public abstract class JmolViewer extends Object implements javajs.api.JSInterface
Modifier and Type | Field and Description |
---|---|
javajs.api.GenericPlatform |
apiPlatform |
String |
menuStructure |
Constructor and Description |
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JmolViewer() |
Modifier and Type | Method and Description |
---|---|
abstract void |
addSelectionListener(JmolSelectionListener listener) |
static JmolViewer |
allocateViewer(Object container,
JmolAdapter jmolAdapter)
a simpler option
|
static JmolViewer |
allocateViewer(Object display,
JmolAdapter modelAdapter,
String fullName,
URL documentBase,
URL codeBase,
String commandOptions,
JmolStatusListener statusListener)
legacy only
|
protected static JmolViewer |
allocateViewer(Object display,
JmolAdapter modelAdapter,
String fullName,
URL documentBase,
URL codeBase,
String commandOptions,
JmolStatusListener statusListener,
javajs.api.GenericPlatform implementedPlatform)
This is the older main access point for creating an application or applet viewer.
|
abstract int |
cacheFileByName(String fileName,
boolean isAdd)
used in JSmolApplet.js for drag-drop behavior.
|
abstract void |
cachePut(String key,
Object data) |
abstract void |
calcAtomsMinMax(BS bs,
BoxInfo boxInfo) |
abstract boolean |
checkHalt(String strCommand,
boolean isInterrupt) |
static boolean |
checkOption(JmolViewer viewer,
String option) |
abstract void |
clearMeasurements() |
abstract void |
clearSelection() |
abstract String |
clipImageOrPasteText(String text) |
abstract void |
deleteMeasurement(int i) |
abstract String |
evalFile(String strFilename) |
abstract String |
evalString(String strScript) |
abstract String |
evalStringQuiet(String script) |
abstract Object |
evaluateExpression(Object expression) |
abstract String |
extractMolData(String what) |
abstract int |
findNearestAtomIndex(int x,
int y) |
abstract String |
generateOutputForExport(Map<String,Object> params) |
abstract String |
getAltLocListInModel(int modelIndex) |
abstract int |
getAtomArgb(int atomIndex) |
abstract int |
getAtomCount() |
abstract int |
getAtomCountInModel(int modelIndex) |
abstract String |
getAtomDefs(Map<String,Object> names) |
abstract String |
getAtomInfo(int atomIndex) |
abstract int |
getAtomModelIndex(int atomIndex) |
abstract String |
getAtomName(int atomIndex) |
abstract int |
getAtomNumber(int atomIndex) |
abstract javajs.util.P3 |
getAtomPoint3f(int atomIndex) |
abstract float |
getAtomRadius(int atomIndex) |
abstract int |
getBackgroundArgb() |
abstract int |
getBondArgb1(int bondIndex) |
abstract int |
getBondArgb2(int bondIndex) |
abstract int |
getBondCount() |
abstract int |
getBondCountInModel(int modelIndex) |
abstract int |
getBondModelIndex(int bondIndex) |
abstract int |
getBondOrder(int bondIndex) |
abstract javajs.util.P3 |
getBondPoint3f1(int bondIndex) |
abstract javajs.util.P3 |
getBondPoint3f2(int bondIndex) |
abstract float |
getBondRadius(int bondIndex) |
abstract boolean |
getBoolean(int tok) |
abstract boolean |
getBooleanProperty(String propertyName) |
abstract javajs.util.P3 |
getBoundBoxCenter() |
abstract javajs.util.V3 |
getBoundBoxCornerVector() |
abstract int |
getChainCount() |
abstract int |
getChainCountInModel(int modelIindex) |
abstract String |
getClipboardText() |
abstract String |
getData(String atomExpression,
String type) |
abstract Object |
getDisplay() |
abstract int |
getDisplayModelIndex() |
abstract BS |
getElementsPresentBitSet(int modelIndex) |
abstract String |
getEmbeddedFileState(String filename) |
abstract String |
getErrorMessage() |
abstract String |
getErrorMessageUn() |
abstract Object |
getFileAsBytes(String fullPathName,
javajs.util.OC out) |
abstract String |
getFileAsString(String filename) |
abstract float |
getFloat(int tok) |
abstract int |
getGroupCount() |
