org.jmol.viewer

Class PropertyManager

java.lang.Object

org.jmol.viewer.PropertyManager

All Implemented Interfaces:

JmolPropertyManager

public class PropertyManager
extends java.lang.Object
implements JmolPropertyManager

The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON(). It is instantiated by reflection

Field Summary

Fields

Modifier and Type	Field and Description
private static java.lang.String	atomExpression
private java.util.Map<java.lang.String,java.lang.Integer>	map
private static int	PROP_ANIMATION_INFO
private static int	PROP_APPLET_INFO
private static int	PROP_ATOM_INFO
private static int	PROP_ATOM_LIST
private static int	PROP_AUXILIARY_INFO
private static int	PROP_BOND_INFO
private static int	PROP_BOUNDBOX_INFO
private static int	PROP_CENTER_INFO
private static int	PROP_CHAIN_INFO
private static int	PROP_CONSOLE_TEXT
private static int	PROP_COUNT
private static int	PROP_DATA_INFO
private static int	PROP_ERROR_MESSAGE
private static int	PROP_EVALUATE
private static int	PROP_EXTRACT_MODEL
private static int	PROP_FILE_INFO
private static int	PROP_FILECONTENTS
private static int	PROP_FILECONTENTS_PATH
private static int	PROP_FILEHEADER
private static int	PROP_FILENAME
private static int	PROP_IMAGE
private static int	PROP_ISOSURFACE_DATA
private static int	PROP_ISOSURFACE_INFO
private static int	PROP_JMOL_STATUS
private static int	PROP_JMOL_VIEWER
private static int	PROP_JSPECVIEW
private static int	PROP_LIGAND_INFO
private static int	PROP_MEASUREMENT_INFO
private static int	PROP_MENU
private static int	PROP_MESSAGE_QUEUE
private static int	PROP_MINIMIZATION_INFO
private static int	PROP_MODEL_INFO
private static int	PROP_MOLECULE_INFO
private static int	PROP_MOUSE_INFO
private static int	PROP_NMR_INFO
private static int	PROP_ORIENTATION_INFO
private static int	PROP_POINTGROUP_INFO
private static int	PROP_POLYMER_INFO
private static int	PROP_SCRIPT_QUEUE_INFO
private static int	PROP_SHAPE_INFO
private static int	PROP_STATE_INFO
private static int	PROP_TRANSFORM_INFO
private static java.lang.String[]	propertyTypes
private static java.lang.String[]	readableTypes
(package private) Viewer	viewer

Constructor Summary

Constructors

Constructor and Description
PropertyManager()

