Revision: 21195
http://sourceforge.net/p/jmol/code/21195
Author: hansonr
Date: 2016-08-10 04:55:19 +0000 (Wed, 10 Aug 2016)
Log Message:
-----------
Refactoring Lst
Modified Paths:
--------------
branches/v14_6/Jmol/jars/JSpecView.jar
branches/v14_6/Jmol/jars/jspecview.properties
branches/v14_6/Jmol/src/javajs/awt/Container.java
branches/v14_6/Jmol/src/javajs/img/GifEncoder.java
branches/v14_6/Jmol/src/javajs/util/Lst.java
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
branches/v14_6/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
branches/v14_6/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java
branches/v14_6/Jmol/src/org/jmol/modelset/AtomCollection.java
branches/v14_6/Jmol/src/org/jmol/modelset/ModelSet.java
branches/v14_6/Jmol/src/org/jmol/script/SV.java
branches/v14_6/Jmol/src/org/jmol/script/ScriptCompiler.java
branches/v14_6/Jmol/src/org/jmol/script/ScriptFunction.java
branches/v14_6/Jmol/src/org/jmol/script/ScriptManager.java
branches/v14_6/Jmol/src/org/jmol/script/ScriptMathProcessor.java
branches/v14_6/Jmol/src/org/jmol/script/ScriptParallelProcessor.java
branches/v14_6/Jmol/src/org/jmol/script/ScriptQueueThread.java
branches/v14_6/Jmol/src/org/jmol/script/ScriptTokenParser.java
branches/v14_6/Jmol/src/org/jmol/shape/Measures.java
branches/v14_6/Jmol/src/org/jmol/shape/Shape.java
branches/v14_6/Jmol/src/org/jmol/shapesurface/Contact.java
branches/v14_6/Jmol/src/org/jmol/smiles/SmilesAromatic.java
branches/v14_6/Jmol/src/org/jmol/smiles/SmilesGenerator.java
branches/v14_6/Jmol/src/org/jmol/util/CommandHistory.java
branches/v14_6/Jmol/src/org/jmol/viewer/OutputManager.java
branches/v14_6/Jmol/src/org/jmol/viewer/StateCreator.java
branches/v14_6/Jmol/src/org/jmol/viewer/StatusManager.java
branches/v14_6/Jmol/src/org/openscience/jmol/app/nbo/NBOJobQueueManager.java
trunk/Jmol/src/javajs/awt/Container.java
trunk/Jmol/src/javajs/img/GifEncoder.java
trunk/Jmol/src/javajs/util/Lst.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptFunction.java
trunk/Jmol/src/org/jmol/script/ScriptManager.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/script/ScriptParallelProcessor.java
trunk/Jmol/src/org/jmol/script/ScriptQueueThread.java
trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java
trunk/Jmol/src/org/jmol/shape/Measures.java
trunk/Jmol/src/org/jmol/shape/Shape.java
trunk/Jmol/src/org/jmol/shapesurface/Contact.java
trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java
trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
trunk/Jmol/src/org/jmol/util/CommandHistory.java
trunk/Jmol/src/org/jmol/viewer/OutputManager.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/StatusManager.java
trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOJobQueueManager.java
Added Paths:
-----------
trunk/Jmol/jars/JSpecView.jar
Removed Paths:
-------------
trunk/Jmol/jars/JSpecView.jar
Modified: branches/v14_6/Jmol/jars/JSpecView.jar
===================================================================
(Binary files differ)
Modified: branches/v14_6/Jmol/jars/jspecview.properties
===================================================================
--- branches/v14_6/Jmol/jars/jspecview.properties 2016-08-10 01:21:37 UTC
(rev 21194)
+++ branches/v14_6/Jmol/jars/jspecview.properties 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -1,5 +1,5 @@
#JSpecView Application Properties
-#Fri Oct 16 09:46:48 CDT 2015
+#Fri May 27 09:51:54 CDT 2016
integralFactor=50
AtoTSeparateWindow=false
useDirectoryLastExportedFile=false
@@ -19,7 +19,7 @@
showXScale=true
showSidePanel=true
showToolBar=true
-recentFilePaths=http\://SIMULATION/propane, http\://SIMULATION/ethanol,
http\://SIMULATION/acetophenone, C\:\\temp\\tt.jdx,
c\:\\temp\\ethanolamine.jdx, c\:\\temp\\acetophenone.jdx, c\:\\temp\\t.jdx
+recentFilePaths=http\://SIMULATION/H1/methanol,
http\://SIMULATION/C13/tylenol, http\://SIMULATION/H1/tylenol,
http\://SIMULATION/propane, http\://SIMULATION/ethanol,
http\://SIMULATION/acetophenone, C\:\\temp\\tt.jdx,
c\:\\temp\\ethanolamine.jdx, c\:\\temp\\acetophenone.jdx, c\:\\temp\\t.jdx
automaticallyOverlay=false
showCoordinates=false
integralMinY=0.1
Modified: branches/v14_6/Jmol/src/javajs/awt/Container.java
