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org::gel::mauve::gui::RearrangementPanel Class Reference

The primary container class for the visualization interface. More...

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

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List of all members.

Public Member Functions

void actionPerformed (ActionEvent e)
void addHintMessageListener (HintMessageListener l)
 Add a HintMessageListener to the list of listeners for the model.

void addKeyMapping (String stroke, String actionName, ActionListener listener)
void attributesChanged (ModelEvent event)
void colorChanged (ModelEvent event)
void drawingSettingsChanged (ModelEvent event)
void genomesReordered (ModelEvent event)
void genomeVisibilityChanged (ModelEvent event)
BaseViewerModel getModel ()
SeqPanel getNewPanel (int i)
Dimension getPreferredScrollableViewportSize ()
Dimension getPreferredSize ()
int getScrollableBlockIncrement (Rectangle visibleRect, int orientation, int direction)
boolean getScrollableTracksViewportHeight ()
boolean getScrollableTracksViewportWidth ()
int getScrollableUnitIncrement (Rectangle visibleRect, int orientation, int direction)
RRSequencePanel getSequencePanel (int i)
void init (BaseViewerModel model)
 Initialize all the GUI elements.

void modeChanged (ModelEvent event)
void modelReloadEnd (ModelEvent event)
void modelReloadStart (ModelEvent event)
void pageSetup ()
void print ()
int print (Graphics g, PageFormat pageFormat, int pageIndex)
void printingEnd (ModelEvent event)
void printingStart (ModelEvent event)
 RearrangementPanel (JToolBar toolbar, MauveFrame parent)
 Does basic initialization for a RearrangementPanel.

void referenceChanged (ModelEvent event)
void removeHintMessageListenerListener (HintMessageListener l)
 Remove a HintMessageListener from the list of listeners for this model.

void removeKeyMapping (String stroke)
void reorderSequences (int new_order[])
 This function reorders sequence data structures when the user has requested a new ordering of sequences in the display.

void setScrollableTracksViewportWidth (boolean matchWidth)
 Match component width to viewport width?

void stateChanged (ChangeEvent e)
void viewableRangeChanged (ModelEvent event)
void viewableRangeChangeEnd (ModelEvent event)
void viewableRangeChangeStart (ModelEvent event)
void weightChanged (ModelEvent event)

Public Attributes

MauveFrame mauveFrame

Static Public Attributes

final Color bg_color = new Color(.85f, .85f, .85f)

Protected Member Functions

void fireHintMessageEvent (String message)
 Invoke HintMessageListener.messageChanged(ModelEvent) on this model's collection of HintMessageListener.

void initLCBTools ()
 Initialize data structures to support LCB display and manipulation.

void initMatchDisplay ()
 Initialize the display environment.


Package Functions

void setNewPanels (Vector v)

Package Attributes

LcbLinePanel lcbLinePanel
BaseViewerModel model
Vector newPanels = new Vector()
PageFormat pageFormat = new PageFormat()
boolean scrollableTracksViewportWidth = true
JPanel sequencePanel
JToolBar toolbar
JSlider weight_slider = new JSlider(0, 100, 0)
JTextField weight_value_text = new JTextField(5)

Static Package Attributes

final int CS_SELECT = 0
final int CS_SEQ_MOVE = 4
final int CS_SEQ_ZOOM = 3
final int CS_UNIV_MOVE = 2
final int CS_UNIV_ZOOM = 1
final double gbc_weighty = 5.0

Private Member Functions

boolean haveBackboneData ()
boolean haveNwayLcbData ()
void initKeyBindings ()
void initToolbar ()

Static Private Member Functions

int determineResolution (PrinterJob printJob)

Private Attributes

CtrlKeyDetector ctrlDetector = new CtrlKeyDetector()
GridBagConstraints gbc = new GridBagConstraints()
GridBagLayout gbl = new GridBagLayout()
 variables controlling the display layout

EventListenerList hintMessageListeners = new EventListenerList()
 a list of objects listening for hint messages

boolean oldDrawMatches
boolean oldFillBoxes
int printingResolution = 600
double printingScale = -1
boolean sliderAdjustmentInProcess = false
JToggleButton zoom_button

Static Private Attributes

final Integer LCB_PANEL = new Integer(2)
final Integer SEQ_PANEL = new Integer(1)

Detailed Description

The primary container class for the visualization interface.