abstract int |
getGroupCountInModel(int modelIndex) |
abstract Map<String,String> |
getHeteroList(int modelIndex) |
abstract byte[] |
getImageAsBytes(String type,
int width,
int height,
int quality,
String[] errMsg) |
abstract int |
getInt(int tok) |
abstract String |
getJavaVendor() |
abstract String |
getJavaVersion() |
static String |
getJmolValueAsString(JmolViewer jmolViewer,
String var) |
static String |
getJmolVersion() |
Object |
getJsObjectInfo(Object[] jsObject,
String method,
Object[] args) |
abstract short |
getMadBond() |
abstract int |
getMeasurementCount() |
abstract int[] |
getMeasurementCountPlusIndices(int i) |
abstract String |
getMeasurementStringValue(int i) |
abstract JmolAdapter |
getModelAdapter() |
abstract Map<String,Object> |
getModelAuxiliaryInfo(int modelIndex) |
abstract Object |
getModelAuxiliaryInfoValue(int modelIndex,
String keyName) |
abstract int |
getModelCount() |
abstract String |
getModelFileName(int modelIndex) |
abstract String |
getModelName(int modelIndex) |
abstract int |
getModelNumber(int modelIndex) |
abstract String |
getModelNumberDotted(int modelIndex) |
abstract Properties |
getModelProperties(int modelIndex) |
abstract String |
getModelProperty(int modelIndex,
String propertyName) |
abstract Map<String,Object> |
getModelSetAuxiliaryInfo() |
abstract String |
getModelSetFileName() |
abstract String |
getModelSetName() |
abstract String |
getModelSetPathName() |
abstract Properties |
getModelSetProperties() |
abstract int |
getMotionEventNumber() |
abstract String |
getOperatingSystemName() |
abstract Object |
getParameter(String name) |
abstract boolean |
getPerspectiveDepth() |
abstract int |
getPolymerCount() |
abstract int |
getPolymerCountInModel(int modelIndex) |
abstract javajs.util.P3[] |
getPolymerLeadMidPoints(int modelIndex,
int polymerIndex) |
abstract Object |
getProperty(String returnType,
String infoType,
Object paramInfo) |
abstract int |
getScreenHeight() |
abstract Object |
getScreenImageBuffer(Object g,
boolean isImageWrite) |
abstract int |
getScreenWidth() |
abstract int |
getSelectionCount() |
abstract String |
getSetHistory(int howFarBack) |
abstract boolean |
getShowAxes() |
abstract boolean |
getShowBbcage() |
abstract BS |
getSmartsMatch(String smarts,
BS bsSelected) |
abstract String |
getStateInfo() |
abstract javajs.util.M4 |
getUnscaledTransformMatrix() |
abstract BS |
getVisibleFramesBitSet() |
abstract int |
getZoomPercent() |
abstract float |
getZoomPercentFloat() |
abstract void |
haltScriptExecution() |
abstract boolean |
haveFrame() |
abstract boolean |
havePartialCharges() |
abstract void |
homePosition() |
abstract boolean |
isApplet() |
abstract boolean |
isScriptExecuting() |
abstract String |
loadInline(List<Object> arrayData,
boolean isAppend)
NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
|
abstract String |
loadInline(String strModel) |
abstract String |
loadInline(String[] arrayModels) |
abstract String |
loadInline(String[] arrayModels,
boolean isAppend) |
abstract String |
loadInline(String strModel,
char newLine) |
abstract String |
loadInlineAppend(String strModel,
boolean isAppend) |
abstract int |
modelGetLastVibrationIndex(int i,
int tok) |
abstract boolean |
modelHasVibrationVectors(int modelIndex) |
void |
mouseEvent(int id,
int x,
int y,
int modifiers,
long when) |
abstract void |
notifyStatusReady(boolean isReady) |
abstract void |
notifyViewerRepaintDone() |
abstract String |
openDOM(Object DOMNode) |
abstract String |
openFile(String fileName) |
void |
openFileAsync(String fileName) |
abstract void |
openFileAsyncSpecial(String fileName,
int flags) |
abstract String |
openFiles(String[] fileNames) |
abstract String |
openReader(String fullPathName,
String fileName,
Reader reader)
Opens the file and creates the model set, given the reader.
