org.jmol.viewer
Class Viewer

java.lang.Object
  org.jmol.api.JmolSimpleViewer
      org.jmol.api.JmolViewer
          org.jmol.viewer.Viewer

public final class Viewer
extends JmolViewer

The JmolViewer can be used to render client molecules. Clients implement the JmolAdapter. JmolViewer uses this interface to extract information from the client data structures and render the molecule to the supplied java.awt.Component The JmolViewer runs on Java 1.1 virtual machines. The 3d graphics rendering package is a software implementation of a z-buffer. It does not use Java3D and does not use Graphics2D from Java 1.2. Therefore, it is well suited to building web browser applets that will run on a wide variety of system configurations.

Field Summary

JPreview	jPreview
static int	MAXIMUM_ZOOM_PERCENTAGE

Method Summary

void	addSelectionListener(JmolSelectionListener listener)
static JmolViewer	allocateViewer(java.awt.Component awtComponent, JmolAdapter modelAdapter)
static JmolViewer	allocateViewer(java.awt.Component awtComponent, JmolAdapter modelAdapter, boolean restricted, javax.swing.JPanel frame, Protein lipid)
void	clearMeasurements() delegated to MeasurementManager
void	clearSelection()
void	deleteMeasurement(int i)
java.lang.String	evalFile(java.lang.String strFilename)
java.lang.String	evalString(java.lang.String strScript)
java.lang.String	evalStringQuiet(java.lang.String strScript)
int	getAnimationFps()
java.awt.Color	getAtomColor(int i)
int	getAtomCount()
int	getAtomModelIndex(int i)
java.lang.String	getAtomName(int i)
int	getAtomNumber(int i)
javax.vecmath.Point3f	getAtomPoint3f(int i)
float	getAtomRadius(int i)
boolean	getAutoBond()
java.awt.Component	getAwtComponent()
boolean	getAxesOrientationRasmol()
java.awt.Color	getBondColor1(int i)
java.awt.Color	getBondColor2(int i)
int	getBondCount()
int	getBondModelIndex(int i)
short	getBondOrder(int i)
javax.vecmath.Point3f	getBondPoint3f1(int i)
javax.vecmath.Point3f	getBondPoint3f2(int i)
float	getBondRadius(int i)
float	getBondTolerance()
boolean	getBooleanProperty(java.lang.String key) mth 2003 05 31 - needs more work this should be implemented using properties or as a hashtable using boxed/wrapped values so that the values could be shared
static java.awt.Image	getBuffImage(java.awt.Image bi, int width, int height) This method creates a new BufferedImage by the given image.
int	getChainCount()
java.awt.Color	getColorBackground()
java.awt.Color	getColorBond()
java.awt.Color	getColorLabel()
java.awt.Color	getColorMeasurement()
java.awt.Color	getColorVector()
int	getDisplayModelIndex()
java.util.BitSet	getElementsPresentBitSet()
FrameRenderer	getFrameRenderer()
int	getGroupCount()
java.util.BitSet	getGroupsPresentBitSet()
java.lang.String	getJavaVendor()
java.lang.String	getJavaVersion()
JPreview	getJPreview() Returns the jPreview.
int	getLipidNumber() new: Returns the lipidNumber.
short	getMadBond()
int	getMeasurementCount()
int[]	getMeasurementCountPlusIndices(int i)
java.lang.String	getMeasurementStringValue(int i)
float	getMinBondDistance()
int	getModelCount()
java.lang.String	getModelName(int modelIndex)
int	getModelNumber(int modelIndex)
java.util.Properties	getModelProperties(int modelIndex)
java.lang.String	getModelProperty(int modelIndex, java.lang.String propertyName)
java.lang.String	getModelSetFileName()
java.lang.String	getModelSetName()
java.lang.String	getModelSetPathName()
java.util.Properties	getModelSetProperties()
int	getMotionEventNumber()
java.lang.String	getOpenFileError()
java.lang.String	getOperatingSystemName()
int	getPercentVdwAtom()
boolean	getPerspectiveDepth()
int	getPolymerCount()
int	getPolymerCountInModel(int modelIndex)
javax.vecmath.Point3f[]	getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
void	getRotation(javax.vecmath.Matrix3f matrixRotation)
float	getRotationRadius()
float	getScalePixelsPerAngstrom()
int	getScreenHeight()
java.awt.Image	getScreenImage()
int	getScreenWidth()
java.util.BitSet	getSelectionSet()
boolean	getShapeShow(int shapeID)
boolean	getShowAxes()
boolean	getShowBbcage()
