org.jmol.viewer
Class StateManager.GlobalSettings

java.lang.Object
  extended by org.jmol.viewer.StateManager.GlobalSettings
Enclosing class:
StateManager

 class StateManager.GlobalSettings
extends java.lang.Object


Field Summary
(package private)  boolean allowEmbeddedScripts
           
(package private)  boolean allowGestures
           
(package private)  boolean allowKeyStrokes
           
(package private)  boolean allowModelkit
           
(package private)  boolean allowMoveAtoms
           
(package private)  boolean allowMultiTouch
           
(package private)  boolean allowRotateSelected
           
(package private)  int ambientPercent
           
(package private)  int animationFps
           
(package private)  boolean antialiasDisplay
           
(package private)  boolean antialiasImages
           
(package private)  boolean antialiasTranslucent
           
(package private)  boolean appendNew
           
(package private)  java.lang.String appletProxy
           
(package private)  boolean applySymmetryToBonds
           
(package private)  boolean atomPicking
           
(package private)  java.lang.String atomTypes
           
(package private)  boolean autoBond
           
(package private)  boolean autoFps
           
(package private)  EnumAxesMode axesMode
           
(package private)  boolean axesOrientationRasmol
           
(package private)  float axesScale
           
(package private)  java.lang.String backgroundImageFileName
           
(package private)  boolean bondModeOr
           
(package private)  boolean bondPicking
           
(package private)  short bondRadiusMilliAngstroms
           
(package private)  float bondTolerance
           
(package private)  float cameraDepth
           
(package private)  boolean cartoonBaseEdges
           
(package private)  boolean cartoonRockets
           
(package private)  boolean chainCaseSensitive
           
(package private)  java.lang.String dataSeparator
           
(package private)  boolean debugScript
           
(package private)  java.lang.String defaultAngleLabel
           
(package private)  java.lang.String defaultDirectory
           
(package private)  java.lang.String defaultDistanceLabel
           
(package private)  float defaultDrawArrowScale
           
(package private)  java.lang.String defaultLabelPDB
           
(package private)  java.lang.String defaultLabelXYZ
           
(package private)  java.lang.String defaultLoadFilter
           
(package private)  java.lang.String defaultLoadScript
           
(package private)  boolean defaultStructureDSSP
           
(package private)  java.lang.String defaultTorsionLabel
           
(package private)  float defaultTranslucent
           
(package private)  int delayMaximumMs
           
(package private)  int diffusePercent
           
(package private)  float dipoleScale
           
(package private)  boolean disablePopupMenu
           
(package private)  boolean displayCellParameters
           
(package private)  int dotDensity
           
(package private)  int dotScale
           
(package private)  boolean dotsSelectedOnly
           
(package private)  boolean dotSurface
           
(package private)  boolean dragSelected
           
(package private)  boolean drawHover
           
(package private)  boolean drawPicking
           
(package private)  boolean dsspCalcHydrogen
           
(package private)  boolean dynamicMeasurements
           
(package private)  java.lang.String edsUrlCutoff
           
(package private)  java.lang.String edsUrlFormat
           
(package private)  java.lang.String edsUrlOptions
           
(package private)  boolean ellipsoidArcs
           
(package private)  boolean ellipsoidAxes
           
(package private)  float ellipsoidAxisDiameter
           
(package private)  boolean ellipsoidBall
           
(package private)  int ellipsoidDotCount
           
(package private)  boolean ellipsoidDots
           
(package private)  boolean ellipsoidFill
           
(package private)  boolean fontCaching
           
(package private)  boolean fontScaling
           
(package private)  boolean forceAutoBond
           
(package private)  boolean fractionalRelative
           
(package private)  boolean greyscaleRendering
           
private  boolean haveSetStructureList
           
(package private)  float hbondsAngleMinimum
           
(package private)  boolean hbondsBackbone
           
(package private)  float hbondsDistanceMaximum
           
(package private)  boolean hbondsRasmol
           
(package private)  boolean hbondsSolid
           
(package private)  int helixStep
           
(package private)  java.lang.String helpPath
           
(package private)  int hermiteLevel
           
(package private)  boolean hideNameInPopup
           
(package private)  boolean hideNavigationPoint
           
(package private)  boolean highResolutionFlag
           
(package private)  int hoverDelayMs
           
(package private)  java.util.Map<java.lang.String,java.lang.Boolean> htBooleanParameterFlags
           
