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

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

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

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List of all members.

Public Member Functions

void colorChanged (ModelEvent event)
void drawingSettingsChanged (ModelEvent event)
void genomesReordered (ModelEvent event)
EditLcbMenuItemBuilder getEditLcbMenuItemBuilder ()
MatchDisplayMenuItemBuilder getMatchDisplayMenuItemBuilder ()
MatchPopupMenuBuilder getMatchPopupMenuBuilder ()
SetReferenceMenuItemBuilder getSetReferenceMenuItemBuilder ()
int goTo (long coordinate)
 centers view on selected coordinate of the genome associated with this MatchPanel and aligns other genomes

void highlightChanged (ModelEvent evt)
boolean isForGenome (Genome comparator)
 isForGenome returns true if this RRSequencePanel is associated with the specified genome, and false otherwise

void markDirty ()
 MatchPanel (RearrangementPanel rrpanel, BaseViewerModel model, Genome genome)
void modelReloadEnd (ModelEvent event)
void mouseClicked (MouseEvent e)
void mouseEntered (MouseEvent e)
 not implemented

void mouseExited (MouseEvent e)
 not implemented

void mousePressed (MouseEvent e)
 not implemented

void mouseReleased (MouseEvent e)
 not implemented

void paintComponent (Graphics graphics)
 paint the sequence display.

void referenceChanged (ModelEvent event)
void viewableRangeChanged (ModelEvent event)
void weightChanged (ModelEvent event)

Protected Member Functions

void getMatchPixelRange (int start_pixel, int end_pixel, int[] match_range)
 Finds all match indices which intersect with the specified range of pixels in the current view.


Package Functions

MatchPopupMenu getPopup (MouseEvent evt)

Package Attributes

RearrangementPanel rrpanel

Private Member Functions

void drawChromosomeBoundaries (Graphics2D g)
void drawLcbBounds (double unitsPerPixel, int box_height, int half_height, Graphics2D matchGraphics, double arc_size)
void drawMatchBoxes (double unitsPerPixel, int box_height, int half_height, Graphics2D g2)
void drawWhiteBackgrounds (int half_height, Graphics2D matchGraphics, double arc_size)
void drawXmfa (int half_height, Graphics2D g, double increment)
void formatBoxes (Graphics2D g2, double similarityIncrement)
 Organize the matches into visual boxes to be displayed on screen.

RoundRectangle2D getLcbRectangle (LCB lcb, int half_height)
void openJdkSafeRect (RoundRectangle2D r)
void updateBuffer ()

Static Private Member Functions

Color getFillColor (Color lcb_color)
 Creates a similarity plot fill color for an LCB of a given color.

Color getFillColorChangeHSB (Color lcb_color, float h, float s, float b)
 Creates a similarity plot fill color for an LCB of a given color.


Private Attributes

Image bufferedImage
int depth = 0
final EditLcbMenuItemBuilder elmib = new EditLcbMenuItemBuilder()
int lastHeight = -1
int lastWidth = -1
final MatchDisplayMenuItemBuilder mdmib = new MatchDisplayMenuItemBuilder()
final MatchPopupMenuBuilder mpmb = new MatchPopupMenuBuilder()
final SetReferenceMenuItemBuilder srmib = new SetReferenceMenuItemBuilder()
long viewEnd

Static Private Attributes

final Color DELETED_COLOR = Color.getHSBColor(0.11f, 1, 1)
final double HALF_PEN_WIDTH = 1.125d
final int HIGHLIGHT_AREA_HEIGHT = 2
final Color highlightAreaColor = new Color(24, 24, 24)
final double LCB_BOUNDARY_WIDTH = 2.25d
final int MAX_POPUP_MATCHES = 15

Constructor & Destructor Documentation

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

Definition at line 78 of file MatchPanel.java.

References org::gel::mauve::BaseViewerModel::addHighlightListener(), org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuBuilder::addMenuItemBuilder(), elmib, org::gel::mauve::gui::sequence::AbstractSequencePanel::getGenome(), org::gel::mauve::Genome::getViewLength(), org::gel::mauve::Genome::getViewStart(), mdmib, mpmb, srmib, and viewEnd.

Member Function Documentation

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

Reimplemented from org::gel::mauve::gui::sequence::AbstractSequencePanel.

Definition at line 985 of file MatchPanel.java.

void org::gel::mauve::gui::sequence::MatchPanel::drawChromosomeBoundaries (  Graphics2D  g  )  [inline, private]
 

Parameters:
g 

Definition at line 536 of file MatchPanel.java.

References org::gel::mauve::Chromosome::getEnd(), and org::gel::mauve::Chromosome::getStart().

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

Reimplemented from org::gel::mauve::gui::sequence::AbstractSequencePanel.