Method Summary

Methods

Modifier and Type	Method and Description
private boolean	addMolFile(SB mol, BS bsAtoms, BS bsBonds, boolean asV3000, boolean asChemDoodle, Quaternion q)
boolean	checkPropertyParameter(java.lang.String name)
java.lang.Object	extractProperty(java.lang.Object property, SV[] args, int ptr)
JmolList<java.util.Map<java.lang.String,java.lang.Object>>	getAllAtomInfo(BS bs)
JmolList<java.util.Map<java.lang.String,java.lang.Object>>	getAllBondInfo(java.lang.Object bsOrArray)
java.util.Map<java.lang.String,JmolList<java.util.Map<java.lang.String,java.lang.Object>>>	getAllChainInfo(BS bs)
java.util.Map<java.lang.String,JmolList<java.util.Map<java.lang.String,java.lang.Object>>>	getAllPolymerInfo(BS bs)
private java.util.Map<java.lang.String,java.lang.Object>	getAtomInfoLong(int i)
private void	getAtomRecordMOL(ModelSet ms, SB mol, int n, Atom a, Quaternion q, P3 pTemp, P3 ptTemp, boolean asV3000, boolean asChemDoodle)
private static void	getAtomResidueInfo(SB info, Atom atom)
private java.lang.String	getBasePairInfo(BS bs)
private java.util.Map<java.lang.String,java.lang.Object>	getBondInfo(int i)
private void	getBondRecordMOL(SB mol, int n, Bond b, int[] atomMap, boolean asV3000, boolean asChemDoodle)
private JmolList<java.util.Map<java.lang.String,JmolList<java.util.Map<java.lang.String,java.lang.Object>>>>	getChainInfo(int modelIndex, BS bs)
java.lang.String	getChimeInfo(int tok, BS bs)
private java.lang.String	getChimeInfoA(Atom[] atoms, int tok, BS bs)
private static BS	getCovalentBondsForAtoms(Bond[] bonds, int bondCount, BS bsAtoms)
java.lang.String	getDefaultPropertyParam(int propID)
(package private) static java.lang.Object	getFileInfo(java.lang.Object objHeader, java.lang.String type)
java.util.Map<java.lang.String,java.lang.Object>	getLigandInfo(java.lang.Object atomExpression)
java.lang.String	getModelExtract(BS bs, boolean doTransform, boolean isModelKit, java.lang.String type)
java.lang.String	getModelFileInfo(BS frames)
java.util.Map<java.lang.String,java.lang.Object>	getModelInfo(java.lang.Object atomExpression)
private java.lang.Object	getModelProperty(java.lang.String propertyName, java.lang.Object propertyValue)
JmolList<java.util.Map<java.lang.String,java.lang.Object>>	getMoleculeInfo(java.lang.Object atomExpression)
private static java.lang.String	getParamType(int propID)
java.lang.Object	getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
private java.lang.Object	getPropertyAsObject(java.lang.String infoType, java.lang.Object paramInfo, java.lang.String returnType)
private static java.lang.String	getPropertyName(int propID)
int	getPropertyNumber(java.lang.String infoType)
java.lang.Object	getSymmetryInfo(BS bsAtoms, java.lang.String xyz, int op, P3 pt, P3 pt2, java.lang.String id, int type)
private static boolean	isReadableAsString(java.lang.String infoType)
void	setViewer(Viewer viewer)

Methods inherited from class java.lang.Object

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

Field Detail

viewer

Viewer viewer

map

private java.util.Map<java.lang.String,java.lang.Integer> map

atomExpression

private static final java.lang.String atomExpression

See Also:

Constant Field Values

propertyTypes

private static final java.lang.String[] propertyTypes

PROP_APPLET_INFO

private static final int PROP_APPLET_INFO

See Also:

Constant Field Values

PROP_FILENAME

private static final int PROP_FILENAME

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Constant Field Values

PROP_FILEHEADER

private static final int PROP_FILEHEADER

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Constant Field Values

PROP_FILECONTENTS_PATH

private static final int PROP_FILECONTENTS_PATH

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Constant Field Values

PROP_FILECONTENTS

private static final int PROP_FILECONTENTS

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Constant Field Values

PROP_ANIMATION_INFO

private static final int PROP_ANIMATION_INFO

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Constant Field Values

PROP_MODEL_INFO

private static final int PROP_MODEL_INFO

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Constant Field Values

PROP_LIGAND_INFO

private static final int PROP_LIGAND_INFO

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Constant Field Values

PROP_SHAPE_INFO

private static final int PROP_SHAPE_INFO

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Constant Field Values

PROP_MEASUREMENT_INFO

private static final int PROP_MEASUREMENT_INFO

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Constant Field Values

PROP_CENTER_INFO

private static final int PROP_CENTER_INFO

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Constant Field Values

PROP_ORIENTATION_INFO

private static final int PROP_ORIENTATION_INFO

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Constant Field Values

PROP_TRANSFORM_INFO

private static final int PROP_TRANSFORM_INFO

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Constant Field Values

PROP_ATOM_LIST

private static final int PROP_ATOM_LIST

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Constant Field Values

PROP_ATOM_INFO

private static final int PROP_ATOM_INFO

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Constant Field Values

PROP_BOND_INFO

private static final int PROP_BOND_INFO

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Constant Field Values

PROP_CHAIN_INFO

private static final int PROP_CHAIN_INFO

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Constant Field Values

PROP_POLYMER_INFO

private static final int PROP_POLYMER_INFO

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Constant Field Values

PROP_MOLECULE_INFO

private static final int PROP_MOLECULE_INFO

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Constant Field Values

PROP_STATE_INFO

private static final int PROP_STATE_INFO

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Constant Field Values

PROP_EXTRACT_MODEL

private static final int PROP_EXTRACT_MODEL

See Also:

