pl.krakow.cmuj.bioinformatics.jellipse
Class jEllipse

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      pl.krakow.cmuj.bioinformatics.jellipse.jEllipse

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class jEllipse
extends javax.swing.JFrame

Main application class serving all grqphic data representations.

See Also:

Serialized Form

Nested Class Summary

class	jEllipse.NotSoGreedyAnimator Prepared out of library sources Animator method that in its original version swamps the CPU not allowing e.g the JMenus to refresh and pop up.
class	jEllipse.QuiteLazyAnimator Prepared out of library sources Animator method that in its original version swamps the CPU not allowing e.g the JMenus to refresh and pop up.

Nested classes/interfaces inherited from class javax.swing.JFrame

javax.swing.JFrame.AccessibleJFrame

Nested classes/interfaces inherited from class java.awt.Frame

java.awt.Frame.AccessibleAWTFrame

Nested classes/interfaces inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

(package private) jEllipse.NotSoGreedyAnimator	animatorMolecule
(package private) jEllipse.QuiteLazyAnimator	animatorPlot
(package private) Peptide	chain
(package private) ColorScheme	Colorscheme
(package private) net.java.games.jogl.GLCanvas	glCanvasMolecule
(package private) net.java.games.jogl.GLCanvas	glCanvasPlot
(package private) net.java.games.jogl.GLCapabilities	glcaps
private javax.swing.JMenuItem	jMenuAnotherAnalyse
private javax.swing.JMenuBar	jMenuBar
private javax.swing.JMenuItem	jMenuColorPB
private javax.swing.JMenu	jMenuColors
private javax.swing.JMenuItem	jMenuColorsRG
private javax.swing.JMenu	jMenuFile
private javax.swing.JMenuItem	jMenuFilePlotExportAsPNG
private javax.swing.JMenuItem	jMenuFileQuit
private javax.swing.JSeparator	jMenuFileSeparator
private javax.swing.JSeparator	jMenuFileSeparator0
private javax.swing.JMenuItem	jMenuFileStructureExportAsPNG
private javax.swing.JMenu	jMenuHelp
private javax.swing.JMenuItem	jMenuHelpAbout
private javax.swing.JMenuItem	jMenuHelpQuickinfo
private javax.swing.JMenuItem	jMenuHelpReferences
private javax.swing.JMenu	jMenuHighlight
private javax.swing.JMenuItem	jMenuHighlightAbsDeviation
private javax.swing.JMenuItem	jMenuHighlightAvgDA
private javax.swing.JMenuItem	jMenuHighlightDeviation
private javax.swing.JMenuItem	jMenuHighlightLnR
private javax.swing.JMenu	jMenuPropertyName
private javax.swing.JMenu	jMenuStructure
private javax.swing.JMenuItem	jMenuStructureBackboneComplete
private javax.swing.JMenuItem	jMenuStructureBackboneVirtual
private javax.swing.JMenu	jMenuView
private javax.swing.JMenuItem	jMenuViewFullscreen
private javax.swing.JMenuItem	jMenuViewRefresh
(package private) javax.swing.JPanel	jPanelLnRvsVPlot
(package private) javax.swing.JPanel	jPanelRamachandranMap
(package private) PdbFile	pdb
(package private) int	plotPbufferHeight
(package private) int	plotPbufferWidth
(package private) PlotRenderer	PlotRer
(package private) Plottable	Property
(package private) boolean	screenshotting_plot
(package private) boolean	screenshotting_structure
(package private) char	selectedchainid
(package private) StructureRenderer	StructureRer
(package private) java.lang.String	titlestr