Definition at line 1003 of file MatchPanel.java.

void org::gel::mauve::gui::sequence::MatchPanel::drawLcbBounds (  double  unitsPerPixel,
int  box_height,
int  half_height,
Graphics2D  matchGraphics,
double  arc_size
)  [inline, private]
 

Definition at line 472 of file MatchPanel.java.

References org::gel::mauve::LCB::color, org::gel::mauve::LcbViewerModel::getDrawLcbBounds(), org::gel::mauve::LcbViewerModel::getFillLcbBoxes(), org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::LCB::getReverse(), org::gel::mauve::LCB::getRightEnd(), org::gel::mauve::LcbViewerModel::getVisibleLcb(), and org::gel::mauve::LcbViewerModel::getVisibleLcbCount().

void org::gel::mauve::gui::sequence::MatchPanel::drawMatchBoxes (  double  unitsPerPixel,
int  box_height,
int  half_height,
Graphics2D  g2
)  [inline, private]
 

Parameters:
end_view 
unitsPerPixel 
box_height 
half_height 
matchGraphics 
highlightAreaGraphics 
half_pen_width 

Definition at line 593 of file MatchPanel.java.

References org::gel::mauve::Match::getLength(), org::gel::mauve::Match::getReverse(), org::gel::mauve::Match::getStart(), org::gel::mauve::Match::highlighted, and org::gel::mauve::Match::lcb.

void org::gel::mauve::gui::sequence::MatchPanel::drawWhiteBackgrounds (  int  half_height,
Graphics2D  matchGraphics,
double  arc_size
)  [inline, private]
 

Definition at line 953 of file MatchPanel.java.

References org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::LCB::getReverse(), and org::gel::mauve::LCB::getRightEnd().

void org::gel::mauve::gui::sequence::MatchPanel::drawXmfa (  int  half_height,
Graphics2D  g,
double  increment
)  [inline, private]
 

Parameters:
half_height 
g 
half_pen_width 

Definition at line 706 of file MatchPanel.java.

References org::gel::mauve::LCB::color, org::gel::mauve::backbone::BackboneList::getBackbone(), org::gel::mauve::XmfaViewerModel::getBackboneList(), org::gel::mauve::backbone::Backbone::getColor(), org::gel::mauve::LcbViewerModel::getDeletedRightNeighbor(), org::gel::mauve::LcbViewerModel::getDrawLcbBounds(), org::gel::mauve::BaseViewerModel::getDrawMatches(), org::gel::mauve::XmfaViewerModel::getDrawSimilarityRanges(), org::gel::mauve::LcbViewerModel::getFillLcbBoxes(), org::gel::mauve::backbone::Backbone::getLeftEnd(), org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::LcbViewerModel::getLeftmostDeletedLCB(), org::gel::mauve::LcbViewerModel::getLeftmostVisibleLCB(), org::gel::mauve::backbone::BackboneList::getNextBackbone(), org::gel::mauve::LCB::getReverse(), org::gel::mauve::backbone::Backbone::getRightEnd(), org::gel::mauve::LCB::getRightEnd(), org::gel::mauve::LcbViewerModel::getVisibleRightNeighbor(), and org::gel::mauve::LCB::multiplicity().

void org::gel::mauve::gui::sequence::MatchPanel::formatBoxes (  Graphics2D  g2,
double  similarityIncrement
)  [inline, private]
 

Organize the matches into visual boxes to be displayed on screen.

formatBoxes will coalesce small matches into a single box to be displayed.

Draws the sequence similarity information, either based on Match objects (ungapped local alignments) or based on a SimilarityIndex

Definition at line 417 of file MatchPanel.java.

References org::gel::mauve::LcbViewerModel::getDrawLcbBounds(), and org::gel::mauve::BaseViewerModel::getDrawMatches().

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

Reimplemented from org::gel::mauve::gui::sequence::AbstractSequencePanel.

Definition at line 1026 of file MatchPanel.java.

EditLcbMenuItemBuilder org::gel::mauve::gui::sequence::MatchPanel::getEditLcbMenuItemBuilder (   )  [inline]
 

Definition at line 94 of file MatchPanel.java.

References elmib.

Color org::gel::mauve::gui::sequence::MatchPanel::getFillColor (  Color  lcb_color  )  [inline, static, private]
 

Creates a similarity plot fill color for an LCB of a given color.

Parameters:
lcb_color The color of the LCB bounding rectangle
Returns:

Definition at line 681 of file MatchPanel.java.

Color org::gel::mauve::gui::sequence::MatchPanel::getFillColorChangeHSB (  Color  lcb_color,
float  h,
float  s,
float  b
)  [inline, static, private]
 

Creates a similarity plot fill color for an LCB of a given color.

