Package org.jmol.viewer
Class TransformManager
java.lang.Object
org.jmol.viewer.TransformManager
- Direct Known Subclasses:
TransformManager4D
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected final javajs.util.A4
protected boolean
protected float
private final javajs.util.A4
javajs.util.BS
(package private) javajs.util.BS
final javajs.util.P3
protected float
protected float
float
protected float
protected float
final javajs.util.P3
(package private) static final float
(package private) static final int
(package private) static final boolean
(package private) static final int
(package private) static final int
(package private) static final int
static final int
static final float
int
static final double
(package private) int
(package private) javajs.util.P4
int
protected boolean
final javajs.util.A4
final javajs.util.P3
final javajs.util.P3
final javajs.util.P3
(package private) final javajs.util.P3
(package private) javajs.util.P3[]
protected final javajs.util.P3
protected boolean
int
private float
final javajs.util.A4
(package private) final javajs.util.P3
boolean
protected javajs.util.V3
protected final javajs.util.P3i
boolean
boolean
(package private) boolean
final javajs.util.M3
protected final javajs.util.M3
protected final javajs.util.M4
protected final javajs.util.M3
private final javajs.util.M4
protected final javajs.util.M3
final javajs.util.M4
final javajs.util.M4
static final int
private static final int
int
static final int
static final int
static final int
float
float
float
private JmolNavigatorInterface
static final int
static final int
static final int
static final int
static final int
static final int
static final int
float
boolean
final javajs.util.P3
float
final javajs.util.P3
final javajs.util.P3
float
int
boolean
float
float
float
boolean
protected int
protected final javajs.util.P3
protected final javajs.util.P3
private final javajs.util.P3
float
float
protected float
(package private) javajs.util.P3
protected final javajs.util.P3
protected final javajs.util.P3
protected final javajs.util.P3
(package private) final Point3fi
float
(package private) javajs.util.V3
private final javajs.util.P3
private float
(package private) float
protected boolean
(package private) float
float
(package private) float
(package private) int
int
(package private) int
boolean
(package private) int
(package private) javajs.util.P4
(package private) float
int
float
private boolean
boolean
float
float
float
(package private) int[]
(package private) float
(package private) boolean
(package private) boolean
(package private) boolean
(package private) STER
(package private) float
protected final javajs.util.P3
private boolean
private final javajs.util.V3
private final javajs.util.V3
protected final javajs.util.V3
boolean
(package private) float
int
private float
private javajs.util.P3
float
protected Viewer
int
boolean
(package private) float
(package private) float
int
int
float
zoom percent zmPct is the current displayed zoom value, AFTER rendering; may not be the same as zmPctSet, particularly if zoom is not enabled(package private) float
zoom percent setting the current setting of zoom; may not be the same as zmPct, particularly if zoom is not enabledboolean
float
private boolean
private float
boolean
int
javajs.util.P3
int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate void
addZoomTranslationNavigationText
(javajs.util.SB sb) (package private) float
angstromsToPixels
(float distance) private javajs.util.P3i
applyPerspective
(javajs.util.T3 ptXYZ, javajs.util.T3 ptRef) adjusts the temporary point for perspective and offsetsprivate void
applyRotation
(javajs.util.M3 mNew, boolean isInternal, javajs.util.BS bsAtoms, javajs.util.V3 translation, boolean translationOnly, javajs.util.M4 m4) void
sets all camera and scale factors needed by the specific perspective model instantiatedprivate void
calcNavCameraFactors
(float offset100) protected void
All the magic happens here.void
sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane.void
void
centerAt
(int x, int y, javajs.util.P3 pt) (package private) void
clear()
private void
(package private) void
private void
float
defaultScaleToScreen
(float radius) (package private) void
depthByPercentagePoints
(int percentage) void
depthToPercent
(int percentDepth) void
float
javajs.util.P3[]
This method returns data needed by the VRML, X3D, and IDTF/U3D exporters.private String
getMoveToText