boolean	getShowHydrogens()
boolean	getShowMeasurements()
javax.vecmath.Matrix4f	getUnscaledTransformMatrix()
boolean	getWireframeRotation()
float	getXTranslationNormalized()
float	getYTranslation()
float	getYTranslationNormalized()
int	getZoomPercent()
void	haltScriptExecution()
boolean	handleOldJvm10Event(java.awt.Event e)
boolean	haveFrame()
void	homePosition()
boolean	isJvm12orGreater()
boolean	isScriptExecuting()
boolean	isShowTransparentLipids() new: Returns the showTransparentLipids.
boolean	modelHasVibrationVectors(int modelIndex)
void	notifyRepainted()
void	openClientFile(java.lang.String fullPathName, java.lang.String fileName, java.lang.Object clientFile)
void	openDOM(java.lang.Object DOMNode)
void	openFile(java.lang.String name)
void	openFiles(java.lang.String modelName, java.lang.String[] names)
void	openReader(java.lang.String fullPathName, java.lang.String name, java.io.Reader reader) Opens the file, given the reader.
void	openStringInline(java.lang.String strModel)
void	paintLipids(java.awt.Graphics g) This method paints the tranparent lipids and calculates the size of the painted images.
void	paintLipidsBorder(java.awt.Graphics g, int quantity) This method paints the tranparent lipids on the left and right border of the JTabbedPane and calculates the size of the painted images.
void	popHoldRepaint()
void	pushHoldRepaint()
void	rebond()
void	refresh()
void	releaseScreenImage()
void	removeSelectionListener(JmolSelectionListener listener)
void	renderScreenImage(java.awt.Graphics g, java.awt.Dimension size, java.awt.Rectangle clip)
void	rotateFront()
void	rotateToX(float angleRadians)
void	rotateToX(int angleDegrees)
void	rotateToY(float angleRadians)
void	rotateToY(int angleDegrees)
void	rotateToZ(float angleRadians)
void	scaleFitToScreen()
void	selectAll()
void	setAnimationFps(int fps)
void	setAppletContext(java.net.URL documentBase, java.net.URL codeBase, java.lang.String appletProxy)
void	setAutoBond(boolean ab)
void	setAxesOrientationRasmol(boolean axesOrientationRasmol)
void	setBondTolerance(float bondTolerance)
void	setBooleanProperty(java.lang.String key, boolean value)
void	setCenterSelected()
void	setColorBackground(java.awt.Color bg)
void	setColorBackground(java.lang.String colorName)
void	setColorBond(java.awt.Color color)
void	setColorLabel(java.awt.Color color)
void	setColorMeasurement(java.awt.Color c)
void	setColorSelection(java.awt.Color c)
void	setColorVector(java.awt.Color c)
void	setDebugScript(boolean debugScript)
void	setFrankOn(boolean frankOn)
void	setJmolDefaults()
void	setJmolStatusListener(JmolStatusListener jmolStatusListener)
void	setJPreview(JPreview preview) Sets the jPreview.
void	setLipidNumber(int lipidNumber) new: lipidNumber The lipidNumber to set.
void	setMarBond(short marBond)
void	setMinBondDistance(float minBondDistance)
void	setModeAtomColorProfile(java.lang.String palette)
void	setModeMouse(int modeMouse)
void	setPercentVdwAtom(int percentVdwAtom)
void	setPerspectiveDepth(boolean perspectiveDepth)
void	setRasmolDefaults()
void	setRotation(javax.vecmath.Matrix3f matrixRotation)
void	setScalePixelsPerAngstrom(float pixelsScale)
void	setScreenDimension(java.awt.Dimension dim)
void	setSelectionHaloEnabled(boolean selectionHaloEnabled)
void	setSelectionSet(java.util.BitSet set)
void	setShapeShow(int shapeID, boolean show)
void	setShowAxes(boolean showAxes)
void	setShowBbcage(boolean showBbcage)
void	setShowHydrogens(boolean showHydrogens)
void	setShowMeasurements(boolean showMeasurements)
void	setShowTransparentLipids(boolean showTransparentLipids) new: showTransparentLipids The showTransparentLipids to set.
void	setVectorScale(float scale)
void	setVibrationPeriod(float period)
void	setVibrationScale(float scale)
void	setWireframeRotation(boolean wireframeRotation)
void	setXTranslationNormalized(float xTranslation)
void	setYTranslationNormalized(float yTranslation)
void	showConsole(boolean showConsole)
boolean	showModelSetDownload()
void	showUrl(java.lang.String urlString)
void	translateXBy(int xDelta)
void	translateYBy(int yDelta)
void	zoomBy(int pixels)

