a layout update.
  - TRANSLATION
```
public static final ChangeType TRANSLATION
```
    Constant TRANSLATION is a ChangeType which indicates a change to the translation, requiring a paint update.
- Constructor Detail
  - PairwiseSequencePanel
```
public PairwiseSequencePanel()
```
    Creates a new PairwiseSequencePanel with the default settings (primary sequence direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, secondary symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font).
- Method Detail
  - getSequence
```
public Sequence getSequence()
```
    getSequence returns the entire Sequence currently being rendered.
    
    Returns:
    a Sequence.
  - setSequence
```
public void setSequence(Sequence sequence)
```
    setSequence sets the Sequence to be rendered.
    
    Parameters:
    sequence - a Sequence.
  - getSecondarySequence
```
public Sequence getSecondarySequence()
```
    getSecondarySequence returns the entire secondary Sequence currently being rendered.
    
    Returns:
    a Sequence.
  - setSecondarySequence
```
public void setSecondarySequence(Sequence sequence)
```
    setSecondarySequence sets the secondary Sequence to be rendered.
    
    Parameters:
    sequence - a Sequence.
  - getSymbols
```
public SymbolList getSymbols()
```
    getSymbols returns all of the Symbols belonging to the currently rendered Sequence.
    
    Specified by:
    
    getSymbols in interface SequenceRenderContext
    
    Returns:
    a SymbolList.
  - getSecondarySymbols
```
public SymbolList getSecondarySymbols()
```
    getSecondarySymbols returns all of the Symbols belonging to the currently rendered secondary Sequence.
    
    Specified by:
    
    getSecondarySymbols in interface PairwiseRenderContext
    
    Returns:
    a SymbolList.
  - getFeatures
```
public FeatureHolder getFeatures()
```
    getFeatures returns all of the Features belonging to the currently rendered Sequence.
    
    Specified by:
    
    getFeatures in interface SequenceRenderContext
    
    Returns:
    a FeatureHolder.
  - getSecondaryFeatures
```
public FeatureHolder getSecondaryFeatures()
```
    getSecondaryFeatures returns all of the Features belonging to the currently rendered secondary Sequence.
    
    Specified by:
    
    getSecondaryFeatures in interface PairwiseRenderContext
    
    Returns:
    a FeatureHolder.
  - getRange
```
public RangeLocation getRange()
```
    getRange returns a RangeLocation representing the region of the sequence currently being rendered. This is calculated from the size of the PairwiseSequencePanel, the current rendering translation and the current scale. The value will therefore change when the PairwiseSequencePanel is resized or "scrolled" by changing the translation.
    
    Specified by:
    
    getRange in interface SequenceRenderContext
    
    Returns:
    a RangeLocation.
  - getSecondaryRange
```
public RangeLocation getSecondaryRange()
```
    getSecondaryRange returns a RangeLocation representing the region of the secondary sequence currently being rendered. This is calculated from the size of the PairwiseSequencePanel, the current rendering translation and the current scale. The value will therefore change when the PairwiseSequencePanel is resized or "scrolled" by changing the translation.
    
    Specified by:
    
    getSecondaryRange in interface PairwiseRenderContext
    
    Returns:
    a RangeLocation.
  - getDirection
```
public int getDirection()
```
    getDirection returns the direction in which this context expects the sequence to be rendered - HORIZONTAL or VERTICAL.
    
    Specified by:
    
    getDirection in interface SequenceRenderContext
    
    Returns:
    an int.
  - setDirection
```
public void setDirection(int direction)
                  throws IllegalArgumentException
```
    setDirection sets the direction in which this context will render the sequence - HORIZONTAL or VERTICAL.
    
    Parameters:
    direction - an int.
    
    Throws:
    
    IllegalArgumentException - if an invalid direction is used.
  - getSecondaryDirection
```
public int getSecondaryDirection()
```
    getSecondaryDirection returns the direction in which this context expects the secondary sequence to be rendered - HORIZONTAL or VERTICAL.
    
    Specified by:
    
    getSecondaryDirection in interface PairwiseRenderContext
    
    Returns:
    an int.
  - getScale
```
public double getScale()
```
    getScale returns the scale in pixels per Symbol.
    
    Specified by:
    
    getScale in interface SequenceRenderContext
    
    Returns:
    a double.
  - setScale
```
public void setScale(double scale)
```
    setScale sets the scale in pixels per Symbol.
    
    Parameters:
    scale - a double.
  - getSymbolTranslation
```
public int getSymbolTranslation()
```
    getSymbolTranslation returns the current translation in Symbols which will be applied when rendering. The sequence will be rendered starting at this translation. Values may be from 0 to the length of the rendered sequence.
    
    Returns:
    an int.
  - setSymbolTranslation
```
public void setSymbolTranslation(int translation)
                          throws IndexOutOfBoundsException
```
    setSymbolTranslation sets the translation in Symbols which will be applied when rendering. The sequence will be rendered starting at that translation. Values may be from 0 to the length of the rendered sequence.
    
