org::gel::mauve::gui::sequence::AbstractSequencePanel Class Reference

Inheritance diagram for org::gel::mauve::gui::sequence::AbstractSequencePanel:

[legend]Collaboration diagram for org::gel::mauve::gui::sequence::AbstractSequencePanel:

[legend]List of all members.

Public Member Functions
	AbstractSequencePanel (BaseViewerModel model, Genome genome)
void	attributesChanged (ModelEvent event)
void	colorChanged (ModelEvent event)
void	drawingSettingsChanged (ModelEvent event)
void	genomesReordered (ModelEvent event)
void	genomeVisibilityChanged (ModelEvent event)
void	modeChanged (ModelEvent event)
void	modelReloadEnd (ModelEvent event)
void	modelReloadStart (ModelEvent event)
final long	pixelToCenterSequenceCoordinate (int pixel)
long	pixelToCenterSequenceCoordinate (double pixel)
final long	pixelToLeftSequenceCoordinate (int pixel)
final long	pixelToRightSequenceCoordinate (int pixel)
void	printingEnd (ModelEvent event)
void	printingStart (ModelEvent event)
void	referenceChanged (ModelEvent event)
final int	sequenceCoordinateToCenterPixel (long pos)
final int	sequenceCoordinateToLeftPixel (long pos)
final int	sequenceCoordinateToRightPixel (long pos)
void	viewableRangeChanged (ModelEvent event)
void	viewableRangeChangeEnd (ModelEvent event)
void	viewableRangeChangeStart (ModelEvent event)
void	weightChanged (ModelEvent event)
Static Public Attributes
final double	BOX_FILL = 0.95
Protected Member Functions
final int	boxHeight ()
final int	boxTop ()
final Genome	getGenome ()
final List	getLCBPixelRange (int start_pixel, int end_pixel)
	Finds all LCBs intersecting a specified range of pixels in the current view.
final void	pixelRangeToSequenceCoordinates (int start_pixel, int end_pixel, long[] seq_range)
	Converts a range of pixel coordinates to sequence coordinates.
Protected Attributes
BaseViewerModel	model
Private Attributes
Genome	genome

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Constructor & Destructor Documentation

org::gel::mauve::gui::sequence::AbstractSequencePanel::AbstractSequencePanel (  BaseViewerModel  model, Genome  genome )  [inline]

Definition at line 23 of file AbstractSequencePanel.java. References org::gel::mauve::BaseViewerModel::addModelListener().

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Member Function Documentation

void org::gel::mauve::gui::sequence::AbstractSequencePanel::attributesChanged (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Definition at line 150 of file AbstractSequencePanel.java.

final int org::gel::mauve::gui::sequence::AbstractSequencePanel::boxHeight (   )  [inline, protected]

Definition at line 35 of file AbstractSequencePanel.java. Referenced by org::gel::mauve::gui::sequence::RRSequencePanel::boxHeight().

final int org::gel::mauve::gui::sequence::AbstractSequencePanel::boxTop (   )  [inline, protected]

Definition at line 30 of file AbstractSequencePanel.java. Referenced by org::gel::mauve::gui::sequence::RRSequencePanel::boxTop().

void org::gel::mauve::gui::sequence::AbstractSequencePanel::colorChanged (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Reimplemented in org::gel::mauve::gui::sequence::MatchPanel. Definition at line 136 of file AbstractSequencePanel.java.

void org::gel::mauve::gui::sequence::AbstractSequencePanel::drawingSettingsChanged (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Reimplemented in org::gel::mauve::gui::sequence::MatchPanel. Definition at line 138 of file AbstractSequencePanel.java.

void org::gel::mauve::gui::sequence::AbstractSequencePanel::genomesReordered (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Reimplemented in org::gel::mauve::gui::sequence::FeaturePanel, and org::gel::mauve::gui::sequence::MatchPanel. Definition at line 147 of file AbstractSequencePanel.java.

void org::gel::mauve::gui::sequence::AbstractSequencePanel::genomeVisibilityChanged (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Reimplemented in org::gel::mauve::gui::sequence::ControlPanel, and org::gel::mauve::gui::sequence::SeqPanel. Definition at line 149 of file AbstractSequencePanel.java.

