org::gel::mauve::gui::LcbLinePanel Class Reference

This class is intended to overlay a RearrangementPanel with lines that connect each locally collinear block. More...

Inheritance diagram for org::gel::mauve::gui::LcbLinePanel:

[legend]Collaboration diagram for org::gel::mauve::gui::LcbLinePanel:


Public Member Functions
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)
void	paint (Graphics g1d)
	Extract the pixel coordinates of visible LCBs and draw lines that connect them.
void	paintComponent (Graphics g)
void	printingEnd (ModelEvent event)
void	printingStart (ModelEvent event)
void	referenceChanged (ModelEvent event)
void	viewableRangeChanged (ModelEvent event)
void	viewableRangeChangeEnd (ModelEvent event)
void	viewableRangeChangeStart (ModelEvent event)
void	weightChanged (ModelEvent event)
Package Functions
boolean	getHidden ()
	LcbLinePanel (RearrangementPanel rrpanel, LcbViewerModel model)
int	nextVisibleGenome (LCB lcb, int fromSeq)
void	setHidden (boolean hidden)
Package Attributes
boolean	draw_strikethrough = true
boolean	hidden = false
boolean[]	highlighted
int	menubar_height
LcbViewerModel	model
RearrangementPanel	rrpanel
Private Member Functions
boolean	barVisible (Rectangle bounds, int start, int end)

Detailed Description

This class is intended to overlay a RearrangementPanel with lines that connect each locally collinear block.

It reads the LCB boundaries and the current view range from various classes contained by a RearrangementPanel. A very, very dirty hack.

Definition at line 25 of file LcbLinePanel.java.

Constructor & Destructor Documentation

org::gel::mauve::gui::LcbLinePanel::LcbLinePanel ( RearrangementPanel rrpanel,

LcbViewerModel model

) [inline, package]

Definition at line 47 of file LcbLinePanel.java.
References org::gel::mauve::BaseViewerModel::addModelListener(), org::gel::mauve::LcbViewerModel::getVisibleLcbCount(), highlighted, and org::gel::mauve::gui::RearrangementPanel::model.

Member Function Documentation

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

Implements org::gel::mauve::ModelListener.
Definition at line 281 of file LcbLinePanel.java.

boolean org::gel::mauve::gui::LcbLinePanel::barVisible ( Rectangle bounds,

int start,

int end

) [inline, private]

Parameters:

bounds

start

end

Returns:

Definition at line 205 of file LcbLinePanel.java.
Referenced by paint().

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

Implements org::gel::mauve::ModelListener.
Definition at line 210 of file LcbLinePanel.java.

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

Implements org::gel::mauve::ModelListener.
Definition at line 220 of file LcbLinePanel.java.

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

Implements org::gel::mauve::ModelListener.
Definition at line 257 of file LcbLinePanel.java.

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

Implements org::gel::mauve::ModelListener.
Definition at line 267 of file LcbLinePanel.java.

boolean org::gel::mauve::gui::LcbLinePanel::getHidden ( ) [inline, package]

Definition at line 37 of file LcbLinePanel.java.
References hidden.
Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed(), viewableRangeChangeEnd(), and viewableRangeChangeStart().

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

Implements org::gel::mauve::ModelListener.
Definition at line 225 of file LcbLinePanel.java.

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

Implements org::gel::mauve::ModelListener.
Definition at line 252 of file LcbLinePanel.java.

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

Implements org::gel::mauve::ModelListener.
Definition at line 247 of file LcbLinePanel.java.

int org::gel::mauve::gui::LcbLinePanel::nextVisibleGenome ( LCB lcb,

int fromSeq

) [inline, package]

Definition at line 65 of file LcbLinePanel.java.
References org::gel::mauve::BaseViewerModel::getGenomeByViewingIndex(), org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::BaseViewerModel::getSequenceCount(), and org::gel::mauve::Genome::getVisible().
Referenced by paint().

void org::gel::mauve::gui::LcbLinePanel::paint ( Graphics g1d ) [inline]

Extract the pixel coordinates of visible LCBs and draw lines that connect them.

Definition at line 81 of file LcbLinePanel.java.
References barVisible(), org::gel::mauve::gui::sequence::RRSequencePanel::boxTop(), org::gel::mauve::LCB::color, draw_strikethrough, org::gel::mauve::BaseViewerModel::getGenomeByViewingIndex(), org::gel::mauve::gui::RearrangementPanel::getNewPanel(), org::gel::mauve::LCB::getReverse(), org::gel::mauve::BaseViewerModel::getSequenceCount(), org::gel::mauve::gui::sequence::SeqPanel::getSequencePanel(), org::gel::mauve::LcbViewerModel::getVisibleLcb(), org::gel::mauve::LcbViewerModel::getVisibleLcbCount(), highlighted, org::gel::mauve::LCB::midpoint(), nextVisibleGenome(), and org::gel::mauve::gui::sequence::RRSequencePanel::sequenceCoordinateToCenterPixel().
Referenced by paintComponent().

void org::gel::mauve::gui::LcbLinePanel::paintComponent ( Graphics g ) [inline]

Definition at line 60 of file LcbLinePanel.java.
References paint().

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

Implements org::gel::mauve::ModelListener.
Definition at line 277 of file LcbLinePanel.java.

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

Implements org::gel::mauve::ModelListener.
Definition at line 272 of file LcbLinePanel.java.

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

Implements org::gel::mauve::ModelListener.
Definition at line 262 of file LcbLinePanel.java.

void org::gel::mauve::gui::LcbLinePanel::setHidden ( boolean hidden ) [inline, package]

Definition at line 38 of file LcbLinePanel.java.
Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed().

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

Implements org::gel::mauve::ModelListener.
Definition at line 230 of file LcbLinePanel.java.

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

Implements org::gel::mauve::ModelListener.
Definition at line 241 of file LcbLinePanel.java.
References getHidden().

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

Implements org::gel::mauve::ModelListener.
Definition at line 235 of file LcbLinePanel.java.
References getHidden().

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

Implements org::gel::mauve::ModelListener.
Definition at line 215 of file LcbLinePanel.java.