org.jmol.viewer
Class TransformManager11

java.lang.Object
  org.jmol.viewer.TransformManager
      org.jmol.viewer.TransformManager11

 class TransformManager11
extends TransformManager

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.viewer.TransformManager

TransformManager.VibrationThread

Field Summary

(package private) boolean	isNavigationCentered
private int	multiplier
private static int	NAV_MODE_NEWXY
private static int	NAV_MODE_NEWXYZ
private static int	NAV_MODE_NEWZ
private static int	NAV_MODE_NONE
private static int	NAV_MODE_RESET
private static int	NAV_MODE_ZOOMED
private float	navigationSlabOffset
private int	navMode
private int	nHits
private float	previousX
private float	previousY
private float	prevZoomSetting
private float	zoomFactor

Fields inherited from class org.jmol.viewer.TransformManager

aaMoveTo, aaStep, aaStepCenter, aaStepNavCenter, aaTest1, aaTotal, cameraDepth, cameraDepthSetting, cameraDistance, cameraScaleFactor, DEFAULT_STEREO_DEGREES, degreesPerRadian, depthPercentSetting, depthPlane, depthValue, fixedRotationAxis, fixedRotationCenter, fixedRotationOffset, fixedTranslation, haveNotifiedNaN, height, internalRotationAxis, internalSlab, isNavigationMode, isSpinFixed, isSpinInternal, isSpinSelected, matrixEnd, matrixRotate, matrixStart, matrixStep, matrixStereo, matrixTemp, matrixTest, matrixTransform, MAXIMUM_ZOOM_PERCENTAGE, MAXIMUM_ZOOM_PERSPECTIVE_DEPTH, modelCenterOffset, modelRadius, modelRadiusPixels, navigating, navigationCenter, navigationOffset, navigationShiftXY, perspectiveDepth, perspectiveModel, point3fScreenTemp, point3iScreenTemp, pointT, ptMoveToCenter, ptTest1, ptTest2, ptTest3, radiansPerDegree, referencePlaneOffset, rotationAxis, rotationRate, scale3D, scale3DAngstromsPerInch, scaleDefaultPixelsPerAngstrom, scalePixelsPerAngstrom, screenHeight, screenPixelCount, screenWidth, slabEnabled, slabPercentSetting, slabPlane, slabValue, spinFps, spinOn, spinX, spinY, spinZ, stereoColors, stereoDegrees, stereoFrame, stereoMode, stereoRadians, twoPI, vectorTemp, vibrationOn, vibrationPeriodMs, viewer, visualRange, width, windowCentered, xTranslationFraction, yTranslationFraction, zoomEnabled, zoomPercent, zoomPercentSetting, zoomRatio

Constructor Summary

TransformManager11()

TransformManager11(Viewer viewer)

TransformManager11(Viewer viewer, int width, int height)

