public class PropertyManager extends java.lang.Object implements JmolPropertyManager
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_DOM_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 int |
PROP_VAL_INFO |
private static int |
PROP_VAR_INFO |
private static java.lang.String[] |
propertyTypes |
private static java.lang.String[] |
readableTypes |
(package private) Viewer |
vwr |
Constructor and Description |
---|
PropertyManager() |
Modifier and Type | Method and Description |
---|---|
private boolean |
addMolFile(javajs.util.SB mol,
BS bsAtoms,
BS bsBonds,
boolean asV3000,
boolean asJSON,
javajs.util.Quat q) |
private java.lang.String |
checkMap(java.util.Map<java.lang.String,?> h,
java.lang.String key,
boolean isWild,
javajs.util.Lst<java.lang.Object> v2,
java.lang.Object args,
int ptr) |
boolean |
checkPropertyParameter(java.lang.String name) |
private java.lang.Object |
compileSelect(SV[] args) |
java.lang.Object |
extractProperty(java.lang.Object prop,
java.lang.Object args,
int ptr,
javajs.util.Lst<java.lang.Object> v2,
boolean isCompiled) |
javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
getAllAtomInfo(BS bs) |
javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
getAllBondInfo(java.lang.Object bsOrArray) |
java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> |
getAllChainInfo(BS bs) |
private java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> |
getAllPolymerInfo(BS bs) |
private java.util.Map<java.lang.String,java.lang.Object> |
getAnimationInfo() |
private SV |
getAnnotationInfo(java.lang.Object atomExpression,
int type) |
private java.util.Map<java.lang.String,java.lang.Object> |
getAppletInfo() |
private SV[] |
getArguments(java.lang.String propertyName) |
private java.util.Map<java.lang.String,java.lang.Object> |
getAtomInfoLong(int i,
javajs.util.P3 ptTemp) |
private void |
getAtomRecordMOL(ModelSet ms,
javajs.util.SB mol,
int n,
Atom a,
javajs.util.Quat q,
javajs.util.P3 pTemp,
javajs.util.P3 ptTemp,
boolean asV3000,
boolean asJSON) |
private static void |
getAtomResidueInfo(javajs.util.SB info,
Atom atom) |
private java.util.Map<java.lang.String,java.lang.Object> |
getAuxiliaryInfo(java.lang.Object atomExpression) |
private java.lang.String |
getBasePairInfo(BS bs) |
private java.util.Map<java.lang.String,java.lang.Object> |
getBondInfo(int i,
javajs.util.P3 ptTemp) |
private void |
getBondRecordMOL(javajs.util.SB mol,
int n,
Bond b,
int[] atomMap,
boolean asV3000,
boolean asJSON) |
private java.util.Map<java.lang.String,java.lang.Object> |
getBoundBoxInfo() |
private javajs.util.Lst<java.util.Map<java.lang.String,javajs.util.Lst<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) |
private java.lang.Object |
getImage(java.lang.String params,
boolean asBytes) |
java.util.Map<java.lang.String,java.lang.Object> |
getLigandInfo(java.lang.Object atomExpression) |
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
getMeasurementInfo() |
java.lang.String |
getModelCml(BS bs,
int atomsMax,
boolean addBonds) |
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) |
javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
getMoleculeInfo(java.lang.Object atomExpression) |
private java.lang.Object |
getMouseInfo() |
private java.lang.Object |
getObj(java.lang.Object prop) |
private static java.lang.String |
getParamType(int propID) |
java.lang.String |
getPdbAtomData(BS bs,
javajs.util.OC out)
PDB or PQR only
|
java.lang.String |
getPdbData(int modelIndex,
java.lang.String type,
BS bsSelected,
java.lang.Object[] parameters,
javajs.util.OC out,
boolean addStructure) |
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) |
private java.util.Map<java.lang.String,java.lang.Object> |
getShapeInfo() |
private java.lang.Object |
getVariables(java.lang.String name) |
private static boolean |
isReadableAsString(java.lang.String infoType) |
void |
setViewer(Viewer vwr) |
Viewer vwr
private java.util.Map<java.lang.String,java.lang.Integer> map
private static final java.lang.String atomExpression
private static final java.lang.String[] propertyTypes
private static final int PROP_APPLET_INFO
private static final int PROP_FILENAME
private static final int PROP_FILEHEADER
private static final int PROP_FILECONTENTS_PATH
private static final int PROP_FILECONTENTS
private static final int PROP_ANIMATION_INFO
private static final int PROP_MODEL_INFO
private static final int PROP_LIGAND_INFO
private static final int PROP_SHAPE_INFO
private static final int PROP_MEASUREMENT_INFO
private static final int PROP_CENTER_INFO
private static final int PROP_ORIENTATION_INFO
private static final int PROP_TRANSFORM_INFO
private static final int PROP_ATOM_LIST
private static final int PROP_ATOM_INFO
private static final int PROP_BOND_INFO
private static final int PROP_CHAIN_INFO
private static final int PROP_POLYMER_INFO
private static final int PROP_MOLECULE_INFO
private static final int PROP_STATE_INFO
private static final int PROP_EXTRACT_MODEL
private static final int PROP_JMOL_STATUS
private static final int PROP_JMOL_VIEWER
private static final int PROP_MESSAGE_QUEUE
private static final int PROP_AUXILIARY_INFO
private static final int PROP_BOUNDBOX_INFO
private static final int PROP_DATA_INFO
private static final int PROP_IMAGE
private static final int PROP_EVALUATE
private static final int PROP_MENU
private static final int PROP_MINIMIZATION_INFO
private static final int PROP_POINTGROUP_INFO