(package private)  java.util.Map<java.lang.String,java.lang.Object> htNonbooleanParameterValues
           
(package private)  java.util.Map<java.lang.String,java.lang.Boolean> htPropertyFlagsRemoved
           
(package private)  java.util.Map<java.lang.String,ScriptVariable> htUserVariables
           
(package private)  boolean imageState
           
(package private)  char inlineNewlineChar
           
(package private)  boolean isosurfaceKey
           
(package private)  boolean isosurfacePropertySmoothing
           
(package private)  int isosurfacePropertySmoothingPower
           
(package private)  boolean justifyMeasurements
           
(package private)  boolean legacyAutoBonding
           
(package private)  float loadAtomDataTolerance
           
(package private)  java.lang.String loadFormat
           
(package private)  java.lang.String loadLigandFormat
           
(package private)  boolean logCommands
           
(package private)  boolean logGestures
           
(package private)  boolean measureAllModels
           
private  java.lang.String measureDistanceUnits
           
(package private)  boolean measurementLabels
           
(package private)  boolean messageStyleChime
           
(package private)  float minBondDistance
           
(package private)  float minimizationCriterion
           
(package private)  boolean minimizationRefresh
           
(package private)  boolean minimizationSilent
           
(package private)  int minimizationSteps
           
(package private)  int minPixelSelRadius
           
(package private)  boolean modelKitMode
           
(package private)  byte modeMultipleBond
           
(package private)  boolean monitorEnergy
           
(package private)  float multipleBondRadiusFactor
           
(package private)  float multipleBondSpacing
           
(package private)  boolean multiProcessor
           
(package private)  boolean navigateSurface
           
(package private)  boolean navigationMode
           
(package private)  boolean navigationPeriodic
           
(package private)  float navigationSpeed
           
(package private)  java.lang.String nihResolverFormat
           
(package private)  int[] objColors
           
(package private)  int[] objMad
           
(package private)  boolean[] objStateOn
           
(package private)  boolean partialDots
           
(package private)  boolean pdbAddHydrogens
           
(package private)  boolean pdbGetHeader
           
(package private)  boolean pdbSequential
           
(package private)  int percentVdwAtom
           
(package private)  boolean perspectiveDepth
           
(package private)  int phongExponent
           
(package private)  int pickingSpinRate
           
(package private)  java.lang.String pickLabel
           
(package private)  float pointGroupDistanceTolerance
           
(package private)  float pointGroupLinearTolerance
           
(package private)  boolean preserveState
           
(package private)  java.lang.String propertyColorScheme
           
(package private)  javax.vecmath.Point3f ptDefaultLattice
           
(package private)  java.lang.String quaternionFrame
           
(package private)  boolean rangeSelected
           
(package private)  boolean rasmolHeteroSetting
           
(package private)  boolean rasmolHydrogenSetting
           
(package private)  int repaintWaitMs
           
(package private)  int ribbonAspectRatio
           
(package private)  boolean ribbonBorder
           
(package private)  boolean rocketBarrels
           
(package private)  boolean saveProteinStructureState
           
(package private)  int scriptDelay
           
(package private)  boolean selectAllModels
           
(package private)  float sheetSmoothing
           
(package private)  boolean showHiddenSelectionHalos
           
(package private)  boolean showHydrogens
           
(package private)  boolean showKeyStrokes
           
(package private)  boolean showMeasurements
           
(package private)  boolean showMultipleBonds
           
(package private)  boolean showNavigationPointAlways
           
(package private)  boolean slabByAtom
           
(package private)  boolean slabByMolecule
           
(package private)  int smallMoleculeMaxAtoms
           
(package private)  boolean smartAromatic
           
(package private)  java.lang.String smilesUrlFormat
           
(package private)  boolean solventOn
           
(package private)  float solventProbeRadius
           
(package private)  boolean specular
           
(package private)  int specularExponent
           