(float timespan, boolean addComments) private boolean
getNav()
javajs.util.P3
float
getNavigationOffsetPercent
(char XorY) protected String
protected String
getNavigationText
(boolean addComments) float
(package private) void
(package private) String
getOrientationText
(int type, boolean isBest) boolean
float
getPerspectiveFactor
(float z) calculate the perspective factor based on zprivate String
private String
getRotateZyzText
(boolean iAddComment) void
getRotation
(javajs.util.M3 m) javajs.util.Quat
(package private) String
protected void
getScreenTemp
(javajs.util.T3 ptXYZ) private javajs.util.P4
getSlabDepthPlane
(boolean isDepth) int
(package private) javajs.util.M3
getStereoRotationMatrix
(boolean stereoFrame) (package private) static TransformManager
getTransformManager
(Viewer vwr, int width, int height, boolean is4D) float
float
javajs.util.T3
getVibrationPoint
(Vibration v, javajs.util.T3 pt, float scale) returnfloat
void
homePosition
(boolean resetSpin) boolean
isInPosition
(javajs.util.V3 axis, float degrees) boolean
(package private) boolean
boolean
(package private) void
move
(JmolScriptEvaluator eval, javajs.util.V3 dRot, float dZoom, javajs.util.V3 dTrans, float dSlab, float floatSecondsTotal, int fps) void
moveRotationCenter
(javajs.util.P3 center, boolean toXY) (package private) void
moveTo
(JmolScriptEvaluator eval, float floatSecondsTotal, javajs.util.P3 center, javajs.util.T3 rotAxis, float degrees, javajs.util.M3 matrixEnd, float zoom, float xTrans, float yTrans, float newRotationRadius, javajs.util.P3 navCenter, float xNav, float yNav, float navDepth, float cameraDepth, float cameraX, float cameraY) boolean
moveToPyMOL
(JmolScriptEvaluator eval, float floatSecondsTotal, float[] pymolView) void
navigateAxis
(javajs.util.V3 rotAxis, float degrees) scripted entry point for navigation(package private) void
navigateKey
(int keyCode, int modifiers) entry point for keyboard-based navigationvoid
navigateList
(JmolScriptEvaluator eval, javajs.util.Lst<Object[]> list) private void
void
navTranslatePercentOrTo
(float seconds, float x, float y) seconds < 0 means "to (x,y)"; >= 0 mean "to (x%, y%)"int
percentToPixels
(char xyz, float percent) private void
resetFitToScreen
(boolean andCenter) protected void
resetNavigationPoint
(boolean doResetSlab) something has arisen that requires resetting of the navigation point.void
private void
resetXYCenter
(int x, int y) protected void
rotate3DBall
(float xDeg, float yDeg, javajs.util.BS bsAtoms) (package private) boolean
rotateAboutPointsInternal
(JmolScriptEvaluator eval, javajs.util.T3 point1, javajs.util.T3 point2, float degreesPerSecond, float endDegrees, boolean isClockwise, boolean isSpin, javajs.util.BS bsAtoms, boolean isGesture, javajs.util.V3 translation, javajs.util.Lst<javajs.util.P3> finalPoints, float[] dihedralList, javajs.util.M4 m4) void
rotateAxisAngle
(javajs.util.V3 rotAxis, float radians) private void
rotateAxisAngle2
(javajs.util.A4 axisAngle, javajs.util.BS bsAtoms) (package private) boolean
rotateAxisAngleAtCenter
(JmolScriptEvaluator eval, javajs.util.P3 rotCenter, javajs.util.V3 rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, javajs.util.BS bsAtoms) void
rotateAxisAngleRadiansFixed
(float angleRadians, javajs.util.BS bsAtoms) void
rotateAxisAngleRadiansInternal
(float radians, javajs.util.BS bsAtoms, javajs.util.M4 m4) void
rotatePoint
(javajs.util.T3 pt, javajs.util.T3 ptRot) void
rotateXRadians
(float angleRadians, javajs.util.BS bsAtoms) protected void
rotateXYBy
(float degX, float degY, javajs.util.BS bsAtoms) void
rotateYRadians
(float angleRadians, javajs.util.BS bsAtoms) (package private) void
rotateZBy
(int zDelta, int x, int y) void
rotateZRadians
(float angleRadians) (package private) void
scaleFitToScreen
(boolean andCenter, boolean zoomLarge, boolean resetSlab, boolean resetZoom) float
scaleToPerspective
(int z, float sizeAngstroms) float
scaleToScreen
(int z, int milliAngstroms) void
setAll
(javajs.util.P3 center, javajs.util.M3 m, javajs.util.P3 navCenter, float zoom, float xTrans, float yTrans, float rotationRadius, float pixelScale, float navDepth, float xNav, float yNav, float cameraDepth, float cameraX, float cameraY) (package private) void
setAntialias
(boolean TF) void
setCamera
(float x, float y) void
setCameraDepthPercent
(float percent, boolean resetSlab) either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model(package private) void
void
setCenterAt