For every genome being displayed, a RearrangementPanel contains a ruler (RulerPanel) and a sequence display (RRSequencePanel). For each genome, the ruler displays sequence coordinates currently in view, while the RRSequencePanel displays some sort of similarity information: either the location of exact matches or a similarity profile. The RearrangementPanel sets up the entire display and coordinates its interface. It mediates shifts in the viewable range and other user interaction. There are three primary information display modes supported by the RearrangementPanel and associated classes. Mode 1) Display a set of ungapped local alignments among multiple genomes. Mode 2) Display a set of ungapped local alignments that have been grouped into locally collinear blocks (LCBs). The LCBs are assumed to not overlap each other. In this display mode, a bounding box around each LCB is usually drawn and an LCBLinePanel can be used to draw connecting lines between LCB bounding boxes Mode 3) Display a gapped global alignment of locally collinear blocks (LCBs) stored in an XMFAAlignment object. A SimilarityIndex object is used to calculate average sequence similarity among the genomes over any arbitrary interval in one sequence. LCB bounding boxes are drawn around each LCB and within each LCB the sequence similarity profile gets displayed. An LCBLinePanel draws connecting lines among LCB bounding boxes in each genome.

Definition at line 95 of file RearrangementPanel.java.

Constructor & Destructor Documentation

org::gel::mauve::gui::RearrangementPanel::RearrangementPanel (  JToolBar  toolbar,
MauveFrame  parent
)  [inline]
 

Does basic initialization for a RearrangementPanel.

Call readRearrangementData() to load and display data.

Parameters:
toolbar A toolbar which can be manipulated by this panel, or null to indicate no toolbar will be available

Definition at line 166 of file RearrangementPanel.java.

References mauveFrame.

Member Function Documentation

void org::gel::mauve::gui::RearrangementPanel::actionPerformed (  ActionEvent  e  )  [inline]
 

Definition at line 571 of file RearrangementPanel.java.

References org::gel::mauve::BaseViewerModel::getMode(), org::gel::mauve::LcbViewerModel::launchGrimmMGR(), mauveFrame, org::gel::mauve::BaseViewerModel::setMode(), org::gel::mauve::ViewerMode::ZOOM, and org::gel::mauve::BaseViewerModel::zoomAndMove().

Referenced by initToolbar().

void org::gel::mauve::gui::RearrangementPanel::addHintMessageListener (  HintMessageListener  l  )  [inline]
 

Add a HintMessageListener to the list of listeners for the model.

Parameters:
l listener to add

Definition at line 484 of file RearrangementPanel.java.

References hintMessageListeners.

Referenced by org::gel::mauve::gui::MauveFrame::setModel().

void org::gel::mauve::gui::RearrangementPanel::addKeyMapping (  String  stroke,
String  actionName,
ActionListener  listener
)  [inline]
 

Definition at line 287 of file RearrangementPanel.java.

Referenced by initKeyBindings(), and org::gel::mauve::gui::StyleMenu::setTarget().

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

Implements org::gel::mauve::ModelListener.

Definition at line 937 of file RearrangementPanel.java.

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

Implements org::gel::mauve::ModelListener.

Definition at line 827 of file RearrangementPanel.java.

int org::gel::mauve::gui::RearrangementPanel::determineResolution (  PrinterJob  printJob  )  [inline, static, private]
 

Parameters:
printJob 

Definition at line 801 of file RearrangementPanel.java.

Referenced by print().

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

Implements org::gel::mauve::ModelListener.

Definition at line 837 of file RearrangementPanel.java.

void org::gel::mauve::gui::RearrangementPanel::fireHintMessageEvent (  String  message  )  [inline, protected]
 

Invoke HintMessageListener.messageChanged(ModelEvent) on this model's collection of HintMessageListener.

Definition at line 501 of file RearrangementPanel.java.

References hintMessageListeners.

Referenced by initLCBTools(), and stateChanged().

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

Implements org::gel::mauve::ModelListener.

Definition at line 922 of file RearrangementPanel.java.

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

Implements org::gel::mauve::ModelListener.

Definition at line 902 of file RearrangementPanel.java.