(package private)  int specularPercent
           
(package private)  int specularPower
           
(package private)  boolean ssbondsBackbone
           
(package private)  boolean statusReporting
           
(package private)  java.lang.String stereoState
           
(package private)  int strandCountForMeshRibbon
           
(package private)  int strandCountForStrands
           
private  java.util.Map<EnumStructure,float[]> structureList
           
(package private)  float strutDefaultRadius
           
(package private)  float strutLengthMaximum
           
(package private)  boolean strutsMultiple
           
(package private)  int strutSpacing
           
(package private)  boolean testFlag1
           
(package private)  boolean testFlag2
           
(package private)  boolean testFlag3
           
(package private)  boolean testFlag4
           
(package private)  boolean traceAlpha
           
(package private)  boolean useArcBall
           
(package private)  boolean useMinimizationThread
           
(package private)  boolean useNumberLocalization
           
(package private)  boolean useScriptQueue
           
(package private)  float vectorScale
           
(package private)  float vibrationPeriod
           
(package private)  float vibrationScale
           
(package private)  float visualRange
           
(package private)  boolean waitForMoveTo
           
(package private)  boolean wireframeRotation
           
(package private)  int zDepth
           
(package private)  boolean zeroBasedXyzRasmol
           
(package private)  boolean zoomLarge
           
(package private)  int zShadePower
           
(package private)  int zSlab
           
 
Constructor Summary
StateManager.GlobalSettings(StateManager.GlobalSettings gsOld)
           
 
Method Summary
private  java.lang.String chop(java.lang.String s)
           
(package private)  void clear()
           
private  boolean doReportProperty(java.lang.String name)
           
(package private)  java.lang.String getAllSettings(java.lang.String prefix)
           
(package private)  javax.vecmath.Point3f getDefaultLattice()
           
(package private)  java.lang.String getLoadState(java.util.Map<java.lang.String,java.lang.Object> htParams)
          these settings are determined when the file is loaded and are kept even though they might later change.
(package private)  java.lang.String getMeasureDistanceUnits()
           
(package private)  ScriptVariable getOrSetNewVariable(java.lang.String name, boolean doSet)
           
(package private)  java.lang.Object getParameter(java.lang.String name)
          strictly a getter -- returns "" if not found
(package private)  java.lang.Object getParameter(java.lang.String name, boolean asVariable)
           
(package private)  java.lang.String getParameterEscaped(java.lang.String name, int nMax)
           
(package private)  java.lang.String getSpecularState()
           
(package private)  java.lang.String getState(java.lang.StringBuffer sfunc)
           
 java.util.Map<EnumStructure,float[]> getStructureList()
           
(package private)  ScriptVariable getUserVariable(java.lang.String name)
           
(package private)  java.lang.String getVariableList()
           
(package private)  java.lang.String getWindowState(java.lang.StringBuffer sfunc, int width, int height)
           
(package private)  boolean isJmolVariable(java.lang.String key)
           
(package private)  void registerAllValues(StateManager.GlobalSettings g)
           
(package private)  void removeJmolParameter(java.lang.String key)
           
(package private)  void removeUserVariable(java.lang.String key)
           
private  void resetParameterStringValue(java.lang.String name, StateManager.GlobalSettings g)
           
(package private)  void setDefaultLattice(javax.vecmath.Point3f ptLattice)
           
(package private)  void setMeasureDistanceUnits(java.lang.String units)
           
(package private)  void setParameterValue(java.lang.String name, boolean value)
           
(package private)  void setParameterValue(java.lang.String name, float value)
           
(package private)  void setParameterValue(java.lang.String name, int value)
           
(package private)  void setParameterValue(java.lang.String name, java.lang.String value)
           
(package private)  void setPicked(int atomIndex)
           
 void setStructureList(float[] list, EnumStructure type)
           
(package private)  ScriptVariable setUserVariable(java.lang.String key, ScriptVariable var)
           