===================================================================
--- branches/v14_6/Jmol/src/javajs/awt/Container.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ branches/v14_6/Jmol/src/javajs/awt/Container.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -52,7 +52,7 @@
}
public void remove(int i) {
- Component c = list.remove(i);
+ Component c = list.removeItemAt(i);
c.parent = null;
cList = null;
}
Modified: branches/v14_6/Jmol/src/javajs/img/GifEncoder.java
===================================================================
--- branches/v14_6/Jmol/src/javajs/img/GifEncoder.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ branches/v14_6/Jmol/src/javajs/img/GifEncoder.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -365,17 +365,17 @@
case 0:
for (int i = n; --i >= 0;)
if (get(i).x >= val)
- newCell.addLast(remove(i));
+ newCell.addLast(removeItemAt(i));
break;
case 1:
for (int i = n; --i >= 0;)
if (get(i).y >= val)
- newCell.addLast(remove(i));
+ newCell.addLast(removeItemAt(i));
break;
case 2:
for (int i = size(); --i >= 0;)
if (get(i).z >= val)
- newCell.addLast(remove(i));
+ newCell.addLast(removeItemAt(i));
break;
}
return true;
Modified: branches/v14_6/Jmol/src/javajs/util/Lst.java
===================================================================
--- branches/v14_6/Jmol/src/javajs/util/Lst.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ branches/v14_6/Jmol/src/javajs/util/Lst.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -65,10 +65,34 @@
* @j2sIgnore
*
*/
+// @Override
+// @Deprecated
+ public V remove(int location) {
+ throw new NullPointerException("use Lst.removeItemAt(location), not
Lst.remove(location)");
+ }
+
+ public V removeItemAt(int location) {
+ /**
+ * no overloading of remove(location) in JavaScript
+ *
+ * @j2sNative
+ *
+ * return this._removeItemAt(location);
+ *
+ */
+ {
+ return super.remove(location);
+ }
+ }
+
+ /**
+ * @j2sIgnore
+ *
+ */
@Override
@Deprecated
public boolean remove(Object v) {
- throw new NullPointerException("use removeObj(obj), not remove(obj) in
List for JavaScript compatibility");
+ throw new NullPointerException("use Lst.removeObj(obj), not
Lst.remove(obj)");
}
public boolean removeObj(Object v) {
@@ -77,7 +101,7 @@
*
* @j2sNative
*
- * return this.removeObject(v);
+ * return this._removeObject(v);
*
*/
{
Modified:
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -350,7 +350,7 @@
Logger.info("PyMOL Pickle reader cached " + memo.size()
+ " tokens; retrieved " + retrieveCount);
- map = (Map<String, Object>) stack.remove(0);
+ map = (Map<String, Object>) stack.removeItemAt(0);
if (map.size() == 0)
for (i = stack.size(); --i >= 0;) {
o = stack.get(i--);
@@ -398,7 +398,7 @@
for (int i = mark; i < stack.size(); ++i)
args.addLast(stack.get(i));
for (int i = stack.size(); --i >= mark;)
- stack.remove(i);
+ stack.removeItemAt(i);
return args;
}
@@ -444,7 +444,7 @@
}
private int getMark() {
- return marks.remove(--markCount).intValue();
+ return marks.removeItemAt(--markCount).intValue();
}
private void push(Object o) {
@@ -459,7 +459,7 @@
}
private Object pop() {
- return stack.remove(stack.size() - 1);
+ return stack.removeItemAt(stack.size() - 1);
}
}
Modified:
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -481,7 +481,7 @@
String name = stringAt(sceneOrder, i);
Lst<Object> thisScene = getMapList(scenes, name);
if (thisScene == null || thisScene.get(2) == null)
- sceneOrder.remove(i--);
+ sceneOrder.removeItemAt(i--);
}
return (sceneOrder != null && sceneOrder.size() != 0);
}
Modified:
branches/v14_6/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -598,7 +598,7 @@
if (bsInputAtomsIgnore.nextSetBit(0) >= 0)
for (int i = n; --i >= 0;)
if (bsInputAtomsIgnore.get(i))
- vCoords.remove(i);
+ vCoords.removeItemAt(i);
ac = vCoords.size();
Logger.info(nPrim + " primitive atoms and " + ac
+ " conventionalAtoms");
Modified: branches/v14_6/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -261,7 +261,7 @@
if (((Boolean) info.get(i)[2]).booleanValue()
&& info.get(i)[0] instanceof P4) {
volumeData.capData((P4) info.get(i)[0], params.cutoff);
- info.remove(i--);
+ info.removeItemAt(i--);
}
}