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

jEllipse()
Creates new form jEllipse

Method Summary

private void	centerWindow(java.awt.Component frame) Displays any java.awt.component in the center of the screen
(package private) void	fadeOthers(javax.swing.JMenu menu, javax.swing.JMenuItem distinguish)
private void	formFocusGained(java.awt.event.FocusEvent evt)
private void	formWindowActivated(java.awt.event.WindowEvent evt)
private void	formWindowGainedFocus(java.awt.event.WindowEvent evt)
private void	initComponents() This method is called from within the constructor to initialize the form.
private void	jMenuAnotherAnalyseActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuColorPBActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuColorsRGActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuFilePlotExportAsPNGActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuFileQuitActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuFileStructureExportAsPNGActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuHelpAboutActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuHelpQuickinfoActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuHelpReferencesActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuHighlightAbsDeviationActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuHighlightAvgDAActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuHighlightDeviationActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuHighlightLnRActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuPropertyNameActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuStructureBackboneCompleteActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuStructureBackboneVirtualActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuViewFullscreenActionPerformed(java.awt.event.ActionEvent evt)
private void	jMenuViewRefreshActionPerformed(java.awt.event.ActionEvent evt)
static void	main(java.lang.String[] args) Main routine.
private void	MainFrameResized(java.awt.event.ComponentEvent evt)
(package private) void	makeLayout() Places components in the main window.
(package private) void	showPropertyName()

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.awt.Frame

addNotify, finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, show, toBack, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusBackward, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

glcaps

final net.java.games.jogl.GLCapabilities glcaps

glCanvasMolecule

net.java.games.jogl.GLCanvas glCanvasMolecule

glCanvasPlot

net.java.games.jogl.GLCanvas glCanvasPlot

jPanelRamachandranMap

javax.swing.JPanel jPanelRamachandranMap

jPanelLnRvsVPlot

javax.swing.JPanel jPanelLnRvsVPlot

animatorMolecule

jEllipse.NotSoGreedyAnimator animatorMolecule

animatorPlot

jEllipse.QuiteLazyAnimator animatorPlot

StructureRer

StructureRenderer StructureRer

PlotRer

PlotRenderer PlotRer

chain

Peptide chain

titlestr

java.lang.String titlestr

Property

Plottable Property

Colorscheme

ColorScheme Colorscheme

screenshotting_plot

boolean screenshotting_plot

screenshotting_structure

boolean screenshotting_structure

plotPbufferWidth

int plotPbufferWidth

plotPbufferHeight

int plotPbufferHeight

pdb

PdbFile pdb

selectedchainid

char selectedchainid

jMenuAnotherAnalyse

private javax.swing.JMenuItem jMenuAnotherAnalyse

jMenuBar

private javax.swing.JMenuBar jMenuBar

jMenuColorPB

private javax.swing.JMenuItem jMenuColorPB

jMenuColors

private javax.swing.JMenu jMenuColors

jMenuColorsRG

private javax.swing.JMenuItem jMenuColorsRG

jMenuFile

private javax.swing.JMenu jMenuFile

jMenuFilePlotExportAsPNG

private javax.swing.JMenuItem jMenuFilePlotExportAsPNG

jMenuFileQuit

private javax.swing.JMenuItem jMenuFileQuit

jMenuFileSeparator

private javax.swing.JSeparator jMenuFileSeparator

jMenuFileSeparator0

private javax.swing.JSeparator jMenuFileSeparator0

jMenuFileStructureExportAsPNG

private javax.swing.JMenuItem jMenuFileStructureExportAsPNG

jMenuHelp

private javax.swing.JMenu jMenuHelp

jMenuHelpAbout

private javax.swing.JMenuItem jMenuHelpAbout

jMenuHelpQuickinfo

private javax.swing.JMenuItem jMenuHelpQuickinfo

jMenuHelpReferences

private javax.swing.JMenuItem jMenuHelpReferences

jMenuHighlight

private javax.swing.JMenu jMenuHighlight

jMenuHighlightAbsDeviation

private javax.swing.JMenuItem jMenuHighlightAbsDeviation

jMenuHighlightAvgDA

private javax.swing.JMenuItem jMenuHighlightAvgDA

jMenuHighlightDeviation

private javax.swing.JMenuItem jMenuHighlightDeviation

jMenuHighlightLnR

private javax.swing.JMenuItem jMenuHighlightLnR

jMenuPropertyName

private javax.swing.JMenu jMenuPropertyName

jMenuStructure

private javax.swing.JMenu jMenuStructure

jMenuStructureBackboneComplete

private javax.swing.JMenuItem jMenuStructureBackboneComplete

jMenuStructureBackboneVirtual

private javax.swing.JMenuItem jMenuStructureBackboneVirtual

jMenuView

private javax.swing.JMenu jMenuView

jMenuViewFullscreen

private javax.swing.JMenuItem jMenuViewFullscreen

jMenuViewRefresh

private javax.swing.JMenuItem jMenuViewRefresh

Constructor Detail

jEllipse

public jEllipse()