Methods inherited from class org.jmol.api.JmolSimpleViewer

allocateSimpleViewer

Methods inherited from class java.lang.Object

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

Field Detail

jPreview

public JPreview jPreview

MAXIMUM_ZOOM_PERCENTAGE

public static int MAXIMUM_ZOOM_PERCENTAGE

Method Detail

allocateViewer

public static JmolViewer allocateViewer(java.awt.Component awtComponent,
                                        JmolAdapter modelAdapter)

allocateViewer

public static JmolViewer allocateViewer(java.awt.Component awtComponent,
                                        JmolAdapter modelAdapter,
                                        boolean restricted,
                                        javax.swing.JPanel frame,
                                        Protein lipid)

getAwtComponent

public java.awt.Component getAwtComponent()

Specified by:

getAwtComponent in class JmolViewer

handleOldJvm10Event

public boolean handleOldJvm10Event(java.awt.Event e)

Specified by:

handleOldJvm10Event in class JmolViewer

homePosition

public void homePosition()

Specified by:

homePosition in class JmolViewer

rotateFront

public void rotateFront()

Specified by:

rotateFront in class JmolViewer

rotateToX

public void rotateToX(float angleRadians)

Specified by:

rotateToX in class JmolViewer

rotateToY

public void rotateToY(float angleRadians)

Specified by:

rotateToY in class JmolViewer

rotateToZ

public void rotateToZ(float angleRadians)

Specified by:

rotateToZ in class JmolViewer

rotateToX

public void rotateToX(int angleDegrees)

Specified by:

rotateToX in class JmolViewer

rotateToY

public void rotateToY(int angleDegrees)

Specified by:

rotateToY in class JmolViewer

translateXBy

public void translateXBy(int xDelta)

Specified by:

translateXBy in class JmolViewer

translateYBy

public void translateYBy(int yDelta)

Specified by:

translateYBy in class JmolViewer

isShowTransparentLipids

public boolean isShowTransparentLipids()

new: Returns the showTransparentLipids.

Specified by:

isShowTransparentLipids in class JmolViewer

setShowTransparentLipids

public void setShowTransparentLipids(boolean showTransparentLipids)

new: showTransparentLipids The showTransparentLipids to set.

Specified by:

setShowTransparentLipids in class JmolViewer

getJPreview

public JPreview getJPreview()

Returns the jPreview.

Specified by:

getJPreview in class JmolViewer

Returns:

JPreview The JPreview panel.

setJPreview

public void setJPreview(JPreview preview)

Sets the jPreview.

