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:

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

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List of all members.

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.


Member Data Documentation

boolean org::gel::mauve::gui::LcbLinePanel::draw_strikethrough = true [package]
 

Definition at line 33 of file LcbLinePanel.java.

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed(), and paint().

boolean org::gel::mauve::gui::LcbLinePanel::hidden = false [package]
 

Definition at line 35 of file LcbLinePanel.java.

Referenced by getHidden().

boolean [] org::gel::mauve::gui::LcbLinePanel::highlighted [package]
 

Definition at line 27 of file LcbLinePanel.java.

Referenced by LcbLinePanel(), and paint().

int org::gel::mauve::gui::LcbLinePanel::menubar_height [package]
 

Definition at line 31 of file LcbLinePanel.java.

LcbViewerModel org::gel::mauve::gui::LcbLinePanel::model [package]
 

Definition at line 45 of file LcbLinePanel.java.

RearrangementPanel org::gel::mauve::gui::LcbLinePanel::rrpanel [package]
 

Definition at line 29 of file LcbLinePanel.java.


The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:04:03 2013 for Mauve by doxygen 1.3.6