Constant Field Values

PROP_JMOL_STATUS

private static final int PROP_JMOL_STATUS

See Also:

Constant Field Values

PROP_JMOL_VIEWER

private static final int PROP_JMOL_VIEWER

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Constant Field Values

PROP_MESSAGE_QUEUE

private static final int PROP_MESSAGE_QUEUE

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Constant Field Values

PROP_AUXILIARY_INFO

private static final int PROP_AUXILIARY_INFO

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Constant Field Values

PROP_BOUNDBOX_INFO

private static final int PROP_BOUNDBOX_INFO

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Constant Field Values

PROP_DATA_INFO

private static final int PROP_DATA_INFO

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Constant Field Values

PROP_IMAGE

private static final int PROP_IMAGE

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Constant Field Values

PROP_EVALUATE

private static final int PROP_EVALUATE

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Constant Field Values

PROP_MENU

private static final int PROP_MENU

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Constant Field Values

PROP_MINIMIZATION_INFO

private static final int PROP_MINIMIZATION_INFO

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Constant Field Values

PROP_POINTGROUP_INFO

private static final int PROP_POINTGROUP_INFO

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Constant Field Values

PROP_FILE_INFO

private static final int PROP_FILE_INFO

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Constant Field Values

PROP_ERROR_MESSAGE

private static final int PROP_ERROR_MESSAGE

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Constant Field Values

PROP_MOUSE_INFO

private static final int PROP_MOUSE_INFO

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Constant Field Values

PROP_ISOSURFACE_INFO

private static final int PROP_ISOSURFACE_INFO

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Constant Field Values

PROP_ISOSURFACE_DATA

private static final int PROP_ISOSURFACE_DATA

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Constant Field Values

PROP_CONSOLE_TEXT

private static final int PROP_CONSOLE_TEXT

See Also:

Constant Field Values

PROP_JSPECVIEW

private static final int PROP_JSPECVIEW

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Constant Field Values

PROP_SCRIPT_QUEUE_INFO

private static final int PROP_SCRIPT_QUEUE_INFO

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Constant Field Values

PROP_NMR_INFO

private static final int PROP_NMR_INFO

See Also:

Constant Field Values

PROP_COUNT

private static final int PROP_COUNT

See Also:

Constant Field Values

readableTypes

private static final java.lang.String[] readableTypes

Constructor Detail

PropertyManager

public PropertyManager()

Method Detail

setViewer

public void setViewer(Viewer viewer)

Specified by:

setViewer in interface JmolPropertyManager

getPropertyNumber

public int getPropertyNumber(java.lang.String infoType)

Specified by:

getPropertyNumber in interface JmolPropertyManager

getDefaultPropertyParam

public java.lang.String getDefaultPropertyParam(int propID)

Specified by:

getDefaultPropertyParam in interface JmolPropertyManager

checkPropertyParameter

public boolean checkPropertyParameter(java.lang.String name)

Specified by:

checkPropertyParameter in interface JmolPropertyManager

getProperty

public java.lang.Object getProperty(java.lang.String returnType,
                           java.lang.String infoType,
                           java.lang.Object paramInfo)

Specified by:

getProperty in interface JmolPropertyManager

getModelProperty

private java.lang.Object getModelProperty(java.lang.String propertyName,
                                java.lang.Object propertyValue)

extractProperty

public java.lang.Object extractProperty(java.lang.Object property,
                               SV[] args,
                               int ptr)