Parameters:
lcb_color The color of the LCB bounding rectangle
brighter A floating point value in range [-1,1] by which the brightness will be adjusted
Returns:

Definition at line 692 of file MatchPanel.java.

RoundRectangle2D org::gel::mauve::gui::sequence::MatchPanel::getLcbRectangle (  LCB  lcb,
int  half_height
)  [inline, private]
 

Parameters:
lcb 
half_height 
arc_size 
Returns:

Definition at line 572 of file MatchPanel.java.

References org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::LCB::getReverse(), and org::gel::mauve::LCB::getRightEnd().

MatchDisplayMenuItemBuilder org::gel::mauve::gui::sequence::MatchPanel::getMatchDisplayMenuItemBuilder (   )  [inline]
 

Definition at line 93 of file MatchPanel.java.

References mdmib.

void org::gel::mauve::gui::sequence::MatchPanel::getMatchPixelRange (  int  start_pixel,
int  end_pixel,
int[]  match_range
)  [inline, protected]
 

Finds all match indices which intersect with the 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
match_range An int array with 2 elements. The resulting range of intersecting match indices will be returned as the first and second elements in the array.

Definition at line 360 of file MatchPanel.java.

MatchPopupMenuBuilder org::gel::mauve::gui::sequence::MatchPanel::getMatchPopupMenuBuilder (   )  [inline]
 

Definition at line 92 of file MatchPanel.java.

References mpmb.

MatchPopupMenu org::gel::mauve::gui::sequence::MatchPanel::getPopup (  MouseEvent  evt  )  [inline, package]
 

Definition at line 303 of file MatchPanel.java.

SetReferenceMenuItemBuilder org::gel::mauve::gui::sequence::MatchPanel::getSetReferenceMenuItemBuilder (   )  [inline]
 

Definition at line 95 of file MatchPanel.java.

References srmib.

int org::gel::mauve::gui::sequence::MatchPanel::goTo (  long  coordinate  )  [inline]
 

centers view on selected coordinate of the genome associated with this MatchPanel and aligns other genomes

Parameters:
coordinate The position to go to
Returns:

Definition at line 186 of file MatchPanel.java.

References org::gel::mauve::BaseViewerModel::zoomAndCenter().

Referenced by org::gel::mauve::gui::sequence::RRSequencePanel::goTo().

void org::gel::mauve::gui::sequence::MatchPanel::highlightChanged (  ModelEvent  evt  )  [inline]
 

Implements org::gel::mauve::HighlightListener.

Definition at line 997 of file MatchPanel.java.

boolean org::gel::mauve::gui::sequence::MatchPanel::isForGenome (  Genome  comparator  )  [inline]
 

isForGenome returns true if this RRSequencePanel is associated with the specified genome, and false otherwise

Parameters:
comparator - the genome in question

Definition at line 202 of file MatchPanel.java.

References org::gel::mauve::gui::sequence::AbstractSequencePanel::getGenome().

Referenced by org::gel::mauve::gui::sequence::RRSequencePanel::isForGenome().

void org::gel::mauve::gui::sequence::MatchPanel::markDirty (   )  [inline]
 

Definition at line 403 of file MatchPanel.java.

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

Reimplemented from org::gel::mauve::gui::sequence::AbstractSequencePanel.

Definition at line 1016 of file MatchPanel.java.

void org::gel::mauve::gui::sequence::MatchPanel::mouseClicked (  MouseEvent  e  )  [inline]
 

Definition at line 118 of file MatchPanel.java.

References org::gel::mauve::BaseViewerModel::addMatchHighlight(), org::gel::mauve::LcbViewerModel::alignView(), org::gel::mauve::XmfaViewerModel::alignView(), org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuBuilder::build(), org::gel::mauve::BaseViewerModel::clearMatchHighlights(), org::gel::mauve::gui::sequence::AbstractSequencePanel::getGenome(), org::gel::mauve::XmfaViewerModel::getSim(), org::gel::mauve::Genome::getSortedMatches(), org::gel::mauve::BaseViewerModel::highlightRange(), mpmb, org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToCenterSequenceCoordinate(), org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToLeftSequenceCoordinate(), and org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToRightSequenceCoordinate().

void org::gel::mauve::gui::sequence::MatchPanel::mouseEntered (  MouseEvent  e  )  [inline]
 

not implemented

Definition at line 99 of file MatchPanel.java.

void org::gel::mauve::gui::sequence::MatchPanel::mouseExited (  MouseEvent  e  )  [inline]
 

not implemented

Definition at line 104 of file MatchPanel.java.

void org::gel::mauve::gui::sequence::MatchPanel::mousePressed (  MouseEvent  e  )  [inline]
 

not implemented

Definition at line 109 of file MatchPanel.java.