    Parameters:
    translation - an int.
    
    Throws:
    
    IndexOutOfBoundsException - if the translation is greater than the sequence length.
  - getSecondarySymbolTranslation
```
public int getSecondarySymbolTranslation()
```
    getSecondarySymbolTranslation returns the current translation in Symbols which will be applied when rendering. The secondary sequence will be rendered starting at this translation. Values may be from 0 to the length of the rendered sequence.
    
    Returns:
    an int.
  - setSecondarySymbolTranslation
```
public void setSecondarySymbolTranslation(int translation)
                                   throws IndexOutOfBoundsException
```
    setSecondarySymbolTranslation sets the translation in Symbols which will be applied when rendering. The secondary sequence will be rendered starting at that translation. Values may be from 0 to the length of the rendered sequence.
    
    Parameters:
    translation - an int.
    
    Throws:
    
    IndexOutOfBoundsException - if the translation is greater than the sequence length.
  - getLeadingBorder
```
public SequenceRenderContext.Border getLeadingBorder()
```
    getLeadingBorder returns the leading border of the primary sequence.
    
    Specified by:
    
    getLeadingBorder in interface SequenceRenderContext
    
    Returns:
    a SequenceRenderContext.Border.
  - getTrailingBorder
```
public SequenceRenderContext.Border getTrailingBorder()
```
    getTrailingBorder returns the trailing border of the primary sequence.
    
    Specified by:
    
    getTrailingBorder in interface SequenceRenderContext
    
    Returns:
    a SequenceRenderContext.Border.
  - getRenderer
```
public PairwiseSequenceRenderer getRenderer()
```
    getRenderer returns the current PairwiseSequenceRenderer.
    
    Returns:
    a PairwiseSequenceRenderer.
  - setRenderer
```
public void setRenderer(PairwiseSequenceRenderer renderer)
                 throws ChangeVetoException
```
    setRenderer sets the current PairwiseSequenceRenderer.
    
    Throws:
    
    ChangeVetoException
  - getRenderingHints
```
public RenderingHints getRenderingHints()
```
    getRenderingHints returns the RenderingHints currently being used by the Graphics2D instances of delegate renderers. If none is set, the constructor creates one with a null Map.
    
    Returns:
    a RenderingHints.
  - setRenderingHints
```
public void setRenderingHints(RenderingHints hints)
```
    setRenderingHints sets the RenderingHints which will be used by the Graphics2D instances of delegate renderers.
    
    Parameters:
    hints - a RenderingHints.
  - sequenceToGraphics
```
public double sequenceToGraphics(int sequencePos)
```
    sequenceToGraphics converts a sequence index to a graphical position.
    
    Specified by:
    
    sequenceToGraphics in interface SequenceRenderContext
    
    Parameters:
    sequencePos - an int.
    
    Returns:
    a double.
  - secondarySequenceToGraphics
```
public double secondarySequenceToGraphics(int sequencePos)
```
    secondarySequenceToGraphics converts a sequence index to a graphical position.
    
    Specified by:
    
    secondarySequenceToGraphics in interface PairwiseRenderContext
    
    Parameters:
    sequencePos - an int.
    
    Returns:
    a double.
  - graphicsToSequence
```
public int graphicsToSequence(double graphicsPos)
```
    graphicsToSequence converts a graphical position to a sequence index.
    
    Specified by:
    
    graphicsToSequence in interface SequenceRenderContext
    
    Parameters:
    graphicsPos - a double.
    
    Returns:
    an int.
  - graphicsToSequence
```
public int graphicsToSequence(Point2D point)
```
    graphicsToSequence converts a graphical position to a sequence index.
    
    Specified by:
    
    graphicsToSequence in interface SequenceRenderContext
    
    Parameters:
    point - a graphic position.
    
    Returns:
    an int.
  - graphicsToSecondarySequence
```
public int graphicsToSecondarySequence(double graphicsPos)
```
    graphicsToSecondarySequence converts a graphical position to a secondary sequence index.
    
    Specified by:
    
    graphicsToSecondarySequence in interface PairwiseRenderContext
    
    Parameters:
    graphicsPos - a double.
    
    Returns:
    an int.
  - graphicsToSecondarySequence
```
public int graphicsToSecondarySequence(Point point)
```
    graphicsToSecondarySequence converts a graphical position to a secondary sequence index.
    
    Specified by:
    
    graphicsToSecondarySequence in interface PairwiseRenderContext
    
    Parameters:
    point - a Point.
    
    Returns:
    an int.
  - getVisibleSymbolCount
```
public int getVisibleSymbolCount()
```
    getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the PairwiseSequencePanel at the current scale. Note that if the translation is greater than 0, the actual number of Symbols rendered will be less.
    