Modified: branches/v14_6/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/modelset/AtomCollection.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/modelset/AtomCollection.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -2612,7 +2612,7 @@
for (int i = list.size(); --i >= 0;) {
Tensor t = (Tensor) list.get(i);
if (bsAtoms.get(t.atomIndex1) || t.atomIndex2 >= 0 &&
bsAtoms.get(t.atomIndex2))
- list.remove(i);
+ list.removeItemAt(i);
}
if (list.size() == 0)
toDelete.addLast(key);
Modified: branches/v14_6/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/modelset/ModelSet.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/modelset/ModelSet.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -640,7 +640,7 @@
moleculeCount = 0;
for (int i = stateScripts.size(); --i >= 0;) {
if (stateScripts.get(i).isConnect()) {
- stateScripts.remove(i);
+ stateScripts.removeItemAt(i);
}
}
deleteAllBonds2();
@@ -809,7 +809,7 @@
// correct stateScripts, particularly CONNECT scripts
for (int i = stateScripts.size(); --i >= 0;) {
if (!stateScripts.get(i).deleteAtoms(modelIndex, bsBonds, bsModelAtoms))
{
- stateScripts.remove(i);
+ stateScripts.removeItemAt(i);
}
}
deleteModelAtoms(firstAtomIndex, nAtoms, bsModelAtoms);
Modified: branches/v14_6/Jmol/src/org/jmol/script/SV.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/script/SV.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/script/SV.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -1524,7 +1524,7 @@
if (i < 0)
i += len;
if (i >= 0 && i < len) {
- v = lst.remove(i);
+ v = lst.removeItemAt(i);
}
} else {
v = m.remove(mapKey.asString());
@@ -1536,7 +1536,7 @@
} else {
Lst<SV> x = getList();
if (value == null || x == null)
- return (x == null || x.size() == 0 ? newS("") : x.remove(x.size() -
1));
+ return (x == null || x.size() == 0 ? newS("") :
x.removeItemAt(x.size() - 1));
x.addLast(newI(0).setv(value));
}
return this;
Modified: branches/v14_6/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/script/ScriptCompiler.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/script/ScriptCompiler.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -720,7 +720,7 @@
// ...{...
if (lastFlowCommand == null) {
parenCount = setBraceCount = braceCount = 0;
- ltoken.remove(0);
+ ltoken.removeItemAt(0);
T t = ContextToken.newContext(true);
addTokenToPrefix(setCommand(t));
pushContext(t);
@@ -729,7 +729,7 @@
parenCount = setBraceCount = 0;
setCommand(lastFlowCommand);
if (lastFlowCommand.tok != T.process && (tokAt(0) == T.leftbrace))
- ltoken.remove(0);
+ ltoken.removeItemAt(0);
lastFlowCommand = null;
forceFlowContext = flowContext;
// lastFlowImplicitEnd = flowContext.nextFlowImplicitEnd;
@@ -753,7 +753,7 @@
case T.define:
break;
default:
- T t = ltoken.remove(2);
+ T t = ltoken.removeItemAt(2);
ltoken.add(
2,
T.o(T.string,
@@ -1005,7 +1005,7 @@
}
private void replaceCommand(T token) {
- ltoken.remove(0);
+ ltoken.removeItemAt(0);
ltoken.add(0, setCommand(token));
}
@@ -1738,7 +1738,7 @@
&& isFlowIfContextOK(forceFlowContext)) {
flowContext = forceFlowContext;
flowContext.forceEndIf = true;
- lltoken.remove(--iCommand);
+ lltoken.removeItemAt(--iCommand);
} else if (flowContext != null && flowContext.addLine > 0) {
while (flowContext != null && !isFlowIfContextOK(flowContext)) {
if (flowContext.checkForceEndIf(0)) {
@@ -2167,8 +2167,8 @@
if (iBrace <= 0 || vBraces.get(iBrace - 1).tok != T.rightbrace)
return OK;
// time to execute end
- vBraces.remove(--iBrace);
- T token = vBraces.remove(--iBrace);
+ vBraces.removeItemAt(--iBrace);
+ T token = vBraces.removeItemAt(--iBrace);
if (theTok == T.leftbrace) {
//
// }
@@ -2178,7 +2178,7 @@
parenCount--;
}
if (token.tok == T.push) {
- vPush.remove(--pushCount);
+ vPush.removeItemAt(--pushCount);
// close this context
addTokenToPrefix(setCommand(ContextToken.newContext(false)));
isEndOfCommand = true;
@@ -2417,7 +2417,7 @@
case T.process:
case T.whilecmd:
if (!isExplicitEnd)
- vPush.remove(--pushCount);
+ vPush.removeItemAt(--pushCount);
break;
case T.parallel:
case T.function:
@@ -2428,10 +2428,10 @@
lineNumbers, lineIndices, lltoken);
}
thisFunction = (vFunctionStack.size() == 0 ? null