(package private)  void unsetUserVariable(java.lang.String key)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

htNonbooleanParameterValues

java.util.Map<java.lang.String,java.lang.Object> htNonbooleanParameterValues

htBooleanParameterFlags

java.util.Map<java.lang.String,java.lang.Boolean> htBooleanParameterFlags

htPropertyFlagsRemoved

java.util.Map<java.lang.String,java.lang.Boolean> htPropertyFlagsRemoved

htUserVariables

java.util.Map<java.lang.String,ScriptVariable> htUserVariables

ambientPercent

int ambientPercent

diffusePercent

int diffusePercent

specular

boolean specular

specularExponent

int specularExponent

phongExponent

int phongExponent

specularPercent

int specularPercent

specularPower

int specularPower

zDepth

int zDepth

zShadePower

int zShadePower

zSlab

int zSlab

slabByMolecule

boolean slabByMolecule

slabByAtom

boolean slabByAtom

allowEmbeddedScripts

boolean allowEmbeddedScripts

appendNew

boolean appendNew

appletProxy

java.lang.String appletProxy

applySymmetryToBonds

boolean applySymmetryToBonds

atomTypes

java.lang.String atomTypes

autoBond

boolean autoBond

axesOrientationRasmol

boolean axesOrientationRasmol

bondRadiusMilliAngstroms

short bondRadiusMilliAngstroms

bondTolerance

float bondTolerance

defaultDirectory

java.lang.String defaultDirectory

defaultStructureDSSP

boolean defaultStructureDSSP

ptDefaultLattice

final javax.vecmath.Point3f ptDefaultLattice

defaultLoadScript

java.lang.String defaultLoadScript

defaultLoadFilter

java.lang.String defaultLoadFilter

forceAutoBond

boolean forceAutoBond

fractionalRelative

boolean fractionalRelative

inlineNewlineChar

char inlineNewlineChar

loadFormat

java.lang.String loadFormat

loadLigandFormat

java.lang.String loadLigandFormat

smilesUrlFormat

java.lang.String smilesUrlFormat

nihResolverFormat

java.lang.String nihResolverFormat

edsUrlFormat

java.lang.String edsUrlFormat

edsUrlCutoff

java.lang.String edsUrlCutoff

edsUrlOptions

java.lang.String edsUrlOptions

minBondDistance

float minBondDistance

minPixelSelRadius

int minPixelSelRadius

pdbAddHydrogens

boolean pdbAddHydrogens

pdbGetHeader

boolean pdbGetHeader

pdbSequential

boolean pdbSequential

percentVdwAtom

int percentVdwAtom

smallMoleculeMaxAtoms

int smallMoleculeMaxAtoms

smartAromatic

boolean smartAromatic

zeroBasedXyzRasmol

boolean zeroBasedXyzRasmol

legacyAutoBonding

boolean legacyAutoBonding

allowRotateSelected

boolean allowRotateSelected

allowMoveAtoms

boolean allowMoveAtoms

perspectiveDepth

boolean perspectiveDepth

visualRange

float visualRange

solventOn

boolean solventOn

defaultAngleLabel

java.lang.String defaultAngleLabel

defaultDistanceLabel

java.lang.String defaultDistanceLabel

defaultTorsionLabel

java.lang.String defaultTorsionLabel

justifyMeasurements

boolean justifyMeasurements

measureAllModels

boolean measureAllModels

minimizationSteps

int minimizationSteps

minimizationRefresh

boolean minimizationRefresh

minimizationSilent

boolean minimizationSilent

minimizationCriterion

float minimizationCriterion

antialiasDisplay

boolean antialiasDisplay

antialiasImages

boolean antialiasImages

imageState

boolean imageState

antialiasTranslucent

boolean antialiasTranslucent

displayCellParameters

boolean displayCellParameters

dotsSelectedOnly

boolean dotsSelectedOnly

dotSurface

boolean dotSurface

dotDensity

int dotDensity

dotScale

int dotScale

dynamicMeasurements

boolean dynamicMeasurements

greyscaleRendering

boolean greyscaleRendering

isosurfaceKey

boolean isosurfaceKey

isosurfacePropertySmoothing

boolean isosurfacePropertySmoothing

isosurfacePropertySmoothingPower

int isosurfacePropertySmoothingPower

repaintWaitMs

int repaintWaitMs

showHiddenSelectionHalos

boolean showHiddenSelectionHalos

showKeyStrokes

boolean showKeyStrokes

showMeasurements

boolean showMeasurements

zoomLarge

boolean zoomLarge

backgroundImageFileName

java.lang.String backgroundImageFileName

partialDots

boolean partialDots