References gbc, gbc_weighty, gbl, org::gel::mauve::BaseViewerModel::getGenomeByViewingIndex(), getNewPanel(), org::gel::mauve::BaseViewerModel::getSequenceCount(), and org::gel::mauve::Genome::getVisible().

BaseViewerModel org::gel::mauve::gui::RearrangementPanel::getModel (   )  [inline]
 

Definition at line 187 of file RearrangementPanel.java.

Referenced by initToolbar().

SeqPanel org::gel::mauve::gui::RearrangementPanel::getNewPanel (  int  i  )  [inline]
 

Definition at line 197 of file RearrangementPanel.java.

References newPanels.

Referenced by org::gel::mauve::gui::sequence::FlatFileFeatureImporter::addedMoreOfTypes(), org::gel::mauve::gui::sequence::FlatFileFeatureImporter::addFeatureType(), genomeVisibilityChanged(), getSequencePanel(), org::gel::mauve::gui::LcbLinePanel::paint(), and reorderSequences().

Dimension org::gel::mauve::gui::RearrangementPanel::getPreferredScrollableViewportSize (   )  [inline]
 

See also:
javax.swing.Scrollable#getPreferredScrollableViewportSize()

Definition at line 719 of file RearrangementPanel.java.

References getPreferredSize().

Dimension org::gel::mauve::gui::RearrangementPanel::getPreferredSize (   )  [inline]
 

Definition at line 667 of file RearrangementPanel.java.

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

Referenced by getPreferredScrollableViewportSize().

int org::gel::mauve::gui::RearrangementPanel::getScrollableBlockIncrement (  Rectangle  visibleRect,
int  orientation,
int  direction
)  [inline]
 

See also:
javax.swing.Scrollable#getScrollableBlockIncrement(java.awt.Rectangle, int, int)

Definition at line 728 of file RearrangementPanel.java.

boolean org::gel::mauve::gui::RearrangementPanel::getScrollableTracksViewportHeight (   )  [inline]
 

See also:
javax.swing.Scrollable#getScrollableTracksViewportHeight()

Definition at line 693 of file RearrangementPanel.java.

boolean org::gel::mauve::gui::RearrangementPanel::getScrollableTracksViewportWidth (   )  [inline]
 

See also:
javax.swing.Scrollable#getScrollableTracksViewportWidth()

Definition at line 710 of file RearrangementPanel.java.

References scrollableTracksViewportWidth.

int org::gel::mauve::gui::RearrangementPanel::getScrollableUnitIncrement (  Rectangle  visibleRect,
int  orientation,
int  direction
)  [inline]
 

See also:
javax.swing.Scrollable#getScrollableUnitIncrement(java.awt.Rectangle, int, int)

Definition at line 737 of file RearrangementPanel.java.

RRSequencePanel org::gel::mauve::gui::RearrangementPanel::getSequencePanel (  int  i  )  [inline]
 

Definition at line 202 of file RearrangementPanel.java.

References getNewPanel(), and org::gel::mauve::gui::sequence::SeqPanel::getSequencePanel().

boolean org::gel::mauve::gui::RearrangementPanel::haveBackboneData (   )  [inline, private]
 

Definition at line 314 of file RearrangementPanel.java.

References org::gel::mauve::XmfaViewerModel::getBackboneList().

boolean org::gel::mauve::gui::RearrangementPanel::haveNwayLcbData (   )  [inline, private]
 

Definition at line 300 of file RearrangementPanel.java.

References org::gel::mauve::LcbViewerModel::isNwayLcbList().

Referenced by initLCBTools(), and initToolbar().

void org::gel::mauve::gui::RearrangementPanel::init (  BaseViewerModel  model  )  [inline]
 

Initialize all the GUI elements.

Definition at line 176 of file RearrangementPanel.java.

References org::gel::mauve::BaseViewerModel::addModelListener(), initLCBTools(), and initMatchDisplay().

Referenced by org::gel::mauve::gui::MauveFrame::setModel().

void org::gel::mauve::gui::RearrangementPanel::initKeyBindings (   )  [inline, private]
 

Definition at line 275 of file RearrangementPanel.java.

References addKeyMapping().

Referenced by initMatchDisplay().

void org::gel::mauve::gui::RearrangementPanel::initLCBTools (   )  [inline, protected]
 

Initialize data structures to support LCB display and manipulation.

