Class SequencePanel

Method Details

• 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