    Returns:
    an int.
  - getVisibleSecondarySymbolCount
```
public int getVisibleSecondarySymbolCount()
```
    getVisibleSecondarySymbolCount returns the maximum number of secondary Symbols which can be rendered in the visible area (excluding all borders) of the PairwiseSequencePanel at the current scale. Note that if the translation is greater than 0, the actual number of Symbols rendered will be less.
    
    Returns:
    an int.
  - paintComponent
```
public void paintComponent(Graphics g)
```
    Overrides:
    
    paintComponent in class JComponent
  - resizeAndValidate
```
public void resizeAndValidate()
```
    resizeAndValidate sets the minimum, preferred and maximum sizes of the component according to the current visible symbol count.
  - addChangeListener
```
public void addChangeListener(ChangeListener cl)
```
    addChangeListener adds a listener for all types of change.
    
    Specified by:
    
    addChangeListener in interface Changeable
    
    Parameters:
    cl - a ChangeListener.
  - addChangeListener
```
public void addChangeListener(ChangeListener cl,
                     ChangeType ct)
```
    addChangeListener adds a listener for specific types of change.
    
    Specified by:
    
    addChangeListener in interface Changeable
    
    Parameters:
    cl - a ChangeListener.
    ct - a ChangeType.
  - removeChangeListener
```
public void removeChangeListener(ChangeListener cl)
```
    removeChangeListener removes a listener.
    
    Specified by:
    
    removeChangeListener in interface Changeable
    
    Parameters:
    cl - a ChangeListener.
  - removeChangeListener
```
public void removeChangeListener(ChangeListener cl,
                        ChangeType ct)
```
    removeChangeListener removes a listener.
    
    Specified by:
    
    removeChangeListener in interface Changeable
    
    Parameters:
    cl - a ChangeListener.
    ct - a ChangeType.
  - 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
  - addSequenceViewerListener
```
public void addSequenceViewerListener(SequenceViewerListener svl)
```
    addSequenceViewerListener adds a listener for mouse click SequenceViewerEvents.
    
    Parameters:
    svl - a SequenceViewerListener.
  - removeSequenceViewerListener
```
public void removeSequenceViewerListener(SequenceViewerListener svl)
```
    removeSequenceViewerListener removes a listener for mouse click SequenceViewerEvents.
    
    Parameters:
    svl - a SequenceViewerListener.
  - addSequenceViewerMotionListener
```
public void addSequenceViewerMotionListener(SequenceViewerMotionListener svml)
```
    addSequenceViewerMotionListener adds a listener for mouse motion SequenceViewerEvents.
    
    Parameters:
    svml - a SequenceViewerMotionListener.
  - removeSequenceViewerMotionListener
```
public void removeSequenceViewerMotionListener(SequenceViewerMotionListener svml)
```
    addSequenceViewerMotionListener removes a listener for mouse motion SequenceViewerEvents.
    
    Parameters:
    svml - a SequenceViewerMotionListener.
  - getChangeSupport
```
protected ChangeSupport getChangeSupport(ChangeType ct)
```
    getChangeSupport lazily instantiates a helper for change listeners.
    
    Parameters:
    ct - a ChangeType.
    
    Returns:
    a ChangeSupport object.
  - hasListeners
```
protected boolean hasListeners()
```
    hasListeners returns true if there are active listeners for BioJava events.
    
    Returns:
    a boolean value.
  - isActive
```
protected boolean isActive()
```
    isActive returns true if both the Sequences to be rendered and the PairwiseHomologyRenderer are not null.
    
    Returns:
    a boolean value.

Class PairwiseSequencePanel

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

Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderContext

Field Summary

Fields inherited from class javax.swing.JComponent

Fields inherited from class java.awt.Component

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

Fields inherited from interface javax.swing.SwingConstants

Fields inherited from interface java.awt.image.ImageObserver

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

TRANSLATION

Constructor Detail

PairwiseSequencePanel

Method Detail

getSequence

setSequence

getSecondarySequence

setSecondarySequence

getSymbols

getSecondarySymbols

getFeatures

getSecondaryFeatures

getRange

getSecondaryRange

getDirection

setDirection

getSecondaryDirection

getScale

setScale

getSymbolTranslation

setSymbolTranslation

getSecondarySymbolTranslation

setSecondarySymbolTranslation

getLeadingBorder

getTrailingBorder

getRenderer

setRenderer

getRenderingHints

setRenderingHints

sequenceToGraphics

secondarySequenceToGraphics

graphicsToSequence

graphicsToSequence

graphicsToSecondarySequence

graphicsToSecondarySequence

getVisibleSymbolCount

getVisibleSecondarySymbolCount

paintComponent

resizeAndValidate

addChangeListener

addChangeListener

removeChangeListener

removeChangeListener

isUnchanging

addSequenceViewerListener

removeSequenceViewerListener

addSequenceViewerMotionListener

removeSequenceViewerMotionListener

getChangeSupport

hasListeners

isActive