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

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

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

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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

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().


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.


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.


The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:04:09 2013 for Mauve by doxygen 1.3.6