(int relativeTo, javajs.util.P3 pt) (package private) void
private void
setFixedRotationCenter
(javajs.util.T3 center) (package private) void
setFrameOffset
(int modelIndex) protected void
setNavFps
(int navFps) void
setNavigatePt
(javajs.util.P3 pt) scripted entry point for navigationvoid
setNavigationDepthPercent
(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
setNavigationMode
(boolean TF) void
(package private) void
setNavigationSlabOffsetPercent
(float percent) void
setNavOn
(boolean navOn) void
setNavXYZ
(float x, float y, float z) (package private) void
setNewRotationCenter
(javajs.util.P3 center, boolean doScale) (package private) void
setPerspectiveDepth
(boolean perspectiveDepth) void
setRotation
(javajs.util.M3 m) private void
setRotationCenterAndRadiusXYZ
(javajs.util.T3 newCenterOfRotation, boolean andRadius) (package private) void
setRotationPointXY
(javajs.util.P3 center) float
setRotationRadius
(float angstroms, boolean doAll) (package private) void
setScaleAngstromsPerInch
(float angstromsPerInch) (package private) void
setScreenParameters
(int screenWidth, int screenHeight, boolean useZoomLarge, boolean antialias, boolean resetSlab, boolean resetZoom) private void
setScreenParameters0
(int screenWidth, int screenHeight, boolean useZoomLarge, boolean antialias, boolean resetSlab, boolean resetZoom) (package private) void
setSelectedTranslation
(javajs.util.BS bsAtoms, char xyz, float xy, float x) void
setSlabDepthInternal
(boolean isDepth) set internal slab or depth from screen-based slab or depth(package private) void
setSlabEnabled
(boolean slabEnabled) void
setSlabRange
(float value) private void
setSpin
(JmolScriptEvaluator eval, boolean spinOn, float endDegrees, javajs.util.Lst<javajs.util.P3> endPositions, float[] dihedralList, javajs.util.BS bsAtoms, boolean isGesture) (package private) void
setSpinFps
(int value) void
void
(package private) void
setSpinXYZ
(float x, float y, float z) (package private) void
setStereoDegrees
(float stereoDegrees) (package private) void
setStereoMode
(STER stereoMode) (package private) void
setStereoMode2
(int[] twoColors) (package private) void
private void
setVibrationOn
(boolean vibrationOn) void
setVibrationPeriod
(float period) sets the period of vibration -- period > 0: sets the period and turns vibration on -- period < 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Float.NaN: uses current setting (frame change)(package private) void
setVibrationScale
(float scale) void
setVibrationT
(float t) (package private) void
setWindowCentered
(boolean TF) (package private) void
setZoomEnabled
(boolean zoomEnabled) void
setZoomHeight
(boolean zoomHeight, boolean zoomLarge) (package private) void
setZShadeEnabled
(boolean zShadeEnabled) (package private) void
slabByPercentagePoints
(int percentage) (package private) void
slabDepthByPercentagePoints
(int percentage) private void
void
slabInternal
(javajs.util.P4 plane, boolean isDepth) void
void
slabToPercent
(int percentSlab) (package private) void
spinXYBy
(int xDelta, int yDelta, float speed) void
javajs.util.P3i
transformPt
(javajs.util.T3 ptXYZ) CAUTION! returns a POINTER TO A TEMPORARY VARIABLEjavajs.util.P3i
transformPt2D
(javajs.util.T3 ptXyp) void
transformPt2Df
(javajs.util.T3 v, javajs.util.P3 pt) void
transformPt3f
(javajs.util.T3 ptXYZ, javajs.util.P3 screen) void
transformPtNoClip
(javajs.util.T3 ptXYZ, javajs.util.T3 pointScreen) void
transformPtScr
(javajs.util.T3 ptXYZ, javajs.util.P3i pointScreen) void
transformPtScrT3
(javajs.util.T3 ptXYZ, javajs.util.T3 pointScreen) void
transformPtScrT32D
(javajs.util.T3 v, javajs.util.P3 pt) javajs.util.P3i
transformPtVib
(javajs.util.P3 ptXYZ, Vibration v) void
translateToPercent
(char type, float percent) (package private) void
translateXYBy
(int xDelta, int yDelta) (package private) void
translateZBy
(int pixels) private static void
truncate0
(javajs.util.SB sb, float val) private static void
truncate2
(javajs.util.SB sb, float val) float
unscaleToScreen
(float z, float screenDistance) void
unTransformPoint
(javajs.util.T3 screenPt, javajs.util.T3 coordPt) boolean
xyzIsSlabbedInternal
(javajs.util.T3 ptRef) (package private) void
zDepthToPercent
(int percentDepth) protected void
zoomBy
(int pixels) standard response to user mouse vertical shift-drag(package private) void
zoomByFactor
(float factor, int x, int y) (package private) void
zoomByPercent
(float percentZoom) void
zoomToPercent