Initializes the LCB weight slider.

Definition at line 427 of file RearrangementPanel.java.

References fireHintMessageEvent(), org::gel::mauve::LcbViewerModel::getLcbChangePoints(), org::gel::mauve::LcbViewerModel::getLcbCount(), org::gel::mauve::LcbViewerModel::getMinLCBWeight(), org::gel::mauve::LcbViewerModel::getVisibleLcbCount(), haveNwayLcbData(), LCB_PANEL, lcbLinePanel, weight_slider, and weight_value_text.

Referenced by init().

void org::gel::mauve::gui::RearrangementPanel::initMatchDisplay (   )  [inline, protected]
 

Initialize the display environment.

Set up a RRSequencePanel and a RulerPanel for each sequence. also populate the toolbar and set up the LCB line panel Register key bindings for various interface elements

Definition at line 245 of file RearrangementPanel.java.

References gbc, gbc_weighty, gbl, org::gel::mauve::BaseViewerModel::getGenomeByViewingIndex(), org::gel::mauve::BaseViewerModel::getSequenceCount(), initKeyBindings(), initToolbar(), newPanels, SEQ_PANEL, and sequencePanel.

Referenced by init().

void org::gel::mauve::gui::RearrangementPanel::initToolbar (   )  [inline, private]
 

Definition at line 327 of file RearrangementPanel.java.

References actionPerformed(), org::gel::mauve::BaseViewerModel::getGenomes(), getModel(), haveNwayLcbData(), and zoom_button.

Referenced by initMatchDisplay().

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

Implements org::gel::mauve::ModelListener.

Definition at line 847 of file RearrangementPanel.java.

References ctrlDetector, org::gel::mauve::BaseViewerModel::getMode(), org::gel::mauve::ViewerMode::NORMAL, org::gel::mauve::ViewerMode::ZOOM, and zoom_button.

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

Implements org::gel::mauve::ModelListener.

Definition at line 917 of file RearrangementPanel.java.

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

Implements org::gel::mauve::ModelListener.

Definition at line 912 of file RearrangementPanel.java.

void org::gel::mauve::gui::RearrangementPanel::pageSetup (   )  [inline]
 

Definition at line 821 of file RearrangementPanel.java.

References pageFormat.

Referenced by org::gel::mauve::gui::MauveFrame::actionPerformed().

void org::gel::mauve::gui::RearrangementPanel::print (   )  [inline]
 

Definition at line 775 of file RearrangementPanel.java.

References determineResolution(), org::gel::mauve::BaseViewerModel::firePrintingEndEvent(), org::gel::mauve::BaseViewerModel::firePrintingStartEvent(), pageFormat, printingResolution, and printingScale.

int org::gel::mauve::gui::RearrangementPanel::print (  Graphics  g,
PageFormat  pageFormat,
int  pageIndex
)  [inline]
 

Definition at line 748 of file RearrangementPanel.java.

References printingResolution, and printingScale.

Referenced by org::gel::mauve::gui::MauveFrame::actionPerformed().

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

Implements org::gel::mauve::ModelListener.

Definition at line 933 of file RearrangementPanel.java.

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

Implements org::gel::mauve::ModelListener.

Definition at line 928 of file RearrangementPanel.java.

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

Implements org::gel::mauve::ModelListener.

Definition at line 842 of file RearrangementPanel.java.

void org::gel::mauve::gui::RearrangementPanel::removeHintMessageListenerListener (  HintMessageListener  l  )  [inline]
 

Remove a HintMessageListener from the list of listeners for this model.

Parameters:
l listener to remove

Definition at line 493 of file RearrangementPanel.java.

References hintMessageListeners.

void org::gel::mauve::gui::RearrangementPanel::removeKeyMapping (  String  stroke  )  [inline]
 

Definition at line 294 of file RearrangementPanel.java.

void org::gel::mauve::gui::RearrangementPanel::reorderSequences (  int  new_order[]  )  [inline]
 

This function reorders sequence data structures when the user has requested a new ordering of sequences in the display.

Definition at line 211 of file RearrangementPanel.java.

