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Classes | Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Static Protected Attributes | Package Functions | Package Attributes | Static Package Attributes | Private Member Functions | Static Private Member Functions | Private Attributes

org::jmol::viewer::TransformManager Class Reference

Inheritance diagram for org::jmol::viewer::TransformManager:
Inheritance graph
Collaboration diagram for org::jmol::viewer::TransformManager:
Collaboration graph

List of all members.


class  MotionThread
class  SpinThread
class  VibrationThread

Public Member Functions

void centerAt (int x, int y, Point3f pt)
void stopMotion ()

Public Attributes

int vibrationPeriodMs

Protected Member Functions

abstract void calcCameraFactors ()
void calcNavigationPoint ()
void calcSlabAndDepthValues ()
synchronized void calcTransformMatrix ()
String getNavigationState ()
abstract float getPerspectiveFactor (float z)
void resetNavigationPoint (boolean doResetSlab)
void rotateAxisAngle (Vector3f rotAxis, float radians)
void setNavFps (int value)
void setNavigationOffsetRelative (boolean navigatingSurface)
void setNavOn (boolean navOn)
void setVibrationT (float t)
void zoomBy (int pixels)

Protected Attributes

final AxisAngle4f aaTest1 = new AxisAngle4f()
boolean antialias
float aperatureAngle
float cameraDepth = Float.NaN
float cameraDepthSetting = 3f
float cameraDistance = 1000f
float cameraDistanceFromCenter
float cameraScaleFactor
int defaultMode = MODE_STANDARD
final AxisAngle4f fixedRotationAxis = new AxisAngle4f()
final Point3f fixedRotationCenter = new Point3f()
final Point3f fixedRotationOffset = new Point3f()
final Point3f fixedTranslation = new Point3f()
boolean haveNotifiedNaN = false
final AxisAngle4f internalRotationAxis = new AxisAngle4f()
Vector3f internalTranslation
final Matrix3f matrixRotate = new Matrix3f()
final Matrix3f matrixStereo = new Matrix3f()
final Matrix4f matrixTemp = new Matrix4f()
final Matrix3f matrixTest = new Matrix3f()
final Matrix4f matrixTransform = new Matrix4f()
final Matrix4f matrixTransformInv = new Matrix4f()
int mode = MODE_STANDARD
float modelCenterOffset
float modelRadius
float modelRadiusPixels
float navFps = Float.NaN
boolean navigating = false
final Point3f navigationCenter = new Point3f()
final Point3f navigationOffset = new Point3f()
final Point3f navigationShiftXY = new Point3f()
boolean navOn
float navX
float navY
float navZ
boolean perspectiveDepth = true
int perspectiveModel = DEFAULT_PERSPECTIVE_MODEL
final Point3f perspectiveOffset = new Point3f()
final Point3f perspectiveShiftXY = new Point3f()
final Point3f point3fScreenTemp = new Point3f()
final Point3i point3iScreenTemp = new Point3i()
float prevZoomSetting
final Point3f ptTest1 = new Point3f()
final Point3f ptTest2 = new Point3f()
final Point3f ptTest3 = new Point3f()
float referencePlaneOffset
boolean scale3D = false
boolean spinOn
final Point3f untransformedPoint = new Point3f()
final Vector3f vectorTemp = new Vector3f()
float visualRange

Static Protected Attributes

static final int MODE_NAVIGATION = 1
static final int MODE_PERSPECTIVE_CENTER = 2
static final int MODE_STANDARD = 0

