java.lang.Object

org.jmol.script.ScriptManager

All Implemented Interfaces:: JmolScriptManager

public class ScriptManager extends Object implements JmolScriptManager

Field Summary

Fields

Modifier and Type

Field

Description

private JmolThread

commandWatcherThread

private ScriptEval

eval

private JmolScriptEvaluator

evalTemp

private boolean

isScriptQueued

private static int

prevCovalentVersion

private Thread[]

queueThreads

private int

scriptIndex

javajs.util.Lst<javajs.util.Lst<Object>>

scriptQueue

private boolean[]

scriptQueueRunning

private boolean

useCommandWatcherThread

private Viewer

vwr

Fields inherited from interface org.jmol.api.JmolScriptManager
CHECK_DIMS, FILE_DROPPED, IS_APPEND, NO_AUTOPLAY, NO_SCRIPT, PDB_CARTOONS, SCRIPT_ONLY
Constructor Summary

Constructors

Constructor

Description

ScriptManager()
Method Summary

Modifier and Type

Method

Description

javajs.util.BS

addHydrogensInline(javajs.util.BS bsAtoms, javajs.util.Lst<Atom> vConnections, javajs.util.P3[] pts, Map<String,Object> htParams)

Add hydrogens to a model

private Object

addScr(String returnType, String strScript, String statusList, boolean isQuiet)

String

addScript(String strScript, boolean isQuiet)

boolean

checkHalt(String str, boolean isInsert)

private void

checkResize(String fname)

private boolean

checkResume(String str)

private String

checkScriptExecution(String strScript, boolean isInsert)

private boolean

checkStepping(String str)

void

clear(boolean isAll)

void

clearCommandWatcherThread()

void

clearQueue()

String

evalFile(String strFilename)

String

evalStringQuietSync(String strScript, boolean isQuiet, boolean allowSyncScript)

Object

evalStringWaitStatusQueued(String returnType, String strScript, String statusList, boolean isQuiet, boolean isQueued)

private void

flushQueue(String command)

javajs.util.BS

getAtomBitSetEval(JmolScriptEvaluator eval, Object atomExpression)

private String

getDragDropFileTypeName(String fileName)

javajs.util.Lst<Object>

getScriptItem(boolean watching, boolean isByCommandWatcher)

javajs.util.Lst<javajs.util.Lst<Object>>

getScriptQueue()

(package private) void

interruptQueueThreads()

boolean

isQueueProcessing()

boolean

isScriptQueued()

private ScriptEval

newScriptEvaluator()

void

openFileAsync(String fname, int flags, String type)

From file dropping.

void

queueThreadFinished(int pt)

void

runScriptNow()

Object

scriptCheckRet(String strScript, boolean returnContext)

static void

setStateScriptVersion(Viewer vwr, String version)

JmolScriptEvaluator

setViewer(Viewer vwr)

void

startCommandWatcher(boolean isStart)

private void

startScriptQueue(boolean startedByCommandWatcher)

void

waitForQueue()

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- vwr
  
  private Viewer vwr
- eval
  
  private ScriptEval eval
- evalTemp
  
  private JmolScriptEvaluator evalTemp
- queueThreads
  
  private Thread[] queueThreads
- scriptQueueRunning
  
  private boolean[] scriptQueueRunning
- commandWatcherThread
  
  private JmolThread commandWatcherThread
- scriptQueue
  
  public javajs.util.Lst<javajs.util.Lst<Object>> scriptQueue
- useCommandWatcherThread
  
  private boolean useCommandWatcherThread
- scriptIndex
  
  private int scriptIndex
- isScriptQueued
  
  private boolean isScriptQueued
- prevCovalentVersion
  
  private static int prevCovalentVersion
Constructor Details
- ScriptManager
  
  public ScriptManager()
Method Details
- getScriptQueue
  
  public javajs.util.Lst<javajs.util.Lst<Object>> getScriptQueue()
  
  Specified by:
  
  getScriptQueue in interface JmolScriptManager
- isScriptQueued
  
  public boolean isScriptQueued()
  
  Specified by:
  
  isScriptQueued in interface JmolScriptManager
- setViewer
  
  public JmolScriptEvaluator setViewer(Viewer vwr)
  
  Specified by:
  
  setViewer in interface JmolScriptManager
- newScriptEvaluator
  
  private ScriptEval newScriptEvaluator()
- clear
  
  public void clear(boolean isAll)
  
  Specified by:
  
  clear in interface JmolScriptManager
- addScript
  
  public String addScript(String strScript, boolean isQuiet)
  
  Specified by:
  
  addScript in interface JmolScriptManager
- addScr
  
  private Object addScr(String returnType, String strScript, String statusList, boolean isQuiet)
- clearQueue
  
  public void clearQueue()
  
  Specified by:
  
  clearQueue in interface JmolScriptManager
- waitForQueue
  
  public void waitForQueue()
  
