Serialized Form

Package org.simtk.console

Class org.simtk.console.ConsolePanel extends javax.swing.JPanel implements Serializable

Serialized Fields

historyText

org.simtk.console.ConsolePanel.HistoryArea historyText

prompt

org.simtk.console.ConsolePanel.Prompt prompt

commandLine

org.simtk.console.ConsolePanel.CommandField commandLine

Package org.simtk.mol.color

Class org.simtk.mol.color.UnknownObjectColorException extends java.lang.Exception implements Serializable

Package org.simtk.mol.toon

Class org.simtk.mol.toon.NoCartoonCreatedException extends java.lang.Exception implements Serializable

Package org.simtk.moleculargraphics

Class org.simtk.moleculargraphics.BufferedCanvas extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

offScreenImage

java.awt.Image offScreenImage

width

int width

height

int height

Class org.simtk.moleculargraphics.CameraPanel extends javax.swing.JPanel implements Serializable

Class org.simtk.moleculargraphics.CylinderPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

renWin

vtk.vtkCanvas renWin

exitButton

javax.swing.JButton exitButton

renderer

vtk.vtkRenderer renderer

vtkPropNames

java.util.Hashtable<K,V> vtkPropNames

vtkPropObjects

java.util.Hashtable<K,V> vtkPropObjects

handCursor

java.awt.Cursor handCursor

defaultCursor

java.awt.Cursor defaultCursor

sphereCount

int sphereCount

cylinderCount

int cylinderCount

picker

vtk.vtkPropPicker picker

Class org.simtk.moleculargraphics.EthaneDemo extends MolApp implements Serializable

Serialized Fields

userAppName

java.lang.String userAppName

ethaneTorsion

org.simtk.moleculargraphics.AtomTorsion ethaneTorsion

actorCartoon

CappedBondActor actorCartoon

ethane

org.simtk.molecularstructure.Molecule ethane

Class org.simtk.moleculargraphics.MolApp extends javax.swing.JFrame implements Serializable

Serialized Fields

classLoader

java.lang.ClassLoader classLoader

canvas

StructureCanvas canvas

Class org.simtk.moleculargraphics.PublicNativeVtkPanel extends vtk.vtkPanel implements Serializable

Class org.simtk.moleculargraphics.SequenceCanvas extends BufferedCanvas implements Serializable

serialVersionUID: 1L

Serialized Fields

numberOfResidues

int numberOfResidues

minHeight

int minHeight

minWidth

int minWidth

myGraphics

java.awt.Graphics myGraphics

parentContainer

javax.swing.JComponent parentContainer

font

java.awt.Font font

symbolWidth

double symbolWidth

symbolHeight

double symbolHeight

characterSpacing

double characterSpacing

baseLine

int baseLine

numberFont

java.awt.Font numberFont

numberHeight

int numberHeight

numberBaseLine

int numberBaseLine

leftEdgeVirtualPixel

int leftEdgeVirtualPixel

sequenceMolecule

org.simtk.molecularstructure.Biopolymer sequenceMolecule

residuePositions

java.util.Map<K,V> residuePositions

positionResidues

java.util.Map<K,V> positionResidues

residueSymbols

java.util.Vector<E> residueSymbols

Class org.simtk.moleculargraphics.SequenceCartoonCanvas extends BufferedCanvas implements Serializable

serialVersionUID: 1L

Serialized Fields

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

sequenceCanvas

TornadoSequenceCanvas sequenceCanvas

highlightedResidues

java.util.Map<K,V> highlightedResidues

residuePositions

java.util.Map<K,V> residuePositions

positionResidues

java.util.Hashtable<K,V> positionResidues

residueCount

int residueCount

cartoonBackgroundColor

java.awt.Color cartoonBackgroundColor

cartoonVisibleColor

java.awt.Color cartoonVisibleColor

cartoonHeight

int cartoonHeight

cartoonTop

int cartoonTop

cartoonBottom

int cartoonBottom

cartoonLeft

int cartoonLeft

cartoonRight

int cartoonRight

cartoonMargin

int cartoonMargin

defaultCursor

java.awt.Cursor defaultCursor

leftRightCursor

java.awt.Cursor leftRightCursor

maxSize

java.awt.Dimension maxSize

minSize

java.awt.Dimension minSize

prefSize

java.awt.Dimension prefSize

mousePressedInCartoon

boolean mousePressedInCartoon

mouseMoveHighlights

boolean mouseMoveHighlights

Class org.simtk.moleculargraphics.SequencePane extends javax.swing.JScrollPane implements Serializable

serialVersionUID: 1L

Serialized Fields

currentHighlightedResidue

org.simtk.molecularstructure.Residue currentHighlightedResidue

firstResidue

org.simtk.molecularstructure.Residue firstResidue

finalResidue

org.simtk.molecularstructure.Residue finalResidue

sequenceCanvas

TornadoSequenceCanvas sequenceCanvas

tornado

Tornado tornado

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

residueCenterBroadcaster

ResidueCenterBroadcaster residueCenterBroadcaster

contentPanel

java.awt.Panel contentPanel

maxSize

java.awt.Dimension maxSize

minSize

java.awt.Dimension minSize

Class org.simtk.moleculargraphics.StructureCanvas extends vtk.vtkPanel implements Serializable