|
abstract String |
openStringInline(String strModel) |
abstract String |
outputToFile(Map<String,Object> params) |
abstract void |
popHoldRepaint(String why) |
abstract boolean |
processMouseEvent(int id,
int x,
int y,
int modifiers,
long when) |
abstract void |
processMultitouchEvent(int groupID,
int eventType,
int touchID,
int iData,
javajs.util.P3 pt,
long time) |
abstract void |
pushHoldRepaint() |
abstract void |
rebond() |
abstract void |
refresh(int isOrientationChange,
String strWhy) |
abstract void |
releaseScreenImage() |
abstract void |
removeSelectionListener(JmolSelectionListener listener) |
abstract void |
renderScreenImage(Object g,
int width,
int height) |
void |
renderScreenImage(Object g,
Object currentSize,
Object rectClip)
old -- not used in 12.2
|
abstract void |
renderScreenImageStereo(Object gLeft,
Object gRight,
int width,
int height)
an added class for rendering stereo in two independent applets
|
abstract javajs.awt.Dimension |
resizeInnerPanel(int width,
int height) |
abstract void |
rotateFront() |
abstract void |
rotateX(float radians) |
abstract void |
rotateXDeg(int degrees) |
abstract void |
rotateY(float radians) |
abstract void |
rotateYDeg(int degrees) |
abstract void |
rotateZ(float radians) |
abstract String |
runScript(String script)
run a script immediately and return output buffer string
Jmol 13.1.15
|
abstract String |
script(String script) |
abstract Object |
scriptCheck(String script) |
abstract String |
scriptWait(String script) |
abstract Object |
scriptWaitStatus(String script,
String statusList) |
abstract void |
selectAll() |
abstract void |
setAnimationFps(int framesPerSecond) |
abstract void |
setAutoBond(boolean autoBond) |
abstract void |
setAxesOrientationRasmol(boolean axesMessedUp) |
abstract void |
setBondTolerance(float bondTolerance) |
abstract void |
setBooleanProperty(String propertyName,
boolean value) |
abstract void |
setCenterSelected() |
abstract void |
setColorBackground(String colorName) |
void |
setConsole(JmolAppConsoleInterface console)
sets a custom console -- should be called IMMEDIATELY following allocateViewer
create your console with, perhaps:
new org.openscience.jmol.app.jmolPanel.AppConsole(viewer, displayFrame,
externalJPanel, buttonsEnabled);
(see examples/basic/org/jmol/Integration.java
|
abstract void |
setDebugScript(boolean debugScript) |
abstract void |
setFloatProperty(String propertyName,
float value) |
abstract void |
setFrankOn(boolean frankOn) |
abstract void |
setInMotion(boolean isInMotion) |
abstract void |
setIntProperty(String propertyName,
int value) |
abstract void |
setJmolCallbackListener(JmolCallbackListener jmolCallbackListener) |
abstract void |
setJmolDefaults() |
abstract void |
setJmolStatusListener(JmolStatusListener jmolStatusListener) |
abstract void |
setMarBond(short marBond) |
abstract void |
setMinBondDistance(float minBondDistance) |
abstract void |
setModeMouse(int modeMouse) |
abstract void |
setPercentVdwAtom(int percentVdwAtom) |
abstract void |
setPerspectiveDepth(boolean perspectiveDepth) |
abstract void |
setRasmolDefaults() |
abstract void |
setScreenDimension(int width,
int height) |
abstract void |
setSelectionHalos(boolean haloEnabled) |
abstract void |
setSelectionSet(BS newSelection) |
abstract void |
setShowAxes(boolean showAxes) |
abstract void |
setShowBbcage(boolean showBbcage) |
abstract void |
setShowHydrogens(boolean showHydrogens) |
abstract void |
setShowMeasurements(boolean showMeasurements) |
abstract void |
setStringProperty(String propertyName,
String value) |
abstract void |
setVectorScale(float vectorScaleValue) |
abstract void |
setVibrationPeriod(float vibrationPeriod) |
abstract void |
setVibrationScale(float vibrationScaleValue) |
abstract void |
showUrl(String urlString) |
abstract void |
syncScript(String script,
String applet,
int port) |
abstract void |
writeTextFile(String string,
String data) |
public String menuStructure
public javajs.api.GenericPlatform apiPlatform
public abstract float getFloat(int tok)
public abstract int getInt(int tok)
public abstract boolean getBoolean(int tok)
protected static JmolViewer allocateViewer(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener, javajs.api.GenericPlatform implementedPlatform)
display
- modelAdapter
- fullName
- documentBase
- codeBase
- commandOptions
- statusListener
- implementedPlatform
- public static JmolViewer allocateViewer(Object container, JmolAdapter jmolAdapter)
container
- jmolAdapter
- public static JmolViewer allocateViewer(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener)