(float percentZoom) (package private) void
zSlabToPercent
(int percentSlab) int
zValueFromPercent
(int zPercent)
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Field Details
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vwr
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DEFAULT_SPIN_Y
static final int DEFAULT_SPIN_Y- See Also:
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DEFAULT_SPIN_FPS
static final int DEFAULT_SPIN_FPS- See Also:
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DEFAULT_NAV_FPS
static final int DEFAULT_NAV_FPS- See Also:
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DEFAULT_VISUAL_RANGE
public static final float DEFAULT_VISUAL_RANGE- See Also:
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DEFAULT_STEREO_DEGREES
public static final int DEFAULT_STEREO_DEGREES- See Also:
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MODE_STANDARD
public static final int MODE_STANDARD- See Also:
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MODE_NAVIGATION
public static final int MODE_NAVIGATION- See Also:
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MODE_PERSPECTIVE_PYMOL
public static final int MODE_PERSPECTIVE_PYMOL- See Also:
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DEFAULT_PERSPECTIVE_MODEL
static final int DEFAULT_PERSPECTIVE_MODEL- See Also:
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DEFAULT_PERSPECTIVE_DEPTH
static final boolean DEFAULT_PERSPECTIVE_DEPTH- See Also:
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DEFAULT_CAMERA_DEPTH
static final float DEFAULT_CAMERA_DEPTH- See Also:
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movetoThread
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vibrationThread
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spinThread
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degreesPerRadian
public static final double degreesPerRadian- See Also:
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perspectiveModel
protected int perspectiveModel -
cameraScaleFactor
protected float cameraScaleFactor -
referencePlaneOffset
public float referencePlaneOffset -
aperatureAngle
protected float aperatureAngle -
cameraDistanceFromCenter
protected float cameraDistanceFromCenter -
modelCenterOffset
public float modelCenterOffset -
modelRadius
public float modelRadius -
modelRadiusPixels
public float modelRadiusPixels -
matrixTemp
protected final javajs.util.M4 matrixTemp -
vectorTemp
protected final javajs.util.V3 vectorTemp -
haveNotifiedNaN
protected boolean haveNotifiedNaN -
spinX
public float spinX -
spinY
public float spinY -
spinZ
public float spinZ -
spinFps
public float spinFps -
isSpinInternal
public boolean isSpinInternal -
isSpinFixed
public boolean isSpinFixed -
isSpinSelected
boolean isSpinSelected -
doTransform4D
protected boolean doTransform4D -
fixedRotationOffset
public final javajs.util.P3 fixedRotationOffset -
fixedRotationCenter
public final javajs.util.P3 fixedRotationCenter -
perspectiveOffset
protected final javajs.util.P3 perspectiveOffset -
perspectiveShiftXY
protected final javajs.util.P3 perspectiveShiftXY -
rotationCenterDefault
private final javajs.util.P3 rotationCenterDefault -
rotationRadiusDefault
private float rotationRadiusDefault -
fixedRotationAxis
public final javajs.util.A4 fixedRotationAxis -
internalRotationAxis
public final javajs.util.A4 internalRotationAxis -
internalTranslation
protected javajs.util.V3 internalTranslation -
internalRotationCenter
final javajs.util.P3 internalRotationCenter -
internalRotationAngle
private float internalRotationAngle -
matrixRotate
public final javajs.util.M3 matrixRotate -
matrixTemp3
protected final javajs.util.M3 matrixTemp3 -
matrixTemp4
private final javajs.util.M4 matrixTemp4 -
axisangleT
private final javajs.util.A4 axisangleT -
vectorT
private final javajs.util.V3 vectorT -
vectorT2
private final javajs.util.V3 vectorT2 -
pointT2
private final javajs.util.P3 pointT2 -
MAXIMUM_ZOOM_PERCENTAGE
public static final int MAXIMUM_ZOOM_PERCENTAGE- See Also:
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MAXIMUM_ZOOM_PERSPECTIVE_DEPTH
private static final int MAXIMUM_ZOOM_PERSPECTIVE_DEPTH- See Also:
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rotationAxis
javajs.util.V3 rotationAxis -
rotationRate
float rotationRate -
fixedTranslation
public final javajs.util.P3 fixedTranslation -
camera
public final javajs.util.P3 camera -
cameraSetting