void org::gel::mauve::gui::sequence::MatchPanel::mouseReleased (  MouseEvent  e  )  [inline]
 

not implemented

Definition at line 114 of file MatchPanel.java.

void org::gel::mauve::gui::sequence::MatchPanel::openJdkSafeRect (  RoundRectangle2D  r  )  [inline, private]
 

Definition at line 944 of file MatchPanel.java.

void org::gel::mauve::gui::sequence::MatchPanel::paintComponent (  Graphics  graphics  )  [inline]
 

paint the sequence display.

copies a pre-computed similarity display and adds any highlighting

Definition at line 371 of file MatchPanel.java.

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

Reimplemented from org::gel::mauve::gui::sequence::AbstractSequencePanel.

Definition at line 1022 of file MatchPanel.java.

void org::gel::mauve::gui::sequence::MatchPanel::updateBuffer (   )  [inline, private]
 

Definition at line 394 of file MatchPanel.java.

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

Reimplemented from org::gel::mauve::gui::sequence::AbstractSequencePanel.

Definition at line 1009 of file MatchPanel.java.

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

Reimplemented from org::gel::mauve::gui::sequence::AbstractSequencePanel.

Definition at line 991 of file MatchPanel.java.

Member Data Documentation

Image org::gel::mauve::gui::sequence::MatchPanel::bufferedImage [private]
 

Definition at line 62 of file MatchPanel.java.

final Color org::gel::mauve::gui::sequence::MatchPanel::DELETED_COLOR = Color.getHSBColor(0.11f, 1, 1) [static, private]
 

Definition at line 44 of file MatchPanel.java.

int org::gel::mauve::gui::sequence::MatchPanel::depth = 0 [private]
 

Definition at line 71 of file MatchPanel.java.

final EditLcbMenuItemBuilder org::gel::mauve::gui::sequence::MatchPanel::elmib = new EditLcbMenuItemBuilder() [private]
 

Definition at line 75 of file MatchPanel.java.

Referenced by getEditLcbMenuItemBuilder(), and MatchPanel().

final double org::gel::mauve::gui::sequence::MatchPanel::HALF_PEN_WIDTH = 1.125d [static, private]
 

Definition at line 56 of file MatchPanel.java.

final int org::gel::mauve::gui::sequence::MatchPanel::HIGHLIGHT_AREA_HEIGHT = 2 [static, private]
 

Definition at line 50 of file MatchPanel.java.

final Color org::gel::mauve::gui::sequence::MatchPanel::highlightAreaColor = new Color(24, 24, 24) [static, private]
 

Definition at line 47 of file MatchPanel.java.

int org::gel::mauve::gui::sequence::MatchPanel::lastHeight = -1 [private]
 

Definition at line 66 of file MatchPanel.java.

int org::gel::mauve::gui::sequence::MatchPanel::lastWidth = -1 [private]
 

Definition at line 65 of file MatchPanel.java.

final double org::gel::mauve::gui::sequence::MatchPanel::LCB_BOUNDARY_WIDTH = 2.25d [static, private]
 

Definition at line 53 of file MatchPanel.java.

final int org::gel::mauve::gui::sequence::MatchPanel::MAX_POPUP_MATCHES = 15 [static, private]
 

Definition at line 45 of file MatchPanel.java.

final MatchDisplayMenuItemBuilder org::gel::mauve::gui::sequence::MatchPanel::mdmib = new MatchDisplayMenuItemBuilder() [private]
 

Definition at line 74 of file MatchPanel.java.

Referenced by getMatchDisplayMenuItemBuilder(), and MatchPanel().

final MatchPopupMenuBuilder org::gel::mauve::gui::sequence::MatchPanel::mpmb = new MatchPopupMenuBuilder() [private]
 

Definition at line 73 of file MatchPanel.java.

Referenced by getMatchPopupMenuBuilder(), MatchPanel(), and mouseClicked().

RearrangementPanel org::gel::mauve::gui::sequence::MatchPanel::rrpanel [package]
 

Definition at line 69 of file MatchPanel.java.

final SetReferenceMenuItemBuilder org::gel::mauve::gui::sequence::MatchPanel::srmib = new SetReferenceMenuItemBuilder() [private]
 

Definition at line 76 of file MatchPanel.java.

Referenced by getSetReferenceMenuItemBuilder(), and MatchPanel().

long org::gel::mauve::gui::sequence::MatchPanel::viewEnd [private]
 

Definition at line 59 of file MatchPanel.java.

Referenced by MatchPanel().

The documentation for this class was generated from the following file:
Generated on Sat May 25 06:04:03 2013 for Mauve by doxygen 1.3.6