display
- modelAdapter
- fullName
- documentBase
- codeBase
- commandOptions
- statusListener
- public void setConsole(JmolAppConsoleInterface console)
console
- the console to usepublic abstract void setInMotion(boolean isInMotion)
public abstract void renderScreenImageStereo(Object gLeft, Object gRight, int width, int height)
gLeft
- gRight
- width
- height
- public static String getJmolVersion()
public static boolean checkOption(JmolViewer viewer, String option)
public abstract void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
public abstract void setJmolStatusListener(JmolStatusListener jmolStatusListener)
public abstract boolean checkHalt(String strCommand, boolean isInterrupt)
public abstract void haltScriptExecution()
public abstract String getOperatingSystemName()
public abstract String getJavaVersion()
public abstract String getJavaVendor()
public abstract boolean haveFrame()
public abstract void pushHoldRepaint()
public abstract void popHoldRepaint(String why)
public abstract void setScreenDimension(int width, int height)
setScreenDimension
in interface javajs.api.JSInterface
public abstract int getScreenWidth()
public abstract int getScreenHeight()
public abstract void releaseScreenImage()
public abstract String outputToFile(Map<String,Object> params)
params
- include type, fileName, text, bytes, quality, width, heightpublic abstract byte[] getImageAsBytes(String type, int width, int height, int quality, String[] errMsg)
type
- width
- height
- quality
- errMsg
- TODOpublic abstract int getMotionEventNumber()
public abstract String openReader(String fullPathName, String fileName, Reader reader)
fullPathName
- fileName
- reader
- public abstract void showUrl(String urlString)
public abstract javajs.util.P3 getBoundBoxCenter()
public abstract javajs.util.V3 getBoundBoxCornerVector()
public abstract int getMeasurementCount()
public abstract String getMeasurementStringValue(int i)
public abstract int[] getMeasurementCountPlusIndices(int i)
public abstract Object getDisplay()
public abstract BS getElementsPresentBitSet(int modelIndex)
public abstract int findNearestAtomIndex(int x, int y)
public abstract String loadInline(String[] arrayModels, boolean isAppend)
arrayModels
- and array of models, each of which is a StringisAppend
- public abstract String loadInline(List<Object> arrayData, boolean isAppend)
arrayData
- a Vector of models, where each model is either a String
or a String[] or a VectorisAppend
- TRUE to append models (no ZAP)public abstract boolean isScriptExecuting()
public abstract String getModelSetName()
public abstract String getModelSetFileName()
public abstract String getModelSetPathName()
public abstract Properties getModelSetProperties()
public abstract int getModelNumber(int modelIndex)
public abstract String getModelName(int modelIndex)
public abstract String getModelNumberDotted(int modelIndex)
public abstract Properties getModelProperties(int modelIndex)
public abstract Object getModelAuxiliaryInfoValue(int modelIndex, String keyName)
public abstract boolean modelHasVibrationVectors(int modelIndex)
public abstract int getModelCount()
public abstract int getDisplayModelIndex()
public abstract BS getVisibleFramesBitSet()
public abstract int getAtomCount()
public abstract int getBondCount()
public abstract int getGroupCount()
public abstract int getChainCount()
public abstract int getPolymerCount()
public abstract int getAtomCountInModel(int modelIndex)
public abstract int getBondCountInModel(int modelIndex)
public abstract int getGroupCountInModel(int modelIndex)
public abstract int getChainCountInModel(int modelIindex)
public abstract int getPolymerCountInModel(int modelIndex)
public abstract int getSelectionCount()
public abstract void addSelectionListener(JmolSelectionListener listener)
public abstract void removeSelectionListener(JmolSelectionListener listener)
public abstract void homePosition()
public abstract boolean getPerspectiveDepth()
public abstract boolean getShowAxes()
public abstract boolean getShowBbcage()
public abstract int getAtomNumber(int atomIndex)
public abstract String getAtomName(int atomIndex)
public abstract String getAtomInfo(int atomIndex)
public abstract int getZoomPercent()
public abstract float getZoomPercentFloat()
public abstract javajs.util.M4 getUnscaledTransformMatrix()
public abstract int getBackgroundArgb()
public abstract float getAtomRadius(int atomIndex)
public abstract javajs.util.P3 getAtomPoint3f(int atomIndex)
public abstract int getAtomArgb(int atomIndex)
public abstract int getAtomModelIndex(int atomIndex)