Serialized Fields

actorCartoons

java.util.Map<K,V> actorCartoons

useScaleBar

boolean useScaleBar

scaleBar

ScaleBar scaleBar

maxSize

java.awt.Dimension maxSize

minSize

java.awt.Dimension minSize

prefSize

java.awt.Dimension prefSize

mouseDragAction

org.simtk.moleculargraphics.StructureCanvas.MouseDragAction mouseDragAction

backgroundColor

java.awt.Color backgroundColor

nutationRangeAngle

double nutationRangeAngle

currentNutationAxis

org.simtk.geometry3d.Vector3D currentNutationAxis

Class org.simtk.moleculargraphics.TestMenu extends MolApp implements Serializable

Class org.simtk.moleculargraphics.Tornado3DCanvas extends StructureCanvas implements Serializable

serialVersionUID: 1L

Serialized Fields

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

residueCenterBroadcaster

ResidueCenterBroadcaster residueCenterBroadcaster

highlightResidues

java.util.Map<K,V> highlightResidues

currentlyDepressedKeyboardKeys

java.util.HashSet<E> currentlyDepressedKeyboardKeys

showLogo

boolean showLogo

doFog

boolean doFog

fogLinear

boolean fogLinear

gl

javax.media.opengl.GL gl

overlayRenderer

vtk.vtkRenderer overlayRenderer

logoImageData

vtk.vtkImageData logoImageData

logoReader

vtk.vtkPNGReader logoReader

logoActor

vtk.vtkActor2D logoActor

logoWidth

int logoWidth

logoHeight

int logoHeight

crosshairCursor

java.awt.Cursor crosshairCursor

defaultCursor

java.awt.Cursor defaultCursor

classLoader

java.lang.ClassLoader classLoader

firstPaint

boolean firstPaint

fpsStopWatch

org.simtk.util.Stopwatch fpsStopWatch

frameCount

int frameCount

fpsRing

org.simtk.util.DoubleRing fpsRing

pickIsPending

boolean pickIsPending

picker

vtk.vtkCellPicker picker

doPick

boolean doPick

Class org.simtk.moleculargraphics.TornadoSequenceCanvas extends SequenceCanvas implements Serializable

serialVersionUID: 1L

Serialized Fields

parent

SequencePane parent

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

residueCenterBroadcaster

ResidueCenterBroadcaster residueCenterBroadcaster

highlightResidue

org.simtk.molecularstructure.Residue highlightResidue

highlightPosition

int highlightPosition

highlightResidues

java.util.Map<K,V> highlightResidues

defaultCursor

java.awt.Cursor defaultCursor

moveCursor

java.awt.Cursor moveCursor

handCursor

java.awt.Cursor handCursor

textCursor

java.awt.Cursor textCursor

waitCursor

java.awt.Cursor waitCursor

leftRightCursor

java.awt.Cursor leftRightCursor

crosshairCursor

java.awt.Cursor crosshairCursor

insertionResidue

org.simtk.molecularstructure.Residue insertionResidue

insertionResidueRightSide

boolean insertionResidueRightSide

temporarilySelectedResidues

java.util.Set<E> temporarilySelectedResidues

highlightColor

java.awt.Color highlightColor

autoScrollThread

org.simtk.moleculargraphics.TornadoSequenceCanvas.AutoScrollThread autoScrollThread

mousePressedInSequenceArea

boolean mousePressedInSequenceArea

mousePressedInNumberArea

boolean mousePressedInNumberArea

mousePressedViewportX

int mousePressedViewportX

mousePressedBarCenter

int mousePressedBarCenter

mousePressedResidue

org.simtk.molecularstructure.Residue mousePressedResidue

mousePressedResidueRightSide

boolean mousePressedResidueRightSide

previousDragResidue

org.simtk.molecularstructure.Residue previousDragResidue

previousAutoscrollTime

long previousAutoscrollTime

Class org.simtk.moleculargraphics.vtkSwingPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

rw

vtk.vtkRenderWindow rw

ren

vtk.vtkRenderer ren

cam

vtk.vtkCamera cam

lgt

vtk.vtkLight lgt

lastX

int lastX

lastY

int lastY

windowset

int windowset

lightingset

int lightingset

LightFollowCamera

int LightFollowCamera

InteractionMode

int InteractionMode

rendering

boolean rendering

windowSetObservable

org.simtk.moleculargraphics.vtkSwingPanel.WindowObservable windowSetObservable

privatePanel

PublicNativeVtkPanel privatePanel

Package org.simtk.parser

Class org.simtk.parser.ParseException extends java.lang.Exception implements Serializable