  Specified by:
  
  waitForQueue in interface JmolScriptManager
- isQueueProcessing
  
  public boolean isQueueProcessing()
  
  Specified by:
  
  isQueueProcessing in interface JmolScriptManager
- flushQueue
  
  private void flushQueue(String command)
- startScriptQueue
  
  private void startScriptQueue(boolean startedByCommandWatcher)
- getScriptItem
  
  public javajs.util.Lst<Object> getScriptItem(boolean watching, boolean isByCommandWatcher)
  
  Specified by:
  
  getScriptItem in interface JmolScriptManager
- startCommandWatcher
  
  public void startCommandWatcher(boolean isStart)
  
  Specified by:
  
  startCommandWatcher in interface JmolScriptManager
- interruptQueueThreads
  
  void interruptQueueThreads()
- clearCommandWatcherThread
  
  public void clearCommandWatcherThread()
- queueThreadFinished
  
  public void queueThreadFinished(int pt)
  
  Specified by:
  
  queueThreadFinished in interface JmolScriptManager
- runScriptNow
  
  public void runScriptNow()
- evalFile
  
  public String evalFile(String strFilename)
  
  Specified by:
  
  evalFile in interface JmolScriptManager
- evalStringWaitStatusQueued
  
  public Object evalStringWaitStatusQueued(String returnType, String strScript, String statusList, boolean isQuiet, boolean isQueued)
  
  Specified by:
  
  evalStringWaitStatusQueued in interface JmolScriptManager
- checkScriptExecution
  
  private String checkScriptExecution(String strScript, boolean isInsert)
- checkResume
  
  private boolean checkResume(String str)
- checkStepping
  
  private boolean checkStepping(String str)
- evalStringQuietSync
  
  public String evalStringQuietSync(String strScript, boolean isQuiet, boolean allowSyncScript)
  
  Specified by:
  
  evalStringQuietSync in interface JmolScriptManager
- checkHalt
  
  public boolean checkHalt(String str, boolean isInsert)
  
  Specified by:
  
  checkHalt in interface JmolScriptManager
- getAtomBitSetEval
  
  public javajs.util.BS getAtomBitSetEval(JmolScriptEvaluator eval, Object atomExpression)
  
  Specified by:
  
  getAtomBitSetEval in interface JmolScriptManager
- scriptCheckRet
  
  public Object scriptCheckRet(String strScript, boolean returnContext)
  
  Specified by:
  
  scriptCheckRet in interface JmolScriptManager
- openFileAsync
  
  public void openFileAsync(String fname, int flags, String type)
  
  From file dropping.
  
  Specified by:
  
  openFileAsync in interface JmolScriptManager
  
  Parameters:
  
  fname -
  
  flags - 1=pdbCartoons, 2=no scripting, 4=append, 8=no autoplay, 16=file dropped, 32=script only (dropped into console) 64=check dims for resize
- checkResize
  
  private void checkResize(String fname)
- getDragDropFileTypeName
  
  private String getDragDropFileTypeName(String fileName)
  
  Parameters:
  
  fileName -
  
  Returns:
  
  "pdb" or "dssr" or "Jmol" or + "::"
- setStateScriptVersion
  
  public static void setStateScriptVersion(Viewer vwr, String version)
- addHydrogensInline
  
  public javajs.util.BS addHydrogensInline(javajs.util.BS bsAtoms, javajs.util.Lst<Atom> vConnections, javajs.util.P3[] pts, Map<String,Object> htParams) throws Exception
  
  Add hydrogens to a model
  
  Specified by:
  
  addHydrogensInline in interface JmolScriptManager
  
  Parameters:
  
  bsAtoms - at least one atom, for identification of a model index
  
  vConnections - return list of atoms added
  
  pts - list of point positions for the added hydrogens?
  
  Throws:
  
  Exception

Class ScriptManager

Field Summary

Fields inherited from interface org.jmol.api.JmolScriptManager

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

vwr

eval

evalTemp

queueThreads

scriptQueueRunning

commandWatcherThread

scriptQueue

useCommandWatcherThread

scriptIndex

isScriptQueued

prevCovalentVersion

Constructor Details

ScriptManager

Method Details

getScriptQueue

isScriptQueued

setViewer

newScriptEvaluator

clear

addScript

addScr

clearQueue

waitForQueue

isQueueProcessing

flushQueue

startScriptQueue

getScriptItem

startCommandWatcher

interruptQueueThreads

clearCommandWatcherThread

queueThreadFinished

runScriptNow

evalFile

evalStringWaitStatusQueued

checkScriptExecution

checkResume

checkStepping

evalStringQuietSync

checkHalt

getAtomBitSetEval

scriptCheckRet

openFileAsync

checkResize

getDragDropFileTypeName

setStateScriptVersion

addHydrogensInline