- : (ScriptFunction) vFunctionStack.remove(0));
+ : (ScriptFunction) vFunctionStack.removeItemAt(0));
tokenCommand.intValue = 0;
if (tok == T.trycmd)
- vPush.remove(--pushCount);
+ vPush.removeItemAt(--pushCount);
break;
default:
return errorStr(ERROR_unrecognizedToken, "end " + ident);
Modified: branches/v14_6/Jmol/src/org/jmol/script/ScriptFunction.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/script/ScriptFunction.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/script/ScriptFunction.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -159,7 +159,7 @@
}
}
for (int i = pt; --i >= cmdpt0;) {
- lltoken.remove(i);
+ lltoken.removeItemAt(i);
lineIndices[i][0] = lineIndices[i][1] = 0;
}
}
Modified: branches/v14_6/Jmol/src/org/jmol/script/ScriptManager.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/script/ScriptManager.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/script/ScriptManager.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -183,7 +183,7 @@
for (int i = scriptQueue.size(); --i >= 0;) {
String strScript = (String) (scriptQueue.get(i).get(0));
if (strScript.indexOf(command) == 0) {
- scriptQueue.remove(i);
+ scriptQueue.removeItemAt(i);
if (Logger.debugging)
Logger.debug(scriptQueue.size() + " scripts; removed: " + strScript);
}
Modified: branches/v14_6/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -143,7 +143,7 @@
for (int i = 0; i <= xPt; i++)
result.addLast(isSpecialAssignment ? xStack[i] :
SV.selectItemVar(xStack[i]));
if (lastAssignedString != null) {
- result.remove(0);
+ result.removeItemAt(0);
result.add(0, lastAssignedString);
lastAssignedString.intValue = xStack[0].intValue;
}
Modified: branches/v14_6/Jmol/src/org/jmol/script/ScriptParallelProcessor.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/script/ScriptParallelProcessor.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/script/ScriptParallelProcessor.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -77,7 +77,7 @@
sm.setParallel();
vShapeManagers.addLast(sm);
}
- runProcess(processes.remove(0), sm);
+ runProcess(processes.removeItemAt(0), sm);
}
synchronized (lock) {
Modified: branches/v14_6/Jmol/src/org/jmol/script/ScriptQueueThread.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/script/ScriptQueueThread.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/script/ScriptQueueThread.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -102,7 +102,7 @@
+ "] scripts; running: " + script);
}
//System.out.println("removing: " + scriptItem + " " + script);
- queue.remove(0);
+ queue.removeItemAt(0);
//System.out.println("removed: " + scriptItem);
// if (isScriptFile) {
// script = "script " + PT.esc(script);
Modified: branches/v14_6/Jmol/src/org/jmol/script/ScriptTokenParser.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/script/ScriptTokenParser.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/script/ScriptTokenParser.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -368,7 +368,7 @@
if (token.tok == T.leftsquare && (lastToken.tok == T.per || lastToken.tok
== T.perper)) {
// new notation
int ipt = ltokenPostfix.size() - 1;
- ltokenPostfix.remove(ipt);
+ ltokenPostfix.removeItemAt(ipt);
ltokenPostfix.addLast(T.tokenRightParen);
int pcount = 0;
int tok;
@@ -592,7 +592,7 @@
if (isHash) {
isImplicitExpression = false;
returnToken();
- ltokenPostfix.remove(ltokenPostfix.size() - 1);
+ ltokenPostfix.removeItemAt(ltokenPostfix.size() - 1);
addNextToken();
int nBrace = 1;
while (nBrace != 0) {
Modified: branches/v14_6/Jmol/src/org/jmol/shape/Measures.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/shape/Measures.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/shape/Measures.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -559,7 +559,7 @@
if (i >= measurements.size() || i < 0)
return;
String msg = getMessage(measurements.get(i), true);
- measurements.remove(i);
+ measurements.removeItemAt(i);
measurementCount--;
vwr.setStatusMeasuring("measureDeleted", i, msg, 0);
}
@@ -578,7 +578,7 @@
break;
case T.delete:
String msg = getMessage(measurements.get(i), true);
- measurements.remove(i);
+ measurements.removeItemAt(i);
measurementCount--;
vwr.setStatusMeasuring("measureDeleted", i, msg, 0);