References gbc, gbc_weighty, gbl, org::gel::mauve::BaseViewerModel::getGenomeByViewingIndex(), getNewPanel(), org::gel::mauve::BaseViewerModel::getSequenceCount(), org::gel::mauve::Genome::getVisible(), org::gel::mauve::BaseViewerModel::reorderSequences(), sequencePanel, org::gel::mauve::gui::sequence::SeqPanel::setBackground(), and setNewPanels().

Referenced by org::gel::mauve::gui::sequence::ControlPanel::ControlPanel().

void org::gel::mauve::gui::RearrangementPanel::setNewPanels (  Vector  v  )  [inline, package]
 

Definition at line 192 of file RearrangementPanel.java.

References newPanels.

Referenced by reorderSequences().

void org::gel::mauve::gui::RearrangementPanel::setScrollableTracksViewportWidth (  boolean  matchWidth  )  [inline]
 

Match component width to viewport width?

Definition at line 703 of file RearrangementPanel.java.

References scrollableTracksViewportWidth.

void org::gel::mauve::gui::RearrangementPanel::stateChanged (  ChangeEvent  e  )  [inline]
 

Definition at line 512 of file RearrangementPanel.java.

References fireHintMessageEvent(), org::gel::mauve::BaseViewerModel::getDrawMatches(), org::gel::mauve::LcbViewerModel::getFillLcbBoxes(), org::gel::mauve::LcbViewerModel::getLcbChangePoints(), org::gel::mauve::LcbViewerModel::getVisibleLcbCount(), oldDrawMatches, oldFillBoxes, org::gel::mauve::BaseViewerModel::setDrawMatches(), org::gel::mauve::LcbViewerModel::setFillLcbBoxes(), sliderAdjustmentInProcess, org::gel::mauve::LcbViewerModel::updateLCBweight(), weight_slider, and weight_value_text.

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

Implements org::gel::mauve::ModelListener.

Definition at line 887 of file RearrangementPanel.java.

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

Implements org::gel::mauve::ModelListener.

Definition at line 897 of file RearrangementPanel.java.

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

Implements org::gel::mauve::ModelListener.

Definition at line 892 of file RearrangementPanel.java.

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

Implements org::gel::mauve::ModelListener.

Definition at line 832 of file RearrangementPanel.java.

Member Data Documentation

final Color org::gel::mauve::gui::RearrangementPanel::bg_color = new Color(.85f, .85f, .85f) [static]
 

Definition at line 130 of file RearrangementPanel.java.

final int org::gel::mauve::gui::RearrangementPanel::CS_SELECT = 0 [static, package]
 

Definition at line 124 of file RearrangementPanel.java.

final int org::gel::mauve::gui::RearrangementPanel::CS_SEQ_MOVE = 4 [static, package]
 

Definition at line 128 of file RearrangementPanel.java.

final int org::gel::mauve::gui::RearrangementPanel::CS_SEQ_ZOOM = 3 [static, package]
 

Definition at line 127 of file RearrangementPanel.java.

final int org::gel::mauve::gui::RearrangementPanel::CS_UNIV_MOVE = 2 [static, package]
 

Definition at line 126 of file RearrangementPanel.java.

final int org::gel::mauve::gui::RearrangementPanel::CS_UNIV_ZOOM = 1 [static, package]
 

Definition at line 125 of file RearrangementPanel.java.

CtrlKeyDetector org::gel::mauve::gui::RearrangementPanel::ctrlDetector = new CtrlKeyDetector() [private]
 

Definition at line 148 of file RearrangementPanel.java.

Referenced by modeChanged().

GridBagConstraints org::gel::mauve::gui::RearrangementPanel::gbc = new GridBagConstraints() [private]
 

Definition at line 155 of file RearrangementPanel.java.

Referenced by genomeVisibilityChanged(), initMatchDisplay(), and reorderSequences().

final double org::gel::mauve::gui::RearrangementPanel::gbc_weighty = 5.0 [static, package]
 

Definition at line 156 of file RearrangementPanel.java.

Referenced by genomeVisibilityChanged(), initMatchDisplay(), and reorderSequences().

GridBagLayout org::gel::mauve::gui::RearrangementPanel::gbl = new GridBagLayout() [private]
 

variables controlling the display layout

Definition at line 154 of file RearrangementPanel.java.