Method Summary

protected void	adjustTemporaryScreenPoint() adjusts the temporary point for perspective and offsets
private void	alignZX(javax.vecmath.Point3f pt0, javax.vecmath.Point3f pt1, javax.vecmath.Point3f ptVectorWing) brings pt0-pt1 vector to [0 0 -1], then rotates about [0 0 1] until ptVectorWing is in xz plane
protected void	calcCameraFactors() sets all camera and scale factors needed by the specific perspective model instantiated
protected void	calcNavigationPoint() All the magic happens here.
protected void	calcNavigationSlabAndDepth()
(package private) boolean	canNavigate()
(package private) javax.vecmath.Point3f	getNavigationCenter()
(package private) float	getNavigationDepthPercent()
(package private) javax.vecmath.Point3f	getNavigationOffset()
(package private) float	getNavigationOffsetPercent(char XorY)
private float	getNavigationSlabOffsetPercent()
protected java.lang.String	getNavigationState()
protected java.lang.String	getNavigationText(boolean addComments)
protected float	getPerspectiveFactor(float z) calculate the perspective factor based on z
(package private) boolean	isNavigationCentered()
(package private) void	navigate(float seconds, javax.vecmath.Point3f pt) scripted entry point for navigation
(package private) void	navigate(float seconds, javax.vecmath.Point3f[][] pathGuide) follows a path guided by orientation and offset vectors (as Point3fs)
private void	navigate(float seconds, javax.vecmath.Point3f[][] pathGuide, javax.vecmath.Point3f[] path, float[] theta, int indexStart, int indexEnd)
(package private) void	navigate(float seconds, javax.vecmath.Point3f[] path, float[] theta, int indexStart, int indexEnd) scripted navigation
(package private) void	navigate(float seconds, javax.vecmath.Vector3f rotAxis, float degrees) scripted entry point for navigation
(package private) void	navigate(int keyCode, int modifiers) entry point for keyboard-based navigation
private void	navigateTo(float floatSecondsTotal, javax.vecmath.Vector3f axis, float degrees, javax.vecmath.Point3f center, float depthPercent, float xTrans, float yTrans)
(package private) void	navTranslate(float seconds, javax.vecmath.Point3f pt) scripted entry point for navigation
(package private) void	navTranslatePercent(float seconds, float x, float y) scripted entry point for navigation
private void	newNavigationCenter() We do not want the fixed navigation offset to change, but we need a new model-based equivalent position.
protected void	resetNavigationPoint(boolean doResetSlab) something has arisen that requires resetting of the navigation point.
private void	setNavigationDepthPercent(float percent)
(package private) void	setNavigationDepthPercent(float timeSec, float percent) sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be <0 or >100)
(package private) void	setNavigationSlabOffsetPercent(float percent)
(package private) void	setScreenParameters(int screenWidth, int screenHeight, boolean useZoomLarge, boolean antialias, boolean resetSlab, boolean resetZoom)

Methods inherited from class org.jmol.viewer.TransformManager

calcSlabAndDepthValues, calcTransformMatrix, checkInternalSlab, clear, depthByPercentagePoints, depthToPercent, finalizeTransformParameters, getAxisAngle, getMatrixRotate, getMatrixtransform, getMoveToText, getNavigating, getNavigationManager, getNewFixedRotationCenter, getOrientationInfo, getOrientationText, getPerspectiveDepth, getRotation, getRotationCenter, getRotationRadius, getRotationText, getSlabDepthPlane, getSlabPercentSetting, getSpinOn, getSpinState, getState, getStereoRotationMatrix, getTransformText, getTranslationScript, getTranslationXPercent, getTranslationYPercent, getTranslationZPercent, getUnscaledTransformMatrix, getZoomPercentFloat, getZoomSetting, homePosition, isInPosition, isVibrationOn, isWindowCentered, matrixUnTransform, move, moveTo, moveTo, rotateAboutPointsInternal, rotateAxisAngle, rotateAxisAngle, rotateAxisAngleAtCenter, rotateAxisAngleRadiansFixed, rotateAxisAngleRadiansInternal, rotateFront, rotatePoint, rotateX, rotateXRadians, rotateXYBy, rotateY, rotateYRadians, rotateZ, rotateZBy, rotateZRadians, scaleFitToScreen, scaleFitToScreen, scaleToPerspective, scaleToScreen, setAntialias, setCameraDepthPercent, setCenter, setCenterAt, setNavigationMode, setNewRotationCenter, setPerspectiveDepth, setRotateFixed, setRotateInternal, setRotateMolecule, setRotation, setRotationPointXY, setRotationRadius, setScaleAngstromsPerInch, setSlabDepthInternal, setSlabEnabled, setSpinFps, setSpinOn, setSpinX, setSpinY, setSpinZ, setStereoDegrees, setStereoMode, setStereoMode, setTranslationFractions, setVibrationPeriod, setVibrationScale, setVibrationT, setVisualRange, setWindowCentered, setZoomEnabled, slabByPercentagePoints, slabDepthByPercentagePoints, slabInternal, slabReset, slabToPercent, transformPoint, transformPoint, transformPoint, transformPoint, transformPointNoClip, transformPointNoClip, transformPoints, transformVector, translateToXPercent, translateToYPercent, translateToZPercent, translateXYBy, unTransformPoint, zoomBy, zoomByFactor, zoomByPercent, zoomToPercent, zValueFromPercent