Specified by:

setJPreview in class JmolViewer

zoomBy

public void zoomBy(int pixels)

Specified by:

zoomBy in class JmolViewer

getZoomPercent

public int getZoomPercent()

Specified by:

getZoomPercent in class JmolViewer

getUnscaledTransformMatrix

public javax.vecmath.Matrix4f getUnscaledTransformMatrix()

Specified by:

getUnscaledTransformMatrix in class JmolViewer

getScalePixelsPerAngstrom

public float getScalePixelsPerAngstrom()

Specified by:

getScalePixelsPerAngstrom in class JmolViewer

setScalePixelsPerAngstrom

public void setScalePixelsPerAngstrom(float pixelsScale)

Specified by:

setScalePixelsPerAngstrom in class JmolViewer

scaleFitToScreen

public void scaleFitToScreen()

Specified by:

scaleFitToScreen in class JmolViewer

getXTranslationNormalized

public float getXTranslationNormalized()

Specified by:

getXTranslationNormalized in class JmolViewer

getYTranslationNormalized

public float getYTranslationNormalized()

Specified by:

getYTranslationNormalized in class JmolViewer

setYTranslationNormalized

public void setYTranslationNormalized(float yTranslation)

Specified by:

setYTranslationNormalized in class JmolViewer

setXTranslationNormalized

public void setXTranslationNormalized(float xTranslation)

Specified by:

setXTranslationNormalized in class JmolViewer

setPerspectiveDepth

public void setPerspectiveDepth(boolean perspectiveDepth)

Specified by:

setPerspectiveDepth in class JmolViewer

setAxesOrientationRasmol

public void setAxesOrientationRasmol(boolean axesOrientationRasmol)

Specified by:

setAxesOrientationRasmol in class JmolViewer

getAxesOrientationRasmol

public boolean getAxesOrientationRasmol()

Specified by:

getAxesOrientationRasmol in class JmolViewer

getPerspectiveDepth

public boolean getPerspectiveDepth()

Specified by:

getPerspectiveDepth in class JmolViewer

setScreenDimension

public void setScreenDimension(java.awt.Dimension dim)

Specified by:

setScreenDimension in class JmolViewer

getScreenWidth

public int getScreenWidth()

Specified by:

getScreenWidth in class JmolViewer

getScreenHeight

public int getScreenHeight()

Specified by:

getScreenHeight in class JmolViewer

setVibrationPeriod

public void setVibrationPeriod(float period)

Specified by:

setVibrationPeriod in class JmolViewer

setRotation

public void setRotation(javax.vecmath.Matrix3f matrixRotation)

Specified by:

setRotation in class JmolViewer

getRotation

public void getRotation(javax.vecmath.Matrix3f matrixRotation)

Specified by:

getRotation in class JmolViewer

getYTranslation

public float getYTranslation()

Specified by:

getYTranslation in class JmolViewer

setModeAtomColorProfile

public void setModeAtomColorProfile(java.lang.String palette)

Specified by:

setModeAtomColorProfile in class JmolViewer

setColorSelection

public void setColorSelection(java.awt.Color c)

Specified by:

setColorSelection in class JmolViewer

setColorLabel

public void setColorLabel(java.awt.Color color)

Specified by:

setColorLabel in class JmolViewer

getColorLabel

public java.awt.Color getColorLabel()

Specified by:

getColorLabel in class JmolViewer

setColorMeasurement

public void setColorMeasurement(java.awt.Color c)

Specified by:

setColorMeasurement in class JmolViewer

getColorMeasurement

public java.awt.Color getColorMeasurement()

Specified by:

getColorMeasurement in class JmolViewer

setColorVector

public void setColorVector(java.awt.Color c)

Specified by:

setColorVector in class JmolViewer

getColorVector

public java.awt.Color getColorVector()

Specified by:

getColorVector in class JmolViewer

setVectorScale

public void setVectorScale(float scale)

Specified by:

setVectorScale in class JmolViewer

setVibrationScale

public void setVibrationScale(float scale)