Package Functions

abstract void adjustTemporaryScreenPoint ()
int angstromsToPixels (float distance)
boolean canNavigate ()
boolean checkInternalSlab (Point3f pt)
void clear ()
float defaultScaleToScreen (float radius)
void depthByPercentagePoints (int percentage)
void depthToPercent (int percentDepth)
synchronized void finalizeTransformParameters ()
void getAxisAngle (AxisAngle4f axisAngle)
Point3f[] getCameraFactors ()
int getFrontPlane ()
Matrix3f getMatrixRotate ()
Matrix4f getMatrixtransform ()
String getMoveToText (float timespan, boolean addComments)
Point3f getNavigationCenter ()
float getNavigationDepthPercent ()
TransformManager getNavigationManager (Viewer viewer, int width, int height)
Point3f getNavigationOffset ()
float getNavigationOffsetPercent (char XorY)
String getNavigationText (boolean addComments)
boolean getNavOn ()
void getNewFixedRotationCenter ()
Hashtable getOrientationInfo ()
String getOrientationText (int type)
boolean getPerspectiveDepth ()
void getRotation (Matrix3f matrixRotation)
Point3f getRotationCenter ()
Quaternion getRotationQuaternion ()
float getRotationRadius ()
String getRotationText ()
Point4f getSlabDepthPlane (boolean isDepth)
int getSlabPercentSetting ()
boolean getSpinOn ()
String getSpinState (boolean isAll)
String getState (StringBuffer sfunc)
synchronized Matrix3f getStereoRotationMatrix (boolean stereoFrame)
String getTransformText ()
String getTranslationScript ()
float getTranslationXPercent ()
float getTranslationYPercent ()
float getTranslationZPercent ()
Matrix4f getUnscaledTransformMatrix ()
float getZoomPercentFloat ()
float getZoomSetting ()
void homePosition (boolean resetSpin)
boolean isInPosition (Vector3f axis, float degrees)
boolean isNavigating ()
boolean isVibrationOn ()
boolean isWindowCentered ()
void move (Vector3f dRot, float dZoom, Vector3f dTrans, float dSlab, float floatSecondsTotal, int fps)
void moveRotationCenter (Point3f center, boolean toXY)
void moveTo (float floatSecondsTotal, Point3f center, Tuple3f rotAxis, float degrees, Matrix3f matrixEnd, float zoom, float xTrans, float yTrans, float newRotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth)
void navigate (float seconds, Vector3f rotAxis, float degrees)
void navigate (float timeSeconds, Point3f[][] pathGuide)
void navigate (float seconds, Point3f[] path, float[] theta, int indexStart, int indexEnd)
synchronized void navigate (int keyCode, int modifiers)
void navigate (float seconds, Point3f center)
void navigateSurface (float timeSeconds, String name)
void navTranslate (float seconds, Point3f pt)
void navTranslatePercent (float seconds, float x, float y)
int percentToPixels (char xyz, float percent)
void rotateAboutPointsInternal (Point3f point1, Point3f point2, float degreesPerSecond, float endDegrees, boolean isClockwise, boolean isSpin, BitSet bsAtoms, boolean isGesture, Vector3f translation, List finalPoints)
void rotateArcBall (float x, float y, float factor)
synchronized void rotateAxisAngle (AxisAngle4f axisAngle, BitSet bsAtoms)
void rotateAxisAngleAtCenter (Point3f rotCenter, Vector3f rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, BitSet bsAtoms)
synchronized void rotateAxisAngleRadiansFixed (float angleRadians, BitSet bsAtoms)
synchronized void rotateAxisAngleRadiansInternal (float radians, BitSet bsAtoms)
void rotateFront ()
void rotatePoint (Point3f pt, Point3f ptRot)
void rotateX (float angleRadians)
synchronized void rotateXRadians (float angleRadians, BitSet bsAtoms)
void rotateXYBy (float xDelta, float yDelta, BitSet bsAtoms)
void rotateY (float angleRadians)
synchronized void rotateYRadians (float angleRadians, BitSet bsAtoms)
void rotateZ (float angleRadians)
void rotateZBy (int zDelta, int x, int y)
synchronized void rotateZRadians (float angleRadians)
void scaleFitToScreen (boolean andCenter)
void scaleFitToScreen (boolean andCenter, boolean zoomLarge, boolean resetSlab, boolean resetZoom)
float scaleToPerspective (int z, float sizeAngstroms)
short scaleToScreen (int z, int milliAngstroms)
void setAntialias (boolean TF)
void setCameraDepthPercent (float percent)
void setCenter ()
void setCenterAt (String relativeTo, Point3f pt)
void setFrameOffset (int modelIndex)
void setFrameOffsets (Point3f[] offsets)
void setNavigationDepthPercent (float timeSec, float percent)
void setNavigationMode (boolean TF)
void setNavigationSlabOffsetPercent (float offset)
void setNavXYZ (float x, float y, float z)
void setNewRotationCenter (Point3f center, boolean doScale)
void setPerspectiveDepth (boolean perspectiveDepth)
void setRotateMolecule (boolean TF)
void setRotation (Matrix3f matrixRotation)
void setRotationPointXY (Point3f center)
float setRotationRadius (float angstroms, boolean doAll)
void setScaleAngstromsPerInch (float angstromsPerInch)
void setScreenParameters (int screenWidth, int screenHeight, boolean useZoomLarge, boolean antialias, boolean resetSlab, boolean resetZoom)
void setSlabDepthInternal (boolean isDepth)
void setSlabEnabled (boolean slabEnabled)
void setSpinFps (int value)
void setSpinOn (boolean spinOn)
void setSpinXYZ (float x, float y, float z)
void setStereoDegrees (float stereoDegrees)
void setStereoMode (int[] twoColors)
void setStereoMode (int stereoMode)
void setTranslationFractions ()
void setVibrationPeriod (float period)
void setVibrationScale (float scale)
void setViewer (Viewer viewer, int width, int height)
void setVisualRange (float angstroms)
void setWindowCentered (boolean TF)
void setZoomEnabled (boolean zoomEnabled)
void setZShadeEnabled (boolean zShadeEnabled)
void slabByPercentagePoints (int percentage)
void slabDepthByPercentagePoints (int percentage)
void slabInternal (Point4f plane, boolean isDepth)
void slabReset ()
void slabToPercent (int percentSlab)
void spinXYBy (int xDelta, int yDelta, float speed)
 TransformManager (Viewer viewer, int width, int height)
 TransformManager (Viewer viewer)
synchronized Point3i transformPoint (Point3f pointAngstroms)
Point3i transformPoint (Point3f pointAngstroms, Vector3f vibrationVector)
void transformPoint (Point3f pointAngstroms, Point3f screen)
void transformPoint (Point3f pointAngstroms, Point3i pointScreen)
void transformPointNoClip (Point3f pointAngstroms, Point3f pointScreen)
synchronized Point3f transformPointNoClip (Point3f pointAngstroms)
void transformPoints (int count, Point3f[] angstroms, Point3i[] screens)
void transformVector (Vector3f vectorAngstroms, Vector3f vectorTransformed)
void translateToPercent (char type, float percent)
void translateXYBy (int xDelta, int yDelta)
void translateZBy (int pixels)
float unscaleToScreen (float z, float screenDistance)
void unTransformPoint (Point3f screenPt, Point3f coordPt)
void zoomByFactor (float factor, int x, int y)
void zoomByPercent (float percentZoom)
void zoomToPercent (float percentZoom)
int zValueFromPercent (int zPercent)