break;
Modified: branches/v14_6/Jmol/src/org/jmol/shape/Shape.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/shape/Shape.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/shape/Shape.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -203,7 +203,7 @@
bsSelected = vwr.bsA();
Lst<Object[]> propertyList = (Lst<Object[]>) value;
while (propertyList.size() > 0) {
- Object[] data = propertyList.remove(0);
+ Object[] data = propertyList.removeItemAt(0);
setProperty(((String) data[0]).intern(), data[1], bsSelected);
}
return;
Modified: branches/v14_6/Jmol/src/org/jmol/shapesurface/Contact.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/shapesurface/Contact.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/shapesurface/Contact.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -464,7 +464,7 @@
}
for (int i = bsBad.length(); --i >= 0;)
if (bsBad.get(i))
- list.remove(i);
+ list.removeItemAt(i);
if (Logger.debugging)
for (int i = 0; i < list.size(); i++)
Logger.debug(list.get(i).toString());
Modified: branches/v14_6/Jmol/src/org/jmol/smiles/SmilesAromatic.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -567,10 +567,10 @@
checkBridges(lstAromatic, bsBad, lstSP2, bsBad2, bs);
for (int i = lstAromatic.size(); --i >= 0;)
if (bsBad.get(i))
- lstAromatic.remove(i);
+ lstAromatic.removeItemAt(i);
for (int i = lstSP2.size(); --i >= 0;)
if (bsBad2.get(i))
- lstSP2.remove(i);
+ lstSP2.removeItemAt(i);
}
private static void checkBridges(Lst<?> lst, BS bsBad, Lst<?> lst2,
Modified: branches/v14_6/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/smiles/SmilesGenerator.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/smiles/SmilesGenerator.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -703,7 +703,7 @@
bondNext = bond0t;
String branch = s2.toString();
// catch is that if there are
- v.remove(i--);
+ v.removeItemAt(i--);
if (bondNext == null)
vBranches.addLast(branch);
else
Modified: branches/v14_6/Jmol/src/org/jmol/util/CommandHistory.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/util/CommandHistory.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/util/CommandHistory.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -94,7 +94,7 @@
if (maxSize < 2)
maxSize = 2;
while (nextCommand > maxSize) {
- commandList.remove(0);
+ commandList.removeItemAt(0);
nextCommand--;
}
if (nextCommand > maxSize)
@@ -228,7 +228,7 @@
public String removeCommand(int n) {
if (n < 0 || n >= nextCommand)
return "";
- String str = commandList.remove(n);
+ String str = commandList.removeItemAt(n);
nextCommand--;
return str;
}
@@ -244,7 +244,7 @@
if (command.endsWith(NOHISTORYLINE_FLAG))
return;
if (nextCommand >= maxSize) {
- commandList.remove(0);
+ commandList.removeItemAt(0);
nextCommand = maxSize - 1;
}
commandList.add(nextCommand, command);
Modified: branches/v14_6/Jmol/src/org/jmol/viewer/OutputManager.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/OutputManager.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/OutputManager.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -276,9 +276,9 @@
return true;
}
objImage = null;
- v.remove(0);
- v.remove(0); // also "_IMAGE_"
- params.put("pngImgData", v.remove(0));
+ v.removeItemAt(0);
+ v.removeItemAt(0); // also "_IMAGE_"
+ params.put("pngImgData", v.removeItemAt(0));
OC oz = getOutputChannel(null, null);
errRet[0] = writeZipFile(oz, v, "OK JMOL", null);
params.put("type", "PNGJ");
@@ -286,7 +286,7 @@
params.put("pngAppPrefix", "Jmol Type");
params.put("pngAppData", oz.toByteArray());
} else if (v.size() == 1) {
- byte[] b = (byte[]) v.remove(0);
+ byte[] b = (byte[]) v.removeItemAt(0);
out.write(b, 0, b.length);
return true;
} else {
Modified: branches/v14_6/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/StateCreator.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/StateCreator.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -1700,7 +1700,7 @@
if (list1.size() == 0 || undoWorking)
return;
undoWorking = true;
- list2.add(0, list1.remove(0));
+ list2.add(0, list1.removeItemAt(0));
s = vwr.actionStatesRedo.get(0);
if (type == T.undomove && list2.size() == 1) {
// must save current state, coord, etc.