final Genome org::gel::mauve::gui::sequence::AbstractSequencePanel::getGenome (   )  [inline, protected]

Definition at line 130 of file AbstractSequencePanel.java. Referenced by org::gel::mauve::gui::sequence::FeaturePanel::adjustScaleAndTranslation(), org::gel::mauve::gui::sequence::RRSequencePanel::attributesChanged(), org::gel::mauve::gui::sequence::SeqPanel::configureLayout(), getLCBPixelRange(), org::gel::mauve::gui::sequence::FeaturePanel::init(), org::gel::mauve::gui::sequence::MatchPanel::isForGenome(), org::gel::mauve::gui::sequence::MatchPanel::MatchPanel(), org::gel::mauve::gui::sequence::SeqPanel::mouseClicked(), org::gel::mauve::gui::sequence::MatchPanel::mouseClicked(), org::gel::mauve::gui::sequence::FeaturePanel::ClickListener::mouseClicked(), org::gel::mauve::gui::sequence::HighlightPanel::mouseMoved(), org::gel::mauve::gui::sequence::HistogramPanel::paintComponent(), org::gel::mauve::gui::sequence::HighlightPanel::paintComponent(), pixelToCenterSequenceCoordinate(), pixelToLeftSequenceCoordinate(), pixelToRightSequenceCoordinate(), org::gel::mauve::gui::sequence::RulerPanel::RulerPanel(), sequenceCoordinateToCenterPixel(), sequenceCoordinateToLeftPixel(), and sequenceCoordinateToRightPixel().

final List org::gel::mauve::gui::sequence::AbstractSequencePanel::getLCBPixelRange (  int  start_pixel, int  end_pixel )  [inline, protected]

Finds all LCBs intersecting a specified range of pixels in the current view. Parameters: start_pixel  The first coordinate of the intersection range end_pixel  The last coordinate of the intersection range Definition at line 115 of file AbstractSequencePanel.java. References getGenome(), and pixelRangeToSequenceCoordinates().

void org::gel::mauve::gui::sequence::AbstractSequencePanel::modeChanged (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Definition at line 139 of file AbstractSequencePanel.java.

void org::gel::mauve::gui::sequence::AbstractSequencePanel::modelReloadEnd (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Reimplemented in org::gel::mauve::gui::sequence::MatchPanel. Definition at line 141 of file AbstractSequencePanel.java.

void org::gel::mauve::gui::sequence::AbstractSequencePanel::modelReloadStart (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Definition at line 140 of file AbstractSequencePanel.java.

final void org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelRangeToSequenceCoordinates (  int  start_pixel, int  end_pixel, long[]  seq_range )  [inline, protected]

Converts a range of pixel coordinates to sequence coordinates. Definition at line 99 of file AbstractSequencePanel.java. References pixelToLeftSequenceCoordinate(), and pixelToRightSequenceCoordinate(). Referenced by getLCBPixelRange().

final long org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToCenterSequenceCoordinate (  int  pixel  )  [inline]

Definition at line 64 of file AbstractSequencePanel.java. References getGenome(), org::gel::mauve::Genome::getViewLength(), and org::gel::mauve::Genome::getViewStart().

long org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToCenterSequenceCoordinate (  double  pixel  )  [inline]

Definition at line 56 of file AbstractSequencePanel.java. References getGenome(), org::gel::mauve::Genome::getViewLength(), and org::gel::mauve::Genome::getViewStart(). Referenced by org::gel::mauve::gui::sequence::SeqPanel::mouseClicked(), org::gel::mauve::gui::sequence::MatchPanel::mouseClicked(), org::gel::mauve::gui::sequence::HighlightPanel::mouseMoved(), and org::gel::mauve::gui::sequence::HistogramPanel::paintComponent().

final long org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToLeftSequenceCoordinate (  int  pixel  )  [inline]

Definition at line 48 of file AbstractSequencePanel.java. References getGenome(), org::gel::mauve::Genome::getViewLength(), and org::gel::mauve::Genome::getViewStart(). Referenced by org::gel::mauve::gui::sequence::MatchPanel::mouseClicked(), org::gel::mauve::gui::sequence::HighlightPanel::mouseMoved(), and pixelRangeToSequenceCoordinates().

final long org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToRightSequenceCoordinate (  int  pixel  )  [inline]