Referenced by genomeVisibilityChanged(), initMatchDisplay(), and reorderSequences().

EventListenerList org::gel::mauve::gui::RearrangementPanel::hintMessageListeners = new EventListenerList() [private]
 

a list of objects listening for hint messages

Definition at line 151 of file RearrangementPanel.java.

Referenced by addHintMessageListener(), fireHintMessageEvent(), and removeHintMessageListenerListener().

final Integer org::gel::mauve::gui::RearrangementPanel::LCB_PANEL = new Integer(2) [static, private]
 

Definition at line 97 of file RearrangementPanel.java.

Referenced by initLCBTools().

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

Definition at line 107 of file RearrangementPanel.java.

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

MauveFrame org::gel::mauve::gui::RearrangementPanel::mauveFrame
 

Definition at line 101 of file RearrangementPanel.java.

Referenced by actionPerformed(), and RearrangementPanel().

BaseViewerModel org::gel::mauve::gui::RearrangementPanel::model [package]
 

Definition at line 140 of file RearrangementPanel.java.

Referenced by org::gel::mauve::gui::LcbLinePanel::LcbLinePanel().

Vector org::gel::mauve::gui::RearrangementPanel::newPanels = new Vector() [package]
 

Definition at line 104 of file RearrangementPanel.java.

Referenced by getNewPanel(), org::gel::mauve::gui::SequenceNavigator::goToPosition(), initMatchDisplay(), and setNewPanels().

boolean org::gel::mauve::gui::RearrangementPanel::oldDrawMatches [private]
 

Definition at line 143 of file RearrangementPanel.java.

Referenced by stateChanged().

boolean org::gel::mauve::gui::RearrangementPanel::oldFillBoxes [private]
 

Definition at line 144 of file RearrangementPanel.java.

Referenced by stateChanged().

PageFormat org::gel::mauve::gui::RearrangementPanel::pageFormat = new PageFormat() [package]
 

Definition at line 133 of file RearrangementPanel.java.

Referenced by org::gel::mauve::gui::MauveFrame::actionPerformed(), pageSetup(), and print().

int org::gel::mauve::gui::RearrangementPanel::printingResolution = 600 [private]
 

Definition at line 137 of file RearrangementPanel.java.

Referenced by print().

double org::gel::mauve::gui::RearrangementPanel::printingScale = -1 [private]
 

Definition at line 136 of file RearrangementPanel.java.

Referenced by print().

boolean org::gel::mauve::gui::RearrangementPanel::scrollableTracksViewportWidth = true [package]
 

Definition at line 699 of file RearrangementPanel.java.

Referenced by getScrollableTracksViewportWidth(), and setScrollableTracksViewportWidth().

final Integer org::gel::mauve::gui::RearrangementPanel::SEQ_PANEL = new Integer(1) [static, private]
 

Definition at line 98 of file RearrangementPanel.java.

Referenced by initMatchDisplay().

JPanel org::gel::mauve::gui::RearrangementPanel::sequencePanel [package]
 

Definition at line 110 of file RearrangementPanel.java.

Referenced by initMatchDisplay(), and reorderSequences().

boolean org::gel::mauve::gui::RearrangementPanel::sliderAdjustmentInProcess = false [private]
 

Definition at line 142 of file RearrangementPanel.java.

Referenced by stateChanged().

JToolBar org::gel::mauve::gui::RearrangementPanel::toolbar [package]
 

Definition at line 114 of file RearrangementPanel.java.

JSlider org::gel::mauve::gui::RearrangementPanel::weight_slider = new JSlider(0, 100, 0) [package]
 

Definition at line 119 of file RearrangementPanel.java.

Referenced by initLCBTools(), and stateChanged().

JTextField org::gel::mauve::gui::RearrangementPanel::weight_value_text = new JTextField(5) [package]
 

Definition at line 122 of file RearrangementPanel.java.

Referenced by initLCBTools(), and stateChanged().

JToggleButton org::gel::mauve::gui::RearrangementPanel::zoom_button [private]
 

Definition at line 145 of file RearrangementPanel.java.

Referenced by initToolbar(), and modeChanged().

The documentation for this class was generated from the following file:
Generated on Sun May 19 06:21:33 2013 for Mauve by doxygen 1.3.6