public final javajs.util.P3 cameraSetting -
xTranslationFraction
float xTranslationFraction -
yTranslationFraction
float yTranslationFraction -
prevZoomSetting
protected float prevZoomSetting -
previousX
public float previousX -
previousY
public float previousY -
zoomEnabled
public boolean zoomEnabled -
zmPct
public float zmPctzoom percent zmPct is the current displayed zoom value, AFTER rendering; may not be the same as zmPctSet, particularly if zoom is not enabled -
zmPctSet
float zmPctSetzoom percent setting the current setting of zoom; may not be the same as zmPct, particularly if zoom is not enabled -
zoomRatio
private float zoomRatio -
slabEnabled
public boolean slabEnabled -
zShadeEnabled
public boolean zShadeEnabled -
internalSlab
public boolean internalSlab -
slabPercentSetting
int slabPercentSetting -
depthPercentSetting
int depthPercentSetting -
slabValue
public int slabValue -
depthValue
public int depthValue -
zSlabPercentSetting
public int zSlabPercentSetting -
zDepthPercentSetting
public int zDepthPercentSetting -
zSlabPoint
public javajs.util.P3 zSlabPoint -
zSlabValue
public int zSlabValue -
zDepthValue
public int zDepthValue -
slabRange
float slabRange -
slabPlane
javajs.util.P4 slabPlane -
depthPlane
javajs.util.P4 depthPlane -
perspectiveDepth
public boolean perspectiveDepth -
scale3D
protected boolean scale3D -
cameraDepth
protected float cameraDepth -
cameraDepthSetting
protected float cameraDepthSetting -
visualRangeAngstroms
public float visualRangeAngstroms -
cameraDistance
public float cameraDistance -
width
public int width -
height
public int height -
screenPixelCount
public int screenPixelCount -
scalePixelsPerAngstrom
float scalePixelsPerAngstrom -
scaleDefaultPixelsPerAngstrom
public float scaleDefaultPixelsPerAngstrom -
scale3DAngstromsPerInch
float scale3DAngstromsPerInch -
antialias
protected boolean antialias -
useZoomLarge
private boolean useZoomLarge -
zoomHeight
private boolean zoomHeight -
screenWidth
int screenWidth -
screenHeight
int screenHeight -
matrixTransform
public final javajs.util.M4 matrixTransform -
matrixTransformInv
public final javajs.util.M4 matrixTransformInv -
fScrPt
protected final javajs.util.P3 fScrPt -
iScrPt
protected final javajs.util.P3i iScrPt -
ptVibTemp
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mode
public int mode -
defaultMode
public int defaultMode -
untransformedPoint
protected final javajs.util.P3 untransformedPoint -
ptTest1
protected final javajs.util.P3 ptTest1 -
ptTest2
protected final javajs.util.P3 ptTest2 -
ptTest3
protected final javajs.util.P3 ptTest3 -
aaTest1
protected final javajs.util.A4 aaTest1 -
matrixTest
protected final javajs.util.M3 matrixTest -
spinOn
public boolean spinOn -
spinIsGesture
private boolean spinIsGesture -
vibrationOn
public boolean vibrationOn -
vibrationPeriod
float vibrationPeriod -
vibrationPeriodMs
public int vibrationPeriodMs -
vibrationScale
private float vibrationScale -
vibrationT
private javajs.util.P3 vibrationT -
stereoMode
STER stereoMode -
stereoColors
int[] stereoColors -
stereoDoubleDTI
boolean stereoDoubleDTI -
stereoDoubleFull
boolean stereoDoubleFull -
stereoDegrees
float stereoDegrees -
stereoRadians
float stereoRadians -
stereoFrame
boolean stereoFrame -
matrixStereo
protected final javajs.util.M3 matrixStereo -
windowCentered
public boolean windowCentered -
frameOffset
final javajs.util.P3 frameOffset -
frameOffsets
javajs.util.P3[] frameOffsets -
bsFrameOffsets
public javajs.util.BS bsFrameOffsets -
bsSelectedAtoms
javajs.util.BS bsSelectedAtoms -
ptOffset
javajs.util.P3 ptOffset -
NAV_MODE_IGNORE
public static final int NAV_MODE_IGNORE- See Also:
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NAV_MODE_ZOOMED
public static final int NAV_MODE_ZOOMED- See Also:
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NAV_MODE_NONE
public static final int NAV_MODE_NONE- See Also:
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NAV_MODE_RESET
public static final int NAV_MODE_RESET- See Also:
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NAV_MODE_NEWXY
public static final int NAV_MODE_NEWXY- See Also:
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NAV_MODE_NEWXYZ
public static final int NAV_MODE_NEWXYZ- See Also:
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NAV_MODE_NEWZ
public static final int NAV_MODE_NEWZ- See Also:
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zoomFactor
public float zoomFactor