Specified by:

extractProperty in interface JmolPropertyManager

getPropertyName

private static java.lang.String getPropertyName(int propID)

getParamType

private static java.lang.String getParamType(int propID)

isReadableAsString

private static boolean isReadableAsString(java.lang.String infoType)

getPropertyAsObject

private java.lang.Object getPropertyAsObject(java.lang.String infoType,
                                   java.lang.Object paramInfo,
                                   java.lang.String returnType)

getFileInfo

static java.lang.Object getFileInfo(java.lang.Object objHeader,
                           java.lang.String type)

getMoleculeInfo

public JmolList<java.util.Map<java.lang.String,java.lang.Object>> getMoleculeInfo(java.lang.Object atomExpression)

getModelInfo

public java.util.Map<java.lang.String,java.lang.Object> getModelInfo(java.lang.Object atomExpression)

Specified by:

getModelInfo in interface JmolPropertyManager

getLigandInfo

public java.util.Map<java.lang.String,java.lang.Object> getLigandInfo(java.lang.Object atomExpression)

Specified by:

getLigandInfo in interface JmolPropertyManager

getSymmetryInfo

public java.lang.Object getSymmetryInfo(BS bsAtoms,
                               java.lang.String xyz,
                               int op,
                               P3 pt,
                               P3 pt2,
                               java.lang.String id,
                               int type)

Specified by:

getSymmetryInfo in interface JmolPropertyManager

getModelExtract

public java.lang.String getModelExtract(BS bs,
                               boolean doTransform,
                               boolean isModelKit,
                               java.lang.String type)

Specified by:

getModelExtract in interface JmolPropertyManager

addMolFile

private boolean addMolFile(SB mol,
                 BS bsAtoms,
                 BS bsBonds,
                 boolean asV3000,
                 boolean asChemDoodle,
                 Quaternion q)

getCovalentBondsForAtoms

private static BS getCovalentBondsForAtoms(Bond[] bonds,
                          int bondCount,
                          BS bsAtoms)

getAtomRecordMOL

private void getAtomRecordMOL(ModelSet ms,
                    SB mol,
                    int n,
                    Atom a,
                    Quaternion q,
                    P3 pTemp,
                    P3 ptTemp,
                    boolean asV3000,
                    boolean asChemDoodle)

getBondRecordMOL

private void getBondRecordMOL(SB mol,
                    int n,
                    Bond b,
                    int[] atomMap,
                    boolean asV3000,
                    boolean asChemDoodle)

getChimeInfo

public java.lang.String getChimeInfo(int tok,
                            BS bs)

Specified by:

getChimeInfo in interface JmolPropertyManager

getChimeInfoA

private java.lang.String getChimeInfoA(Atom[] atoms,
                             int tok,
                             BS bs)

getModelFileInfo

public java.lang.String getModelFileInfo(BS frames)

Specified by:

getModelFileInfo in interface JmolPropertyManager

getAllAtomInfo

public JmolList<java.util.Map<java.lang.String,java.lang.Object>> getAllAtomInfo(BS bs)

getAtomInfoLong

private java.util.Map<java.lang.String,java.lang.Object> getAtomInfoLong(int i)

getAllBondInfo

public JmolList<java.util.Map<java.lang.String,java.lang.Object>> getAllBondInfo(java.lang.Object bsOrArray)

getBondInfo

private java.util.Map<java.lang.String,java.lang.Object> getBondInfo(int i)

getAllChainInfo

public java.util.Map<java.lang.String,JmolList<java.util.Map<java.lang.String,java.lang.Object>>> getAllChainInfo(BS bs)

getChainInfo

private JmolList<java.util.Map<java.lang.String,JmolList<java.util.Map<java.lang.String,java.lang.Object>>>> getChainInfo(int modelIndex,
                                                                                                                BS bs)

getAllPolymerInfo

public java.util.Map<java.lang.String,JmolList<java.util.Map<java.lang.String,java.lang.Object>>> getAllPolymerInfo(BS bs)

getBasePairInfo

private java.lang.String getBasePairInfo(BS bs)

getAtomResidueInfo

private static void getAtomResidueInfo(SB info,
                      Atom atom)