Methods inherited from class java.lang.Object

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

Field Detail

navigationSlabOffset

private float navigationSlabOffset

zoomFactor

private float zoomFactor

prevZoomSetting

private float prevZoomSetting

previousX

private float previousX

previousY

private float previousY

isNavigationCentered

boolean isNavigationCentered

nHits

private int nHits

multiplier

private int multiplier

NAV_MODE_ZOOMED

private static final int NAV_MODE_ZOOMED

See Also:

Constant Field Values

NAV_MODE_NONE

private static final int NAV_MODE_NONE

See Also:

Constant Field Values

NAV_MODE_RESET

private static final int NAV_MODE_RESET

See Also:

Constant Field Values

NAV_MODE_NEWXY

private static final int NAV_MODE_NEWXY

See Also:

Constant Field Values

NAV_MODE_NEWXYZ

private static final int NAV_MODE_NEWXYZ

See Also:

Constant Field Values

NAV_MODE_NEWZ

private static final int NAV_MODE_NEWZ

See Also:

Constant Field Values

navMode

private int navMode

Constructor Detail

TransformManager11

TransformManager11()

TransformManager11

TransformManager11(Viewer viewer)

TransformManager11

TransformManager11(Viewer viewer,
                   int width,
                   int height)

Method Detail

calcCameraFactors

protected void calcCameraFactors()

Description copied from class: TransformManager

sets all camera and scale factors needed by the specific perspective model instantiated

Specified by:

calcCameraFactors in class TransformManager

getPerspectiveFactor

protected float getPerspectiveFactor(float z)

Description copied from class: TransformManager

calculate the perspective factor based on z

Specified by:

getPerspectiveFactor in class TransformManager

Returns:

perspectiveFactor

adjustTemporaryScreenPoint

protected void adjustTemporaryScreenPoint()

Description copied from class: TransformManager

adjusts the temporary point for perspective and offsets

Specified by:

adjustTemporaryScreenPoint in class TransformManager

setScreenParameters

void setScreenParameters(int screenWidth,
                         int screenHeight,
                         boolean useZoomLarge,
                         boolean antialias,
                         boolean resetSlab,
                         boolean resetZoom)

Overrides:

setScreenParameters in class TransformManager

calcNavigationPoint

protected void calcNavigationPoint()

All the magic happens here.

Overrides:

calcNavigationPoint in class TransformManager

calcNavigationSlabAndDepth

protected void calcNavigationSlabAndDepth()

newNavigationCenter

private void newNavigationCenter()

We do not want the fixed navigation offset to change, but we need a new model-based equivalent position. The fixed rotation center is at a fixed offset as well. This means that the navigationCenter must be recalculated based on its former offset in the new context. We have two points, N(navigation) and R(rotation). We know where they ARE: fixedNavigationOffset and fixedRotationOffset. From these we must derive navigationCenter.

canNavigate

boolean canNavigate()

Overrides:

canNavigate in class TransformManager

resetNavigationPoint

protected void resetNavigationPoint(boolean doResetSlab)

Description copied from class: TransformManager

something has arisen that requires resetting of the navigation point.