private static final int PROP_FILE_INFO
private static final int PROP_ERROR_MESSAGE
private static final int PROP_MOUSE_INFO
private static final int PROP_ISOSURFACE_INFO
private static final int PROP_ISOSURFACE_DATA
private static final int PROP_CONSOLE_TEXT
private static final int PROP_JSPECVIEW
private static final int PROP_SCRIPT_QUEUE_INFO
private static final int PROP_NMR_INFO
private static final int PROP_VAR_INFO
private static final int PROP_DOM_INFO
private static final int PROP_VAL_INFO
private static final int PROP_COUNT
private static final java.lang.String[] readableTypes
public void setViewer(Viewer vwr)
setViewer
in interface JmolPropertyManager
public int getPropertyNumber(java.lang.String infoType)
getPropertyNumber
in interface JmolPropertyManager
public java.lang.String getDefaultPropertyParam(int propID)
getDefaultPropertyParam
in interface JmolPropertyManager
public boolean checkPropertyParameter(java.lang.String name)
checkPropertyParameter
in interface JmolPropertyManager
public java.lang.Object getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
getProperty
in interface JmolPropertyManager
private SV[] getArguments(java.lang.String propertyName)
public java.lang.Object extractProperty(java.lang.Object prop, java.lang.Object args, int ptr, javajs.util.Lst<java.lang.Object> v2, boolean isCompiled)
extractProperty
in interface JmolPropertyManager
private java.lang.Object compileSelect(SV[] args)
private java.lang.String checkMap(java.util.Map<java.lang.String,?> h, java.lang.String key, boolean isWild, javajs.util.Lst<java.lang.Object> v2, java.lang.Object args, int ptr)
private java.lang.Object getObj(java.lang.Object prop)
private static java.lang.String getPropertyName(int propID)
private static java.lang.String getParamType(int propID)
private static boolean isReadableAsString(java.lang.String infoType)
private java.lang.Object getPropertyAsObject(java.lang.String infoType, java.lang.Object paramInfo, java.lang.String returnType)
private java.lang.Object getImage(java.lang.String params, boolean asBytes)
private java.lang.Object getVariables(java.lang.String name)
static java.lang.Object getFileInfo(java.lang.Object objHeader, java.lang.String type)
public javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getMoleculeInfo(java.lang.Object atomExpression)
public java.util.Map<java.lang.String,java.lang.Object> getModelInfo(java.lang.Object atomExpression)
getModelInfo
in interface JmolPropertyManager
public java.util.Map<java.lang.String,java.lang.Object> getLigandInfo(java.lang.Object atomExpression)
getLigandInfo
in interface JmolPropertyManager
public java.lang.String getModelExtract(BS bs, boolean doTransform, boolean isModelKit, java.lang.String type)
getModelExtract
in interface JmolPropertyManager
private boolean addMolFile(javajs.util.SB mol, BS bsAtoms, BS bsBonds, boolean asV3000, boolean asJSON, javajs.util.Quat q)
private static BS getCovalentBondsForAtoms(Bond[] bonds, int bondCount, BS bsAtoms)
private void getAtomRecordMOL(ModelSet ms, javajs.util.SB mol, int n, Atom a, javajs.util.Quat q, javajs.util.P3 pTemp, javajs.util.P3 ptTemp, boolean asV3000, boolean asJSON)
private void getBondRecordMOL(javajs.util.SB mol, int n, Bond b, int[] atomMap, boolean asV3000, boolean asJSON)
public java.lang.String getChimeInfo(int tok, BS bs)
getChimeInfo
in interface JmolPropertyManager
public java.lang.String getModelFileInfo(BS frames)
getModelFileInfo
in interface JmolPropertyManager
public javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getAllAtomInfo(BS bs)
private java.util.Map<java.lang.String,java.lang.Object> getAtomInfoLong(int i, javajs.util.P3 ptTemp)
public javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getAllBondInfo(java.lang.Object bsOrArray)
private java.util.Map<java.lang.String,java.lang.Object> getBondInfo(int i, javajs.util.P3 ptTemp)
public java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> getAllChainInfo(BS bs)
private javajs.util.Lst<java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>>> getChainInfo(int modelIndex, BS bs)
private java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> getAllPolymerInfo(BS bs)
private java.lang.String getBasePairInfo(BS bs)
private static void getAtomResidueInfo(javajs.util.SB info, Atom atom)
private java.util.Map<java.lang.String,java.lang.Object> getAppletInfo()
private java.util.Map<java.lang.String,java.lang.Object> getAnimationInfo()
private java.util.Map<java.lang.String,java.lang.Object> getBoundBoxInfo()
private java.util.Map<java.lang.String,java.lang.Object> getShapeInfo()
private java.util.Map<java.lang.String,java.lang.Object> getAuxiliaryInfo(java.lang.Object atomExpression)
private SV getAnnotationInfo(java.lang.Object atomExpression, int type)
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getMeasurementInfo()
private java.lang.Object getMouseInfo()
public java.lang.String getPdbAtomData(BS bs, javajs.util.OC out)
getPdbAtomData
in interface JmolPropertyManager
bs
- selected atomsout
- StringXBuilder or BufferedWriterpublic java.lang.String getPdbData(int modelIndex, java.lang.String type, BS bsSelected, java.lang.Object[] parameters, javajs.util.OC out, boolean addStructure)
getPdbData
in interface JmolPropertyManager
public java.lang.String getModelCml(BS bs, int atomsMax, boolean addBonds)
getModelCml
in interface JmolPropertyManager