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Constructor Details
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TransformManager
public TransformManager()
-
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Method Details
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getTransformManager
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setDefaultPerspective
void setDefaultPerspective() -
homePosition
public void homePosition(boolean resetSpin) -
setRotation
public void setRotation(javajs.util.M3 m) -
resetRotation
public void resetRotation() -
clearThreads
void clearThreads() -
clear
void clear() -
setFixedRotationCenter
private void setFixedRotationCenter(javajs.util.T3 center) -
setRotationPointXY
void setRotationPointXY(javajs.util.P3 center) -
spinXYBy
void spinXYBy(int xDelta, int yDelta, float speed) -
rotateXYBy
protected void rotateXYBy(float degX, float degY, javajs.util.BS bsAtoms) -
rotateZBy
void rotateZBy(int zDelta, int x, int y) -
applyRotation
private void applyRotation(javajs.util.M3 mNew, boolean isInternal, javajs.util.BS bsAtoms, javajs.util.V3 translation, boolean translationOnly, javajs.util.M4 m4) -
rotate3DBall
protected void rotate3DBall(float xDeg, float yDeg, javajs.util.BS bsAtoms) -
rotateXRadians
public void rotateXRadians(float angleRadians, javajs.util.BS bsAtoms) -
rotateYRadians
public void rotateYRadians(float angleRadians, javajs.util.BS bsAtoms) -
rotateZRadians
public void rotateZRadians(float angleRadians) -
rotateAxisAngle
public void rotateAxisAngle(javajs.util.V3 rotAxis, float radians) -
rotateAxisAngle2
private void rotateAxisAngle2(javajs.util.A4 axisAngle, javajs.util.BS bsAtoms) -
rotateAxisAngleAtCenter
boolean rotateAxisAngleAtCenter(JmolScriptEvaluator eval, javajs.util.P3 rotCenter, javajs.util.V3 rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, javajs.util.BS bsAtoms) -
rotateAxisAngleRadiansFixed
public void rotateAxisAngleRadiansFixed(float angleRadians, javajs.util.BS bsAtoms) -
rotateAboutPointsInternal
boolean rotateAboutPointsInternal(JmolScriptEvaluator eval, javajs.util.T3 point1, javajs.util.T3 point2, float degreesPerSecond, float endDegrees, boolean isClockwise, boolean isSpin, javajs.util.BS bsAtoms, boolean isGesture, javajs.util.V3 translation, javajs.util.Lst<javajs.util.P3> finalPoints, float[] dihedralList, javajs.util.M4 m4) - Parameters:
eval
-point1
-point2
-degreesPerSecond
-endDegrees
-isClockwise
-isSpin
-bsAtoms
-isGesture
-translation
-finalPoints
-dihedralList
-m4
-- Returns:
- true if synchronous so that JavaScript can restart properly
-
rotateAxisAngleRadiansInternal
public void rotateAxisAngleRadiansInternal(float radians, javajs.util.BS bsAtoms, javajs.util.M4 m4) -
getNewFixedRotationCenter
void getNewFixedRotationCenter() -
setTranslationFractions
void setTranslationFractions() -
centerAt
public void centerAt(int x, int y, javajs.util.P3 pt) -
percentToPixels
public int percentToPixels(char xyz, float percent) -
angstromsToPixels
float angstromsToPixels(float distance) -
translateXYBy
void translateXYBy(int xDelta, int yDelta) -
setCamera
public void setCamera(float x, float y) -
translateToPercent
public void translateToPercent(char type, float percent) -
getTranslationXPercent
public float getTranslationXPercent() -
getTranslationYPercent
public float getTranslationYPercent() -
getTranslationScript
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getOrientationText
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getRotationQ
public javajs.util.Quat getRotationQ() -
getOrientationInfo
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getRotation
public void getRotation(javajs.util.M3 m) -
setZoomHeight
public void setZoomHeight(boolean zoomHeight, boolean zoomLarge) -
zoomBy
protected void zoomBy(int pixels) standard response to user mouse vertical shift-drag- Parameters:
pixels
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zoomByFactor
void zoomByFactor(float factor, int x, int y) -
zoomToPercent
public void zoomToPercent(float percentZoom) -
translateZBy
void translateZBy(int pixels) -
resetXYCenter
private void resetXYCenter(int x, int y) -
zoomByPercent
void zoomByPercent(float percentZoom) -
setScaleAngstromsPerInch
void setScaleAngstromsPerInch(float angstromsPerInch) -
setSlabRange
public void setSlabRange(float value) -
setSlabEnabled
void setSlabEnabled(boolean slabEnabled) -
setZShadeEnabled
void setZShadeEnabled(boolean zShadeEnabled) -