public abstract float getBondRadius(int bondIndex)
public abstract javajs.util.P3 getBondPoint3f1(int bondIndex)
public abstract javajs.util.P3 getBondPoint3f2(int bondIndex)
public abstract int getBondArgb1(int bondIndex)
public abstract int getBondArgb2(int bondIndex)
public abstract int getBondOrder(int bondIndex)
public abstract int getBondModelIndex(int bondIndex)
public abstract javajs.util.P3[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
public abstract short getMadBond()
public abstract void rebond()
public abstract void refresh(int isOrientationChange, String strWhy)
public abstract void notifyViewerRepaintDone()
public abstract boolean getBooleanProperty(String propertyName)
public abstract String getSetHistory(int howFarBack)
public abstract boolean havePartialCharges()
public abstract boolean isApplet()
public abstract String getAltLocListInModel(int modelIndex)
public abstract String getStateInfo()
public abstract void setColorBackground(String colorName)
public abstract void setShowAxes(boolean showAxes)
public abstract void setShowBbcage(boolean showBbcage)
public abstract void setJmolDefaults()
public abstract void setRasmolDefaults()
public abstract void setBooleanProperty(String propertyName, boolean value)
public abstract void setIntProperty(String propertyName, int value)
public abstract void setFloatProperty(String propertyName, float value)
public abstract void setModeMouse(int modeMouse)
public abstract void setShowHydrogens(boolean showHydrogens)
public abstract void setShowMeasurements(boolean showMeasurements)
public abstract void setPerspectiveDepth(boolean perspectiveDepth)
public abstract void setAutoBond(boolean autoBond)
public abstract void setMarBond(short marBond)
public abstract void setBondTolerance(float bondTolerance)
public abstract void setMinBondDistance(float minBondDistance)
public abstract void setAxesOrientationRasmol(boolean axesMessedUp)
public abstract void setPercentVdwAtom(int percentVdwAtom)
public abstract void setAnimationFps(int framesPerSecond)
public abstract void setFrankOn(boolean frankOn)
public abstract void setDebugScript(boolean debugScript)
public abstract void deleteMeasurement(int i)
public abstract void clearMeasurements()
public abstract void setVectorScale(float vectorScaleValue)
public abstract void setVibrationScale(float vibrationScaleValue)
public abstract void setVibrationPeriod(float vibrationPeriod)
public abstract void selectAll()
public abstract void clearSelection()
public abstract void setSelectionSet(BS newSelection)
public abstract void setSelectionHalos(boolean haloEnabled)
public abstract void setCenterSelected()
public abstract void rotateFront()
public abstract void rotateXDeg(int degrees)
public abstract void rotateYDeg(int degrees)
public abstract void rotateX(float radians)
public abstract void rotateY(float radians)
public abstract void rotateZ(float radians)
public abstract JmolAdapter getModelAdapter()
public abstract void openFileAsyncSpecial(String fileName, int flags)
openFileAsyncSpecial
in interface javajs.api.JSInterface
public void openFileAsync(String fileName)
public abstract String getErrorMessage()
public abstract String getErrorMessageUn()
public abstract String getModelFileName(int modelIndex)
public abstract void processMultitouchEvent(int groupID, int eventType, int touchID, int iData, javajs.util.P3 pt, long time)
public abstract boolean processMouseEvent(int id, int x, int y, int modifiers, long when)
processMouseEvent
in interface javajs.api.JSInterface
public void mouseEvent(int id, int x, int y, int modifiers, long when)
public void renderScreenImage(Object g, Object currentSize, Object rectClip)
g
- currentSize
- rectClip
- // unusedpublic static String getJmolValueAsString(JmolViewer jmolViewer, String var)
public abstract void cachePut(String key, Object data)
cachePut
in interface javajs.api.JSInterface
public abstract void renderScreenImage(Object g, int width, int height)
public abstract Object getProperty(String returnType, String infoType, Object paramInfo)
returnType
- "JSON", "string", "readable", and anything else returns the Java object.infoType
- paramInfo
- public abstract javajs.awt.Dimension resizeInnerPanel(int width, int height)
public abstract String runScript(String script)
script
- public abstract int modelGetLastVibrationIndex(int i, int tok)
public abstract int cacheFileByName(String fileName, boolean isAdd)
cacheFileByName
in interface javajs.api.JSInterface
fileName
- isAdd
- public abstract String getClipboardText()
public abstract void notifyStatusReady(boolean isReady)