Specified by:

setVibrationScale in class JmolViewer

setColorBackground

public void setColorBackground(java.awt.Color bg)

Specified by:

setColorBackground in class JmolViewer

getColorBackground

public java.awt.Color getColorBackground()

Specified by:

getColorBackground in class JmolViewer

setColorBackground

public void setColorBackground(java.lang.String colorName)

Specified by:

setColorBackground in class JmolViewer

setSelectionHaloEnabled

public void setSelectionHaloEnabled(boolean selectionHaloEnabled)

Specified by:

setSelectionHaloEnabled in class JmolViewer

selectAll

public void selectAll()

Specified by:

selectAll in class JmolViewer

clearSelection

public void clearSelection()

Specified by:

clearSelection in class JmolViewer

setSelectionSet

public void setSelectionSet(java.util.BitSet set)

Specified by:

setSelectionSet in class JmolViewer

getSelectionSet

public java.util.BitSet getSelectionSet()

Specified by:

getSelectionSet in class JmolViewer

addSelectionListener

public void addSelectionListener(JmolSelectionListener listener)

Specified by:

addSelectionListener in class JmolViewer

removeSelectionListener

public void removeSelectionListener(JmolSelectionListener listener)

Specified by:

removeSelectionListener in class JmolViewer

setModeMouse

public void setModeMouse(int modeMouse)

Specified by:

setModeMouse in class JmolViewer

setAppletContext

public void setAppletContext(java.net.URL documentBase,
                             java.net.URL codeBase,
                             java.lang.String appletProxy)

Specified by:

setAppletContext in class JmolViewer

openFile

public void openFile(java.lang.String name)

Specified by:

openFile in class JmolSimpleViewer

openFiles

public void openFiles(java.lang.String modelName,
                      java.lang.String[] names)

openStringInline

public void openStringInline(java.lang.String strModel)

Specified by:

openStringInline in class JmolSimpleViewer

openDOM

public void openDOM(java.lang.Object DOMNode)

Specified by:

openDOM in class JmolSimpleViewer

openReader

public void openReader(java.lang.String fullPathName,
                       java.lang.String name,
                       java.io.Reader reader)

Opens the file, given the reader. name is a text name of the file ... to be displayed in the window no need to pass a BufferedReader ... ... the FileManager will wrap a buffer around it

Specified by:

openReader in class JmolViewer

Parameters:

fullPathName -

name -

reader -

getOpenFileError

public java.lang.String getOpenFileError()

Specified by:

getOpenFileError in class JmolSimpleViewer

openClientFile

public void openClientFile(java.lang.String fullPathName,
                           java.lang.String fileName,
                           java.lang.Object clientFile)

Specified by:

openClientFile in class JmolViewer

getModelSetName

public java.lang.String getModelSetName()

Specified by:

getModelSetName in class JmolViewer

getModelSetFileName

public java.lang.String getModelSetFileName()

Specified by:

getModelSetFileName in class JmolViewer

getModelSetPathName

public java.lang.String getModelSetPathName()

Specified by:

getModelSetPathName in class JmolViewer

haveFrame

public boolean haveFrame()

Specified by:

haveFrame in class JmolViewer

getRotationRadius

public float getRotationRadius()

Specified by:

getRotationRadius in class JmolViewer

getModelCount

public int getModelCount()

Specified by:

getModelCount in class JmolViewer

getModelSetProperties

public java.util.Properties getModelSetProperties()

Specified by:

getModelSetProperties in class JmolViewer

getModelNumber

public int getModelNumber(int modelIndex)

Specified by:

getModelNumber in class JmolViewer

getModelName

public java.lang.String getModelName(int modelIndex)

Specified by:

getModelName in class JmolViewer

getModelProperties

public java.util.Properties getModelProperties(int modelIndex)

Specified by:

getModelProperties in class JmolViewer

getModelProperty

public java.lang.String getModelProperty(int modelIndex,
                                         java.lang.String propertyName)