@@ -1753,7 +1753,7 @@
vwr.actionStatesRedo.add(1, sb.toString());
}
if (vwr.actionStates.size() == MAX_ACTION_UNDO) {
- vwr.actionStates.remove(MAX_ACTION_UNDO - 1);
+ vwr.actionStates.removeItemAt(MAX_ACTION_UNDO - 1);
}
}
undoWorking = !clearRedo;
Modified: branches/v14_6/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/StatusManager.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/StatusManager.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -198,7 +198,7 @@
if (statusRecordSet == null)
messageQueue.put(statusName, statusRecordSet = new Lst<Lst<Object>>());
else if (statusRecordSet.size() == MAXIMUM_QUEUE_LENGTH)
- statusRecordSet.remove(0);
+ statusRecordSet.removeItemAt(0);
statusRecordSet.addLast(msgRecord);
}
Modified:
branches/v14_6/Jmol/src/org/openscience/jmol/app/nbo/NBOJobQueueManager.java
===================================================================
---
branches/v14_6/Jmol/src/org/openscience/jmol/app/nbo/NBOJobQueueManager.java
2016-08-10 01:21:37 UTC (rev 21194)
+++
branches/v14_6/Jmol/src/org/openscience/jmol/app/nbo/NBOJobQueueManager.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -115,7 +115,7 @@
if (!running || interrupted())
break;
busy = true;
- thisJob = list.remove(0);
+ thisJob = list.removeItemAt(0);
thisJob.service.jobCanceled = false;
thisJob.run();
busy = false;
Deleted: trunk/Jmol/jars/JSpecView.jar
===================================================================
(Binary files differ)
Added: trunk/Jmol/jars/JSpecView.jar
===================================================================
(Binary files differ)
Index: trunk/Jmol/jars/JSpecView.jar
===================================================================
--- trunk/Jmol/jars/JSpecView.jar 2016-08-10 01:21:37 UTC (rev 21194)
+++ trunk/Jmol/jars/JSpecView.jar 2016-08-10 04:55:19 UTC (rev 21195)
Property changes on: trunk/Jmol/jars/JSpecView.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Modified: trunk/Jmol/src/javajs/awt/Container.java
===================================================================
--- trunk/Jmol/src/javajs/awt/Container.java 2016-08-10 01:21:37 UTC (rev
21194)
+++ trunk/Jmol/src/javajs/awt/Container.java 2016-08-10 04:55:19 UTC (rev
21195)
@@ -52,7 +52,7 @@
}
public void remove(int i) {
- Component c = list.remove(i);
+ Component c = list.removeItemAt(i);
c.parent = null;
cList = null;
}
Modified: trunk/Jmol/src/javajs/img/GifEncoder.java
===================================================================
--- trunk/Jmol/src/javajs/img/GifEncoder.java 2016-08-10 01:21:37 UTC (rev
21194)
+++ trunk/Jmol/src/javajs/img/GifEncoder.java 2016-08-10 04:55:19 UTC (rev
21195)
@@ -365,17 +365,17 @@
case 0:
for (int i = n; --i >= 0;)
if (get(i).x >= val)
- newCell.addLast(remove(i));
+ newCell.addLast(removeItemAt(i));
break;
case 1:
for (int i = n; --i >= 0;)
if (get(i).y >= val)
- newCell.addLast(remove(i));
+ newCell.addLast(removeItemAt(i));
break;
case 2:
for (int i = size(); --i >= 0;)
if (get(i).z >= val)
- newCell.addLast(remove(i));
+ newCell.addLast(removeItemAt(i));
break;
}
return true;
Modified: trunk/Jmol/src/javajs/util/Lst.java
===================================================================
--- trunk/Jmol/src/javajs/util/Lst.java 2016-08-10 01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/javajs/util/Lst.java 2016-08-10 04:55:19 UTC (rev 21195)
@@ -65,10 +65,34 @@
* @j2sIgnore
*
*/
+// @Override
+// @Deprecated
+ public V remove(int location) {
+ throw new NullPointerException("use Lst.removeItemAt(location), not
Lst.remove(location)");
+ }
+
+ public V removeItemAt(int location) {
+ /**
+ * no overloading of remove(location) in JavaScript
+ *
+ * @j2sNative
+ *
+ * return this._removeItemAt(location);
+ *
+ */
+ {
+ return super.remove(location);