setZoomEnabled
void setZoomEnabled(boolean zoomEnabled) -
slabReset
public void slabReset() -
getSlabPercentSetting
public int getSlabPercentSetting() -
slabDepthChanged
private void slabDepthChanged() -
slabByPercentagePoints
void slabByPercentagePoints(int percentage) -
depthByPercentagePoints
void depthByPercentagePoints(int percentage) -
slabDepthByPercentagePoints
void slabDepthByPercentagePoints(int percentage) -
slabToPercent
public void slabToPercent(int percentSlab) -
depthToPercent
public void depthToPercent(int percentDepth) -
zSlabToPercent
void zSlabToPercent(int percentSlab) -
zDepthToPercent
void zDepthToPercent(int percentDepth) -
slabInternal
public void slabInternal(javajs.util.P4 plane, boolean isDepth) -
setSlabDepthInternal
public void setSlabDepthInternal(boolean isDepth) set internal slab or depth from screen-based slab or depth- Parameters:
isDepth
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getSlabDepthPlane
private javajs.util.P4 getSlabDepthPlane(boolean isDepth) -
getCameraFactors
public javajs.util.P3[] getCameraFactors()This method returns data needed by the VRML, X3D, and IDTF/U3D exporters. It also should serve as a valuable resource for anyone adapting Jmol and wanting to know how the Jmol 11+ camera business works.- Returns:
- a set of camera data
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setPerspectiveDepth
void setPerspectiveDepth(boolean perspectiveDepth) -
getPerspectiveDepth
public boolean getPerspectiveDepth() -
setCameraDepthPercent
public void setCameraDepthPercent(float percent, boolean resetSlab) either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model- Parameters:
percent
-resetSlab
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getCameraDepth
public float getCameraDepth() -
setScreenParameters0
private void setScreenParameters0(int screenWidth, int screenHeight, boolean useZoomLarge, boolean antialias, boolean resetSlab, boolean resetZoom) -
setAntialias
void setAntialias(boolean TF) -
defaultScaleToScreen
public float defaultScaleToScreen(float radius) -
resetFitToScreen
private void resetFitToScreen(boolean andCenter) -
scaleFitToScreen
void scaleFitToScreen(boolean andCenter, boolean zoomLarge, boolean resetSlab, boolean resetZoom) -
scaleToScreen
public float scaleToScreen(int z, int milliAngstroms) -
unscaleToScreen
public float unscaleToScreen(float z, float screenDistance) -
scaleToPerspective
public float scaleToPerspective(int z, float sizeAngstroms) -
finalizeTransformParameters
public void finalizeTransformParameters() -
getZoomSetting
public float getZoomSetting() -
calcSlabAndDepthValues
public void calcSlabAndDepthValues()sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane. (slab on; slab 0) superceded in navigation mode -
zValueFromPercent
public int zValueFromPercent(int zPercent) -
calcTransformMatrix
public void calcTransformMatrix() -
rotatePoint
public void rotatePoint(javajs.util.T3 pt, javajs.util.T3 ptRot) -
getScreenTemp
protected void getScreenTemp(javajs.util.T3 ptXYZ) -
transformPtScr
public void transformPtScr(javajs.util.T3 ptXYZ, javajs.util.P3i pointScreen) -
transformPtScrT3
public void transformPtScrT3(javajs.util.T3 ptXYZ, javajs.util.T3 pointScreen) -
transformPt3f
public void transformPt3f(javajs.util.T3 ptXYZ, javajs.util.P3 screen) -
transformPtNoClip
public void transformPtNoClip(javajs.util.T3 ptXYZ, javajs.util.T3 pointScreen) -
transformPt
public javajs.util.P3i transformPt(javajs.util.T3 ptXYZ) CAUTION! returns a POINTER TO A TEMPORARY VARIABLE- Parameters:
ptXYZ
-- Returns:
- POINTER TO point3iScreenTemp
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transformPtVib
- Parameters:
ptXYZ
-v
-- Returns:
- POINTER TO TEMPORARY VARIABLE (caution!) point3iScreenTemp
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getVibrationPoint
return- Parameters:
v
-pt
- temporary value; also returnedscale
-- Returns:
- pt
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transformPt2Df
public void transformPt2Df(javajs.util.T3 v, javajs.util.P3 pt) -
transformPtScrT32D
public void transformPtScrT32D(javajs.util.T3 v, javajs.util.P3 pt) -
transformPt2D
public javajs.util.P3i transformPt2D(javajs.util.T3 ptXyp) -
applyPerspective
private javajs.util.P3i applyPerspective(javajs.util.T3 ptXYZ, javajs.util.T3 ptRef) adjusts the temporary point for perspective and offsets- Parameters:
ptXYZ
-ptRef
-- Returns:
- temporary point!!!