Specified by:

getModelProperty in class JmolViewer

modelHasVibrationVectors

public boolean modelHasVibrationVectors(int modelIndex)

Specified by:

modelHasVibrationVectors in class JmolViewer

getChainCount

public int getChainCount()

Specified by:

getChainCount in class JmolViewer

getGroupCount

public int getGroupCount()

Specified by:

getGroupCount in class JmolViewer

getPolymerCount

public int getPolymerCount()

Specified by:

getPolymerCount in class JmolViewer

getPolymerCountInModel

public int getPolymerCountInModel(int modelIndex)

Specified by:

getPolymerCountInModel in class JmolViewer

getAtomCount

public int getAtomCount()

Specified by:

getAtomCount in class JmolViewer

getBondCount

public int getBondCount()

Specified by:

getBondCount in class JmolViewer

setCenterSelected

public void setCenterSelected()

Specified by:

setCenterSelected in class JmolViewer

rebond

public void rebond()

Specified by:

rebond in class JmolViewer

setBondTolerance

public void setBondTolerance(float bondTolerance)

Specified by:

setBondTolerance in class JmolViewer

getBondTolerance

public float getBondTolerance()

Specified by:

getBondTolerance in class JmolViewer

setMinBondDistance

public void setMinBondDistance(float minBondDistance)

Specified by:

setMinBondDistance in class JmolViewer

getMinBondDistance

public float getMinBondDistance()

Specified by:

getMinBondDistance in class JmolViewer

setAutoBond

public void setAutoBond(boolean ab)

Specified by:

setAutoBond in class JmolViewer

getAutoBond

public boolean getAutoBond()

Specified by:

getAutoBond in class JmolViewer

getElementsPresentBitSet

public java.util.BitSet getElementsPresentBitSet()

Specified by:

getElementsPresentBitSet in class JmolViewer

getGroupsPresentBitSet

public java.util.BitSet getGroupsPresentBitSet()

Specified by:

getGroupsPresentBitSet in class JmolViewer

clearMeasurements

public void clearMeasurements()

delegated to MeasurementManager

Specified by:

clearMeasurements in class JmolViewer

getMeasurementCount

public int getMeasurementCount()

Specified by:

getMeasurementCount in class JmolViewer

getMeasurementStringValue

public java.lang.String getMeasurementStringValue(int i)

Specified by:

getMeasurementStringValue in class JmolViewer

getMeasurementCountPlusIndices

public int[] getMeasurementCountPlusIndices(int i)

Specified by:

getMeasurementCountPlusIndices in class JmolViewer

deleteMeasurement

public void deleteMeasurement(int i)

Specified by:

deleteMeasurement in class JmolViewer

setAnimationFps

public void setAnimationFps(int fps)

Specified by:

setAnimationFps in class JmolViewer

getAnimationFps

public int getAnimationFps()

Specified by:

getAnimationFps in class JmolViewer

getDisplayModelIndex

public int getDisplayModelIndex()

Specified by:

getDisplayModelIndex in class JmolViewer

getFrameRenderer

public FrameRenderer getFrameRenderer()

Specified by:

getFrameRenderer in class JmolViewer

getMotionEventNumber

public int getMotionEventNumber()

Specified by:

getMotionEventNumber in class JmolViewer

pushHoldRepaint

public void pushHoldRepaint()

Specified by:

pushHoldRepaint in class JmolViewer

popHoldRepaint

public void popHoldRepaint()

Specified by:

popHoldRepaint in class JmolViewer

refresh

public void refresh()

Specified by:

refresh in class JmolViewer

notifyRepainted

public void notifyRepainted()

Specified by:

notifyRepainted in class JmolViewer

renderScreenImage

public void renderScreenImage(java.awt.Graphics g,
                              java.awt.Dimension size,
                              java.awt.Rectangle clip)

Specified by:

renderScreenImage in class JmolSimpleViewer

paintLipidsBorder

public void paintLipidsBorder(java.awt.Graphics g,
                              int quantity)

This method paints the tranparent lipids on the left and right border of the JTabbedPane and calculates the size of the painted images.