+ }
+ }
+
+ /**
+ * @j2sIgnore
+ *
+ */
@Override
@Deprecated
public boolean remove(Object v) {
- throw new NullPointerException("use removeObj(obj), not remove(obj) in
List for JavaScript compatibility");
+ throw new NullPointerException("use Lst.removeObj(obj), not
Lst.remove(obj)");
}
public boolean removeObj(Object v) {
@@ -77,7 +101,7 @@
*
* @j2sNative
*
- * return this.removeObject(v);
+ * return this._removeObject(v);
*
*/
{
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -350,7 +350,7 @@
Logger.info("PyMOL Pickle reader cached " + memo.size()
+ " tokens; retrieved " + retrieveCount);
- map = (Map<String, Object>) stack.remove(0);
+ map = (Map<String, Object>) stack.removeItemAt(0);
if (map.size() == 0)
for (i = stack.size(); --i >= 0;) {
o = stack.get(i--);
@@ -398,7 +398,7 @@
for (int i = mark; i < stack.size(); ++i)
args.addLast(stack.get(i));
for (int i = stack.size(); --i >= mark;)
- stack.remove(i);
+ stack.removeItemAt(i);
return args;
}
@@ -444,7 +444,7 @@
}
private int getMark() {
- return marks.remove(--markCount).intValue();
+ return marks.removeItemAt(--markCount).intValue();
}
private void push(Object o) {
@@ -459,7 +459,7 @@
}
private Object pop() {
- return stack.remove(stack.size() - 1);
+ return stack.removeItemAt(stack.size() - 1);
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -481,7 +481,7 @@
String name = stringAt(sceneOrder, i);
Lst<Object> thisScene = getMapList(scenes, name);
if (thisScene == null || thisScene.get(2) == null)
- sceneOrder.remove(i--);
+ sceneOrder.removeItemAt(i--);
}
return (sceneOrder != null && sceneOrder.size() != 0);
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -598,7 +598,7 @@
if (bsInputAtomsIgnore.nextSetBit(0) >= 0)
for (int i = n; --i >= 0;)
if (bsInputAtomsIgnore.get(i))
- vCoords.remove(i);
+ vCoords.removeItemAt(i);
ac = vCoords.size();
Logger.info(nPrim + " primitive atoms and " + ac
+ " conventionalAtoms");
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -261,7 +261,7 @@
if (((Boolean) info.get(i)[2]).booleanValue()
&& info.get(i)[0] instanceof P4) {
volumeData.capData((P4) info.get(i)[0], params.cutoff);
- info.remove(i--);
+ info.removeItemAt(i--);
}
}
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -2612,7 +2612,7 @@
for (int i = list.size(); --i >= 0;) {
Tensor t = (Tensor) list.get(i);
if (bsAtoms.get(t.atomIndex1) || t.atomIndex2 >= 0 &&
bsAtoms.get(t.atomIndex2))
- list.remove(i);
+ list.removeItemAt(i);
}
if (list.size() == 0)
toDelete.addLast(key);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -640,7 +640,7 @@
moleculeCount = 0;
for (int i = stateScripts.size(); --i >= 0;) {
if (stateScripts.get(i).isConnect()) {
- stateScripts.remove(i);
+ stateScripts.removeItemAt(i);
}
}
deleteAllBonds2();
@@ -809,7 +809,7 @@
// correct stateScripts, particularly CONNECT scripts
for (int i = stateScripts.size(); --i >= 0;) {
if (!stateScripts.get(i).deleteAtoms(modelIndex, bsBonds, bsModelAtoms))
{
- stateScripts.remove(i);
+ stateScripts.removeItemAt(i);
}
}
deleteModelAtoms(firstAtomIndex, nAtoms, bsModelAtoms);
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2016-08-10 01:21:37 UTC (rev
21194)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2016-08-10 04:55:19 UTC (rev
21195)
@@ -1524,7 +1524,7 @@
if (i < 0)
i += len;
if (i >= 0 && i < len) {
- v = lst.remove(i);
+ v = lst.removeItemAt(i);
}
} else {
v = m.remove(mapKey.asString());
@@ -1536,7 +1536,7 @@
} else {
Lst<SV> x = getList();
if (value == null || x == null)
- return (x == null || x.size() == 0 ? newS("") : x.remove(x.size() -
1));
+ return (x == null || x.size() == 0 ? newS("") :
x.removeItemAt(x.size() - 1));
x.addLast(newI(0).setv(value));
}
return this;
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -720,7 +720,7 @@
// ...{...