Overrides:

resetNavigationPoint in class TransformManager

navigate

void navigate(int keyCode,
              int modifiers)

Description copied from class: TransformManager

entry point for keyboard-based navigation

Overrides:

navigate in class TransformManager

Parameters:

keyCode - 0 indicates key released

modifiers - shift,alt,ctrl

navigate

void navigate(float seconds,
              javax.vecmath.Point3f pt)

Description copied from class: TransformManager

scripted entry point for navigation

Overrides:

navigate in class TransformManager

navigate

void navigate(float seconds,
              javax.vecmath.Vector3f rotAxis,
              float degrees)

Description copied from class: TransformManager

scripted entry point for navigation

Overrides:

navigate in class TransformManager

setNavigationDepthPercent

void setNavigationDepthPercent(float timeSec,
                               float percent)

Description copied from class: TransformManager

sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be <0 or >100)

Overrides:

setNavigationDepthPercent in class TransformManager

navTranslate

void navTranslate(float seconds,
                  javax.vecmath.Point3f pt)

Description copied from class: TransformManager

scripted entry point for navigation

Overrides:

navTranslate in class TransformManager

navTranslatePercent

void navTranslatePercent(float seconds,
                         float x,
                         float y)

Description copied from class: TransformManager

scripted entry point for navigation

Overrides:

navTranslatePercent in class TransformManager

navigateTo

private void navigateTo(float floatSecondsTotal,
                        javax.vecmath.Vector3f axis,
                        float degrees,
                        javax.vecmath.Point3f center,
                        float depthPercent,
                        float xTrans,
                        float yTrans)

navigate

void navigate(float seconds,
              javax.vecmath.Point3f[][] pathGuide)

Description copied from class: TransformManager

follows a path guided by orientation and offset vectors (as Point3fs)

Overrides:

navigate in class TransformManager

navigate

void navigate(float seconds,
              javax.vecmath.Point3f[] path,
              float[] theta,
              int indexStart,
              int indexEnd)

Description copied from class: TransformManager

scripted navigation

Overrides:

navigate in class TransformManager

Parameters:

seconds - number of seconds to allow for total movement, like moveTo

path - sequence of points to turn into a hermetian path

theta - orientation angle along path (0 aligns with window Y axis) [or Z axis if path is vertical]

indexStart - index of first "station"

indexEnd - index of last "station" not implemented yet

navigate

private void navigate(float seconds,
                      javax.vecmath.Point3f[][] pathGuide,
                      javax.vecmath.Point3f[] path,
                      float[] theta,
                      int indexStart,
                      int indexEnd)

alignZX

private void alignZX(javax.vecmath.Point3f pt0,
                     javax.vecmath.Point3f pt1,
                     javax.vecmath.Point3f ptVectorWing)

brings pt0-pt1 vector to [0 0 -1], then rotates about [0 0 1] until ptVectorWing is in xz plane

Parameters:

pt0 -

pt1 -

ptVectorWing -

getNavigationCenter

javax.vecmath.Point3f getNavigationCenter()

Overrides:

getNavigationCenter in class TransformManager

isNavigationCentered

boolean isNavigationCentered()

Overrides:

isNavigationCentered in class TransformManager

setNavigationSlabOffsetPercent

void setNavigationSlabOffsetPercent(float percent)

Overrides:

setNavigationSlabOffsetPercent in class TransformManager

getNavigationSlabOffsetPercent

private float getNavigationSlabOffsetPercent()

getNavigationOffset

javax.vecmath.Point3f getNavigationOffset()

Overrides:

getNavigationOffset in class TransformManager

setNavigationDepthPercent

private void setNavigationDepthPercent(float percent)

getNavigationDepthPercent

float getNavigationDepthPercent()

Overrides:

getNavigationDepthPercent in class TransformManager

getNavigationOffsetPercent

float getNavigationOffsetPercent(char XorY)

Overrides:

getNavigationOffsetPercent in class TransformManager

getNavigationText

protected java.lang.String getNavigationText(boolean addComments)

Overrides:

getNavigationText in class TransformManager

getNavigationState

protected java.lang.String getNavigationState()

Overrides:

getNavigationState in class TransformManager

Returns:

the script that defines the current navigation state