bondModeOr

boolean bondModeOr

hbondsBackbone

boolean hbondsBackbone

hbondsAngleMinimum

float hbondsAngleMinimum

hbondsDistanceMaximum

float hbondsDistanceMaximum

hbondsRasmol

boolean hbondsRasmol

hbondsSolid

boolean hbondsSolid

modeMultipleBond

byte modeMultipleBond

showHydrogens

boolean showHydrogens

showMultipleBonds

boolean showMultipleBonds

ssbondsBackbone

boolean ssbondsBackbone

multipleBondSpacing

float multipleBondSpacing

multipleBondRadiusFactor

float multipleBondRadiusFactor

cartoonBaseEdges

boolean cartoonBaseEdges

cartoonRockets

boolean cartoonRockets

chainCaseSensitive

boolean chainCaseSensitive

hermiteLevel

int hermiteLevel

highResolutionFlag

boolean highResolutionFlag

rangeSelected

boolean rangeSelected

rasmolHydrogenSetting

boolean rasmolHydrogenSetting

rasmolHeteroSetting

boolean rasmolHeteroSetting

ribbonAspectRatio

int ribbonAspectRatio

ribbonBorder

boolean ribbonBorder

rocketBarrels

boolean rocketBarrels

sheetSmoothing

float sheetSmoothing

traceAlpha

boolean traceAlpha

allowGestures

boolean allowGestures

allowModelkit

boolean allowModelkit

allowMultiTouch

boolean allowMultiTouch

allowKeyStrokes

boolean allowKeyStrokes

animationFps

int animationFps

autoFps

boolean autoFps

axesMode

EnumAxesMode axesMode

axesScale

float axesScale

cameraDepth

float cameraDepth

dataSeparator

java.lang.String dataSeparator

debugScript

boolean debugScript

defaultDrawArrowScale

float defaultDrawArrowScale

defaultLabelXYZ

java.lang.String defaultLabelXYZ

defaultLabelPDB

java.lang.String defaultLabelPDB

defaultTranslucent

float defaultTranslucent

delayMaximumMs

int delayMaximumMs

dipoleScale

float dipoleScale

disablePopupMenu

boolean disablePopupMenu

dragSelected

boolean dragSelected

drawHover

boolean drawHover

drawPicking

boolean drawPicking

dsspCalcHydrogen

boolean dsspCalcHydrogen

bondPicking

boolean bondPicking

atomPicking

boolean atomPicking

helpPath

java.lang.String helpPath

fontScaling

boolean fontScaling

fontCaching

boolean fontCaching

helixStep

int helixStep

hideNameInPopup

boolean hideNameInPopup

hoverDelayMs

int hoverDelayMs

loadAtomDataTolerance

float loadAtomDataTolerance

logCommands

boolean logCommands

logGestures

boolean logGestures

measurementLabels

boolean measurementLabels

messageStyleChime

boolean messageStyleChime

monitorEnergy

boolean monitorEnergy

multiProcessor

boolean multiProcessor

pickingSpinRate

int pickingSpinRate

pickLabel

java.lang.String pickLabel

pointGroupDistanceTolerance

float pointGroupDistanceTolerance

pointGroupLinearTolerance

float pointGroupLinearTolerance

preserveState

boolean preserveState

propertyColorScheme

java.lang.String propertyColorScheme

quaternionFrame

java.lang.String quaternionFrame

saveProteinStructureState

boolean saveProteinStructureState

solventProbeRadius

float solventProbeRadius

scriptDelay

int scriptDelay

selectAllModels

boolean selectAllModels

statusReporting

boolean statusReporting

strandCountForStrands

int strandCountForStrands

strandCountForMeshRibbon

int strandCountForMeshRibbon

strutSpacing

int strutSpacing

strutLengthMaximum

float strutLengthMaximum

strutDefaultRadius

float strutDefaultRadius

strutsMultiple

boolean strutsMultiple

useArcBall

boolean useArcBall

useMinimizationThread

boolean useMinimizationThread

useNumberLocalization

boolean useNumberLocalization

useScriptQueue

boolean useScriptQueue

waitForMoveTo

boolean waitForMoveTo

vectorScale

float vectorScale

vibrationPeriod

float vibrationPeriod

vibrationScale

float vibrationScale

wireframeRotation

boolean wireframeRotation

hideNavigationPoint

boolean hideNavigationPoint

navigationMode

boolean navigationMode

navigateSurface

boolean navigateSurface

navigationPeriodic

boolean navigationPeriodic

navigationSpeed

float navigationSpeed

showNavigationPointAlways

boolean showNavigationPointAlways

stereoState

java.lang.String stereoState

modelKitMode