Package Attributes

final Vector3f arcBall0 = new Vector3f()
final Matrix3f arcBall0Rotation = new Matrix3f()
final Vector3f arcBall1 = new Vector3f()
final Vector3f arcBallAxis = new Vector3f()
int depthPercentSetting
Point4f depthPlane = null
int depthValue
final Point3f frameOffset = new Point3f()
Point3f[] frameOffsets
int height
boolean internalSlab = false
boolean isSpinFixed = false
boolean isSpinInternal = false
boolean isSpinSelected = false
MotionThread motion
float previousX
float previousY
Vector3f rotationAxis = new Vector3f()
float rotationRate = 0
float scale3DAngstromsPerInch
float scaleDefaultPixelsPerAngstrom
float scalePixelsPerAngstrom
int screenHeight
int screenPixelCount
int screenWidth
boolean slabEnabled = false
int slabPercentSetting
Point4f slabPlane = null
int slabValue
float spinFps = DEFAULT_SPIN_FPS
float spinX
float spinY = DEFAULT_SPIN_Y
float spinZ
int[] stereoColors
float stereoDegrees = Float.NaN
boolean stereoFrame
int stereoMode
float stereoRadians
boolean vibrationOn
Viewer viewer
int width
boolean windowCentered
float xTranslationFraction = 0.5f
float yTranslationFraction = 0.5f
int zDepthValue
boolean zoomEnabled = true
float zoomPercent = 100
float zoomPercentSetting = 100
float zoomRatio
boolean zShadeEnabled = false
int zSlabValue

Static Package Attributes

static final int DEFAULT_NAV_FPS = 10
static final int DEFAULT_PERSPECTIVE_MODEL = 11
static final int DEFAULT_SPIN_FPS = 30
static final int DEFAULT_SPIN_Y = 30
static final double degreesPerRadian = 180 / Math.PI
static final int MAXIMUM_ZOOM_PERCENTAGE = 200000
static final int MAXIMUM_ZOOM_PERSPECTIVE_DEPTH = 10000
static final double twoPI = 2 * Math.PI

Private Member Functions

void addZoomTranslationNavigationText (StringBuffer sb)
void applyRotation (Matrix3f mNew, boolean isInternal, BitSet bsAtoms)
void clearSpin ()
void clearVibration ()
String getCenterText ()
String getRotateXyzText ()
String getRotateZyzText (boolean iAddComment)
void resetXYCenter (int x, int y)
void setFixedRotationCenter (Point3f center)
void setRotationCenterAndRadiusXYZ (Point3f newCenterOfRotation, boolean andRadius)
void setRotationCenterAndRadiusXYZ (String relativeTo, Point3f pt)
void setSpinOn (boolean spinOn, float endDegrees, List endPositions, BitSet bsAtoms, boolean isGesture)
void setVibrationOn (boolean vibrationOn)
Point3i transformScreenPoint (Point3f ptXyp)

Static Private Member Functions

static void truncate0 (StringBuffer sb, float val)
static void truncate2 (StringBuffer sb, float val)

Private Attributes

final AxisAngle4f axisangleT = new AxisAngle4f()
float internalRotationAngle = 0
final Point3f internalRotationCenter = new Point3f(0, 0, 0)
final Matrix3f matrixTemp3 = new Matrix3f()
final Matrix4f matrixTemp4 = new Matrix4f()
final Point3f point3fVibrationTemp = new Point3f()
final Point3f pointT2 = new Point3f()
final Point3f pointTsp = new Point3f()
boolean rotateMolecule
final Point3f rotationCenterDefault = new Point3f()
float rotationRadiusDefault
SpinThread spinThread
boolean useZoomLarge
final Vector3f vectorT = new Vector3f()
final Vector3f vectorT2 = new Vector3f()
float vibrationAmplitude
float vibrationPeriod
float vibrationRadians
float vibrationScale
VibrationThread vibrationThread

Detailed Description

Definition at line 47 of file TransformManager.java.

The documentation for this class was generated from the following file:

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