Parameters:

g - Graphics to paint on

quantity - This integer defines how much lipids will be drawn at the borders

paintLipids

public void paintLipids(java.awt.Graphics g)

This method paints the tranparent lipids and calculates the size of the painted images.

Parameters:

g - Graphics object to point on

getBuffImage

public static java.awt.Image getBuffImage(java.awt.Image bi,
                                          int width,
                                          int height)

This method creates a new BufferedImage by the given image. The new size of the BufferedImage is the given width and height

Parameters:

bi - Image which is used to create the buffered image

width - the width of the bufferedImage

height - the height of the bufferedImage

Returns:

the new bufferedImage

getScreenImage

public java.awt.Image getScreenImage()

Specified by:

getScreenImage in class JmolViewer

releaseScreenImage

public void releaseScreenImage()

Specified by:

releaseScreenImage in class JmolViewer

evalFile

public java.lang.String evalFile(java.lang.String strFilename)

Specified by:

evalFile in class JmolSimpleViewer

evalString

public java.lang.String evalString(java.lang.String strScript)

Specified by:

evalString in class JmolSimpleViewer

evalStringQuiet

public java.lang.String evalStringQuiet(java.lang.String strScript)

Specified by:

evalStringQuiet in class JmolViewer

isScriptExecuting

public boolean isScriptExecuting()

Specified by:

isScriptExecuting in class JmolViewer

haltScriptExecution

public void haltScriptExecution()

Specified by:

haltScriptExecution in class JmolViewer

setColorBond

public void setColorBond(java.awt.Color color)

Specified by:

setColorBond in class JmolViewer

getColorBond

public java.awt.Color getColorBond()

Specified by:

getColorBond in class JmolViewer

setMarBond

public void setMarBond(short marBond)

Specified by:

setMarBond in class JmolViewer

setShapeShow

public void setShapeShow(int shapeID,
                         boolean show)

Specified by:

setShapeShow in class JmolViewer

getShapeShow

public boolean getShapeShow(int shapeID)

Specified by:

getShapeShow in class JmolViewer

setJmolStatusListener

public void setJmolStatusListener(JmolStatusListener jmolStatusListener)

Specified by:

setJmolStatusListener in class JmolViewer

setDebugScript

public void setDebugScript(boolean debugScript)

Specified by:

setDebugScript in class JmolViewer

showUrl

public void showUrl(java.lang.String urlString)

Specified by:

showUrl in class JmolViewer

showConsole

public void showConsole(boolean showConsole)

getBooleanProperty

public boolean getBooleanProperty(java.lang.String key)

mth 2003 05 31 - needs more work this should be implemented using properties or as a hashtable using boxed/wrapped values so that the values could be shared

Specified by:

getBooleanProperty in class JmolViewer

Parameters:

key -

Returns:

the boolean property mth 2005 06 24 and/or these property names should be interned strings so that we can just do == comparisions between strings

setBooleanProperty

public void setBooleanProperty(java.lang.String key,
                               boolean value)

Specified by:

setBooleanProperty in class JmolViewer

setPercentVdwAtom

public void setPercentVdwAtom(int percentVdwAtom)

Specified by:

setPercentVdwAtom in class JmolViewer

setFrankOn

public void setFrankOn(boolean frankOn)

Specified by:

setFrankOn in class JmolViewer

getPercentVdwAtom

public int getPercentVdwAtom()

Specified by:

getPercentVdwAtom in class JmolViewer

getMadBond

public short getMadBond()

Specified by:

getMadBond in class JmolViewer

setShowHydrogens

public void setShowHydrogens(boolean showHydrogens)

Specified by:

setShowHydrogens in class JmolViewer

getShowHydrogens

public boolean getShowHydrogens()