Definition at line 40 of file AbstractSequencePanel.java. References getGenome(), org::gel::mauve::Genome::getViewLength(), and org::gel::mauve::Genome::getViewStart(). Referenced by org::gel::mauve::gui::sequence::MatchPanel::mouseClicked(), org::gel::mauve::gui::sequence::HighlightPanel::mouseMoved(), and pixelRangeToSequenceCoordinates().

void org::gel::mauve::gui::sequence::AbstractSequencePanel::printingEnd (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Reimplemented in org::gel::mauve::gui::sequence::SeqPanel. Definition at line 146 of file AbstractSequencePanel.java.

void org::gel::mauve::gui::sequence::AbstractSequencePanel::printingStart (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Reimplemented in org::gel::mauve::gui::sequence::SeqPanel. Definition at line 145 of file AbstractSequencePanel.java.

void org::gel::mauve::gui::sequence::AbstractSequencePanel::referenceChanged (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Reimplemented in org::gel::mauve::gui::sequence::MatchPanel. Definition at line 148 of file AbstractSequencePanel.java.

final int org::gel::mauve::gui::sequence::AbstractSequencePanel::sequenceCoordinateToCenterPixel (  long  pos  )  [inline]

Definition at line 88 of file AbstractSequencePanel.java. References getGenome(), org::gel::mauve::Genome::getViewLength(), and org::gel::mauve::Genome::getViewStart(). Referenced by org::gel::mauve::gui::sequence::HighlightPanel::paintComponent(), and org::gel::mauve::gui::sequence::RRSequencePanel::sequenceCoordinateToCenterPixel().

final int org::gel::mauve::gui::sequence::AbstractSequencePanel::sequenceCoordinateToLeftPixel (  long  pos  )  [inline]

Definition at line 80 of file AbstractSequencePanel.java. References getGenome(), org::gel::mauve::Genome::getViewLength(), and org::gel::mauve::Genome::getViewStart(). Referenced by org::gel::mauve::gui::sequence::RangeHighlightPanel::paintComponent().

final int org::gel::mauve::gui::sequence::AbstractSequencePanel::sequenceCoordinateToRightPixel (  long  pos  )  [inline]

Definition at line 72 of file AbstractSequencePanel.java. References getGenome(), org::gel::mauve::Genome::getViewLength(), and org::gel::mauve::Genome::getViewStart(). Referenced by org::gel::mauve::gui::sequence::RangeHighlightPanel::paintComponent().

void org::gel::mauve::gui::sequence::AbstractSequencePanel::viewableRangeChanged (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Reimplemented in org::gel::mauve::gui::sequence::FeaturePanel, org::gel::mauve::gui::sequence::MatchPanel, and org::gel::mauve::gui::sequence::RulerPanel. Definition at line 143 of file AbstractSequencePanel.java.

void org::gel::mauve::gui::sequence::AbstractSequencePanel::viewableRangeChangeEnd (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Definition at line 144 of file AbstractSequencePanel.java.

void org::gel::mauve::gui::sequence::AbstractSequencePanel::viewableRangeChangeStart (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Definition at line 142 of file AbstractSequencePanel.java.

void org::gel::mauve::gui::sequence::AbstractSequencePanel::weightChanged (  ModelEvent  event  )  [inline]

Implements org::gel::mauve::ModelListener. Reimplemented in org::gel::mauve::gui::sequence::MatchPanel. Definition at line 137 of file AbstractSequencePanel.java.

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Member Data Documentation

final double org::gel::mauve::gui::sequence::AbstractSequencePanel::BOX_FILL = 0.95 [static]

Definition at line 21 of file AbstractSequencePanel.java.

Genome org::gel::mauve::gui::sequence::AbstractSequencePanel::genome [private]

Reimplemented in org::gel::mauve::gui::sequence::ControlPanel. Definition at line 17 of file AbstractSequencePanel.java.

BaseViewerModel org::gel::mauve::gui::sequence::AbstractSequencePanel::model [protected]

Reimplemented in org::gel::mauve::gui::sequence::ControlPanel. Definition at line 19 of file AbstractSequencePanel.java.

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The documentation for this class was generated from the following file:

• src/org/gel/mauve/gui/sequence/AbstractSequencePanel.java

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