boolean modelKitMode

objColors

int[] objColors

objStateOn

boolean[] objStateOn

objMad

int[] objMad

ellipsoidAxes

boolean ellipsoidAxes

ellipsoidDots

boolean ellipsoidDots

ellipsoidArcs

boolean ellipsoidArcs

ellipsoidFill

boolean ellipsoidFill

ellipsoidBall

boolean ellipsoidBall

ellipsoidDotCount

int ellipsoidDotCount

ellipsoidAxisDiameter

float ellipsoidAxisDiameter

testFlag1

boolean testFlag1

testFlag2

boolean testFlag2

testFlag3

boolean testFlag3

testFlag4

boolean testFlag4

measureDistanceUnits

private java.lang.String measureDistanceUnits

structureList

private java.util.Map<EnumStructure,float[]> structureList

haveSetStructureList

private boolean haveSetStructureList
Constructor Detail

StateManager.GlobalSettings

StateManager.GlobalSettings(StateManager.GlobalSettings gsOld)
Method Detail

clear

void clear()

registerAllValues

void registerAllValues(StateManager.GlobalSettings g)

getLoadState

java.lang.String getLoadState(java.util.Map<java.lang.String,java.lang.Object> htParams)
these settings are determined when the file is loaded and are kept even though they might later change. So we list them here and ALSO let them be defined in the settings. 10.9.98 missed this.

Parameters:
htParams -
Returns:
script command

setDefaultLattice

void setDefaultLattice(javax.vecmath.Point3f ptLattice)

getDefaultLattice

javax.vecmath.Point3f getDefaultLattice()

getWindowState

java.lang.String getWindowState(java.lang.StringBuffer sfunc,
                                int width,
                                int height)

getSpecularState

java.lang.String getSpecularState()

setMeasureDistanceUnits

void setMeasureDistanceUnits(java.lang.String units)

getMeasureDistanceUnits

java.lang.String getMeasureDistanceUnits()

isJmolVariable

boolean isJmolVariable(java.lang.String key)

resetParameterStringValue

private void resetParameterStringValue(java.lang.String name,
                                       StateManager.GlobalSettings g)

setParameterValue

void setParameterValue(java.lang.String name,
                       boolean value)

setParameterValue

void setParameterValue(java.lang.String name,
                       int value)

setParameterValue

void setParameterValue(java.lang.String name,
                       float value)

setParameterValue

void setParameterValue(java.lang.String name,
                       java.lang.String value)

removeJmolParameter

void removeJmolParameter(java.lang.String key)

setUserVariable

ScriptVariable setUserVariable(java.lang.String key,
                               ScriptVariable var)

unsetUserVariable

void unsetUserVariable(java.lang.String key)

removeUserVariable

void removeUserVariable(java.lang.String key)

getUserVariable

ScriptVariable getUserVariable(java.lang.String name)

getParameterEscaped

java.lang.String getParameterEscaped(java.lang.String name,
                                     int nMax)

getParameter

java.lang.Object getParameter(java.lang.String name)
strictly a getter -- returns "" if not found

Parameters:
name -
Returns:
a Integer, Float, String, BitSet, or Variable

getOrSetNewVariable

ScriptVariable getOrSetNewVariable(java.lang.String name,
                                   boolean doSet)
Parameters:
name -
doSet -
Returns:
a new variable if possible, but null if "_xxx"

getParameter

java.lang.Object getParameter(java.lang.String name,
                              boolean asVariable)

getAllSettings

java.lang.String getAllSettings(java.lang.String prefix)

chop

private java.lang.String chop(java.lang.String s)

getState

java.lang.String getState(java.lang.StringBuffer sfunc)

doReportProperty

private boolean doReportProperty(java.lang.String name)

getVariableList

java.lang.String getVariableList()

setStructureList

public void setStructureList(float[] list,
                             EnumStructure type)

getStructureList

public java.util.Map<EnumStructure,float[]> getStructureList()

setPicked

void setPicked(int atomIndex)