Creates new form jEllipse

Method Detail

initComponents

private void initComponents()

This method is called from within the constructor to initialize the form. WARNING: Do NOT modify this code. The content of this method is always regenerated by the Form Editor.

jMenuFileStructureExportAsPNGActionPerformed

private void jMenuFileStructureExportAsPNGActionPerformed(java.awt.event.ActionEvent evt)

jMenuAnotherAnalyseActionPerformed

private void jMenuAnotherAnalyseActionPerformed(java.awt.event.ActionEvent evt)

jMenuPropertyNameActionPerformed

private void jMenuPropertyNameActionPerformed(java.awt.event.ActionEvent evt)

jMenuViewFullscreenActionPerformed

private void jMenuViewFullscreenActionPerformed(java.awt.event.ActionEvent evt)

jMenuFilePlotExportAsPNGActionPerformed

private void jMenuFilePlotExportAsPNGActionPerformed(java.awt.event.ActionEvent evt)

jMenuHelpReferencesActionPerformed

private void jMenuHelpReferencesActionPerformed(java.awt.event.ActionEvent evt)

jMenuHelpAboutActionPerformed

private void jMenuHelpAboutActionPerformed(java.awt.event.ActionEvent evt)

jMenuHelpQuickinfoActionPerformed

private void jMenuHelpQuickinfoActionPerformed(java.awt.event.ActionEvent evt)

jMenuColorPBActionPerformed

private void jMenuColorPBActionPerformed(java.awt.event.ActionEvent evt)

jMenuColorsRGActionPerformed

private void jMenuColorsRGActionPerformed(java.awt.event.ActionEvent evt)

jMenuHighlightAbsDeviationActionPerformed

private void jMenuHighlightAbsDeviationActionPerformed(java.awt.event.ActionEvent evt)

jMenuHighlightDeviationActionPerformed

private void jMenuHighlightDeviationActionPerformed(java.awt.event.ActionEvent evt)

jMenuHighlightAvgDAActionPerformed

private void jMenuHighlightAvgDAActionPerformed(java.awt.event.ActionEvent evt)

jMenuHighlightLnRActionPerformed

private void jMenuHighlightLnRActionPerformed(java.awt.event.ActionEvent evt)

jMenuStructureBackboneVirtualActionPerformed

private void jMenuStructureBackboneVirtualActionPerformed(java.awt.event.ActionEvent evt)

jMenuStructureBackboneCompleteActionPerformed

private void jMenuStructureBackboneCompleteActionPerformed(java.awt.event.ActionEvent evt)

jMenuFileQuitActionPerformed

private void jMenuFileQuitActionPerformed(java.awt.event.ActionEvent evt)

jMenuViewRefreshActionPerformed

private void jMenuViewRefreshActionPerformed(java.awt.event.ActionEvent evt)

formWindowGainedFocus

private void formWindowGainedFocus(java.awt.event.WindowEvent evt)

formWindowActivated

private void formWindowActivated(java.awt.event.WindowEvent evt)

formFocusGained

private void formFocusGained(java.awt.event.FocusEvent evt)

MainFrameResized

private void MainFrameResized(java.awt.event.ComponentEvent evt)

makeLayout

void makeLayout()

Places components in the main window.

fadeOthers

void fadeOthers(javax.swing.JMenu menu,
                javax.swing.JMenuItem distinguish)

showPropertyName

void showPropertyName()

centerWindow

private void centerWindow(java.awt.Component frame)

Displays any java.awt.component in the center of the screen

Parameters:

frame - usu a window

main

public static void main(java.lang.String[] args)

Main routine.

Parameters:

args - the command line arguments