Serialized Fields

specialConstructor

boolean specialConstructor

This variable determines which constructor was used to create this object and thereby affects the semantics of the "getMessage" method (see below).

currentToken

Token currentToken

This is the last token that has been consumed successfully. If this object has been created due to a parse error, the token followng this token will (therefore) be the first error token.

expectedTokenSequences

int[][] expectedTokenSequences

Each entry in this array is an array of integers. Each array of integers represents a sequence of tokens (by their ordinal values) that is expected at this point of the parse.

tokenImage

java.lang.String[] tokenImage

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred. This array is defined in the generated ...Constants interface.

eol

java.lang.String eol

The end of line string for this machine.

Class org.simtk.parser.TokenMgrError extends java.lang.Error implements Serializable

Serialized Fields

errorCode

int errorCode

Indicates the reason why the exception is thrown. It will have one of the above 4 values.

Package org.simtk.splashscreen

Class org.simtk.splashscreen.SplashWindow extends java.awt.Window implements Serializable

Serialized Fields

paintCalled

boolean paintCalled

Package org.simtk.toon.secstruct

Class org.simtk.toon.secstruct.SecondaryStructureCanvas extends javax.swing.JPanel implements Serializable

Serialized Fields

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

characterDensity

double characterDensity

fonts

java.util.List<E> fonts

fontHeights

java.util.Map<K,V> fontHeights

fontWidths

java.util.Map<K,V> fontWidths

diagram

SecondaryStructureDiagram diagram

transform

org.simtk.toon.secstruct.SecondaryStructureCanvas.Transform2D transform

worstBasePairs

java.util.Set<E> worstBasePairs

previousHeight

double previousHeight

finiteHeightWasSeen

boolean finiteHeightWasSeen

maxSize

java.awt.Dimension maxSize

minSize

java.awt.Dimension minSize

prefSize

java.awt.Dimension prefSize

oldMouseX

int oldMouseX

oldMouseY

int oldMouseY

Package org.simtk.tornado

Class org.simtk.tornado.Tornado extends MolApp implements Serializable

Serialized Fields

applicationName

java.lang.String applicationName

background

org.simtk.tornado.Tornado.TornadoBackground background

canvas2D

SecondaryStructureCanvas canvas2D

initialLoadStructurePanel

javax.swing.JPanel initialLoadStructurePanel

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

residueCenterBroadcaster

ResidueCenterBroadcaster residueCenterBroadcaster

activeMoleculeBroadcaster

ActiveMoleculeBroadcaster activeMoleculeBroadcaster

initialBackgroundColor

java.awt.Color initialBackgroundColor

highlightColor

java.awt.Color highlightColor

currentPath

java.lang.String currentPath

saveImagePath

java.lang.String saveImagePath

loadStructureDialog

org.simtk.tornado.Tornado.LoadStructureDialog loadStructureDialog

colorScheme

ColorScheme colorScheme

currentCartoon

MoleculeCartoon currentCartoon

toonRange

org.simtk.tornado.Tornado.ToonRange toonRange

selectedSourceTypes

java.util.List<E> selectedSourceTypes

undoRedoMechanism

org.simtk.gui.UndoRedoMechanism undoRedoMechanism

userIsInteracting

boolean userIsInteracting

viewMenu

javax.swing.JMenu viewMenu

sequencePane

SequencePane sequencePane

sequenceCartoonCanvas

SequenceCartoonCanvas sequenceCartoonCanvas

sequencePanel

java.awt.Panel sequencePanel

messageArea

javax.swing.JLabel messageArea

currentHighlightedResidue

org.simtk.molecularstructure.Residue currentHighlightedResidue

useRotationThread

boolean useRotationThread

rotationThread

InertialRotationThread rotationThread

drawSecondaryStructure

boolean drawSecondaryStructure

moleculeCollection

org.simtk.molecularstructure.MoleculeCollection moleculeCollection

handCursor

java.awt.Cursor handCursor

defaultCursor

java.awt.Cursor defaultCursor

waitCursor

java.awt.Cursor waitCursor

titleBase

java.lang.String titleBase

Package org.simtk.tornado.command

Class org.simtk.tornado.command.BackgroundColorAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

color

java.awt.Color color

colorName

java.lang.String colorName

colorable

Colorable colorable

undoRedoMechanism

org.simtk.gui.UndoRedoMechanism undoRedoMechanism