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xyzIsSlabbedInternal
public boolean xyzIsSlabbedInternal(javajs.util.T3 ptRef) -
move
void move(JmolScriptEvaluator eval, javajs.util.V3 dRot, float dZoom, javajs.util.V3 dTrans, float dSlab, float floatSecondsTotal, int fps) -
isInPosition
public boolean isInPosition(javajs.util.V3 axis, float degrees) -
moveToPyMOL
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moveTo
void moveTo(JmolScriptEvaluator eval, float floatSecondsTotal, javajs.util.P3 center, javajs.util.T3 rotAxis, float degrees, javajs.util.M3 matrixEnd, float zoom, float xTrans, float yTrans, float newRotationRadius, javajs.util.P3 navCenter, float xNav, float yNav, float navDepth, float cameraDepth, float cameraX, float cameraY) -
setAll
public void setAll(javajs.util.P3 center, javajs.util.M3 m, javajs.util.P3 navCenter, float zoom, float xTrans, float yTrans, float rotationRadius, float pixelScale, float navDepth, float xNav, float yNav, float cameraDepth, float cameraX, float cameraY) -
stopMotion
public void stopMotion() -
getRotationText
String getRotationText() -
getMoveToText
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getCenterText
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getRotateXyzText
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getRotateZyzText
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truncate0
private static void truncate0(javajs.util.SB sb, float val) -
truncate2
private static void truncate2(javajs.util.SB sb, float val) -
setSpinXYZ
void setSpinXYZ(float x, float y, float z) -
setSpinFps
void setSpinFps(int value) -
clearSpin
private void clearSpin() -
setSpinOn
public void setSpinOn() -
setSpinOff
public void setSpinOff() -
setSpin
private void setSpin(JmolScriptEvaluator eval, boolean spinOn, float endDegrees, javajs.util.Lst<javajs.util.P3> endPositions, float[] dihedralList, javajs.util.BS bsAtoms, boolean isGesture) -
setVibrationScale
void setVibrationScale(float scale) -
setVibrationPeriod
public void setVibrationPeriod(float period) sets the period of vibration -- period > 0: sets the period and turns vibration on -- period < 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Float.NaN: uses current setting (frame change)- Parameters:
period
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setVibrationT
public void setVibrationT(float t) -
isVibrationOn
boolean isVibrationOn() -
setVibrationOn
private void setVibrationOn(boolean vibrationOn) -
clearVibration
private void clearVibration() -
setStereoMode2
void setStereoMode2(int[] twoColors) -
setStereoMode
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setStereoDegrees
void setStereoDegrees(float stereoDegrees) -
getStereoRotationMatrix
javajs.util.M3 getStereoRotationMatrix(boolean stereoFrame) -
isWindowCentered
public boolean isWindowCentered() -
setWindowCentered
void setWindowCentered(boolean TF) -
setRotationRadius
public float setRotationRadius(float angstroms, boolean doAll) -
setRotationCenterAndRadiusXYZ
private void setRotationCenterAndRadiusXYZ(javajs.util.T3 newCenterOfRotation, boolean andRadius) -
setNewRotationCenter
void setNewRotationCenter(javajs.util.P3 center, boolean doScale) -
moveRotationCenter
public void moveRotationCenter(javajs.util.P3 center, boolean toXY) -
setCenter
void setCenter() -
setCenterAt
public void setCenterAt(int relativeTo, javajs.util.P3 pt) -
setFrameOffset
void setFrameOffset(int modelIndex) -
setSelectedTranslation
void setSelectedTranslation(javajs.util.BS bsAtoms, char xyz, float xy, float x) -
calcCameraFactors
public void calcCameraFactors()sets all camera and scale factors needed by the specific perspective model instantiated -
getPerspectiveFactor
public float getPerspectiveFactor(float z) calculate the perspective factor based on z- Parameters:
z
-- Returns:
- perspectiveFactor
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unTransformPoint
public void unTransformPoint(javajs.util.T3 screenPt, javajs.util.T3 coordPt) -
setScreenParameters
void setScreenParameters(int screenWidth, int screenHeight, boolean useZoomLarge, boolean antialias, boolean resetSlab, boolean resetZoom)
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