Specified by:

getShowHydrogens in class JmolViewer

setShowBbcage

public void setShowBbcage(boolean showBbcage)

Specified by:

setShowBbcage in class JmolViewer

getShowBbcage

public boolean getShowBbcage()

Specified by:

getShowBbcage in class JmolViewer

setShowAxes

public void setShowAxes(boolean showAxes)

Specified by:

setShowAxes in class JmolViewer

getShowAxes

public boolean getShowAxes()

Specified by:

getShowAxes in class JmolViewer

setShowMeasurements

public void setShowMeasurements(boolean showMeasurements)

Specified by:

setShowMeasurements in class JmolViewer

getShowMeasurements

public boolean getShowMeasurements()

Specified by:

getShowMeasurements in class JmolViewer

setWireframeRotation

public void setWireframeRotation(boolean wireframeRotation)

Specified by:

setWireframeRotation in class JmolViewer

getWireframeRotation

public boolean getWireframeRotation()

Specified by:

getWireframeRotation in class JmolViewer

setJmolDefaults

public void setJmolDefaults()

Specified by:

setJmolDefaults in class JmolViewer

setRasmolDefaults

public void setRasmolDefaults()

Specified by:

setRasmolDefaults in class JmolViewer

getAtomName

public java.lang.String getAtomName(int i)

Specified by:

getAtomName in class JmolViewer

getAtomNumber

public int getAtomNumber(int i)

Specified by:

getAtomNumber in class JmolViewer

getAtomPoint3f

public javax.vecmath.Point3f getAtomPoint3f(int i)

Specified by:

getAtomPoint3f in class JmolViewer

getAtomRadius

public float getAtomRadius(int i)

Specified by:

getAtomRadius in class JmolViewer

getAtomColor

public java.awt.Color getAtomColor(int i)

Specified by:

getAtomColor in class JmolViewer

getAtomModelIndex

public int getAtomModelIndex(int i)

Specified by:

getAtomModelIndex in class JmolViewer

getBondPoint3f1

public javax.vecmath.Point3f getBondPoint3f1(int i)

Specified by:

getBondPoint3f1 in class JmolViewer

getBondPoint3f2

public javax.vecmath.Point3f getBondPoint3f2(int i)

Specified by:

getBondPoint3f2 in class JmolViewer

getBondRadius

public float getBondRadius(int i)

Specified by:

getBondRadius in class JmolViewer

getBondOrder

public short getBondOrder(int i)

Specified by:

getBondOrder in class JmolViewer

getBondColor1

public java.awt.Color getBondColor1(int i)

Specified by:

getBondColor1 in class JmolViewer

getBondModelIndex

public int getBondModelIndex(int i)

Specified by:

getBondModelIndex in class JmolViewer

getBondColor2

public java.awt.Color getBondColor2(int i)

Specified by:

getBondColor2 in class JmolViewer

getPolymerLeadMidPoints

public javax.vecmath.Point3f[] getPolymerLeadMidPoints(int modelIndex,
                                                       int polymerIndex)

Specified by:

getPolymerLeadMidPoints in class JmolViewer

isJvm12orGreater

public boolean isJvm12orGreater()

Specified by:

isJvm12orGreater in class JmolViewer

getOperatingSystemName

public java.lang.String getOperatingSystemName()

Specified by:

getOperatingSystemName in class JmolViewer

getJavaVendor

public java.lang.String getJavaVendor()

Specified by:

getJavaVendor in class JmolViewer

getJavaVersion

public java.lang.String getJavaVersion()

Specified by:

getJavaVersion in class JmolViewer

showModelSetDownload

public boolean showModelSetDownload()

Specified by:

showModelSetDownload in class JmolViewer

getLipidNumber

public int getLipidNumber()

new: Returns the lipidNumber.

Specified by:

getLipidNumber in class JmolViewer

setLipidNumber

public void setLipidNumber(int lipidNumber)

new: lipidNumber The lipidNumber to set.

Specified by:

setLipidNumber in class JmolViewer