if (lastFlowCommand == null) {
parenCount = setBraceCount = braceCount = 0;
- ltoken.remove(0);
+ ltoken.removeItemAt(0);
T t = ContextToken.newContext(true);
addTokenToPrefix(setCommand(t));
pushContext(t);
@@ -729,7 +729,7 @@
parenCount = setBraceCount = 0;
setCommand(lastFlowCommand);
if (lastFlowCommand.tok != T.process && (tokAt(0) == T.leftbrace))
- ltoken.remove(0);
+ ltoken.removeItemAt(0);
lastFlowCommand = null;
forceFlowContext = flowContext;
// lastFlowImplicitEnd = flowContext.nextFlowImplicitEnd;
@@ -753,7 +753,7 @@
case T.define:
break;
default:
- T t = ltoken.remove(2);
+ T t = ltoken.removeItemAt(2);
ltoken.add(
2,
T.o(T.string,
@@ -1005,7 +1005,7 @@
}
private void replaceCommand(T token) {
- ltoken.remove(0);
+ ltoken.removeItemAt(0);
ltoken.add(0, setCommand(token));
}
@@ -1738,7 +1738,7 @@
&& isFlowIfContextOK(forceFlowContext)) {
flowContext = forceFlowContext;
flowContext.forceEndIf = true;
- lltoken.remove(--iCommand);
+ lltoken.removeItemAt(--iCommand);
} else if (flowContext != null && flowContext.addLine > 0) {
while (flowContext != null && !isFlowIfContextOK(flowContext)) {
if (flowContext.checkForceEndIf(0)) {
@@ -2167,8 +2167,8 @@
if (iBrace <= 0 || vBraces.get(iBrace - 1).tok != T.rightbrace)
return OK;
// time to execute end
- vBraces.remove(--iBrace);
- T token = vBraces.remove(--iBrace);
+ vBraces.removeItemAt(--iBrace);
+ T token = vBraces.removeItemAt(--iBrace);
if (theTok == T.leftbrace) {
//
// }
@@ -2178,7 +2178,7 @@
parenCount--;
}
if (token.tok == T.push) {
- vPush.remove(--pushCount);
+ vPush.removeItemAt(--pushCount);
// close this context
addTokenToPrefix(setCommand(ContextToken.newContext(false)));
isEndOfCommand = true;
@@ -2417,7 +2417,7 @@
case T.process:
case T.whilecmd:
if (!isExplicitEnd)
- vPush.remove(--pushCount);
+ vPush.removeItemAt(--pushCount);
break;
case T.parallel:
case T.function:
@@ -2428,10 +2428,10 @@
lineNumbers, lineIndices, lltoken);
}
thisFunction = (vFunctionStack.size() == 0 ? null
- : (ScriptFunction) vFunctionStack.remove(0));
+ : (ScriptFunction) vFunctionStack.removeItemAt(0));
tokenCommand.intValue = 0;
if (tok == T.trycmd)
- vPush.remove(--pushCount);
+ vPush.removeItemAt(--pushCount);
break;
default:
return errorStr(ERROR_unrecognizedToken, "end " + ident);
Modified: trunk/Jmol/src/org/jmol/script/ScriptFunction.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptFunction.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/script/ScriptFunction.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -159,7 +159,7 @@
}
}
for (int i = pt; --i >= cmdpt0;) {
- lltoken.remove(i);
+ lltoken.removeItemAt(i);
lineIndices[i][0] = lineIndices[i][1] = 0;
}
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptManager.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/script/ScriptManager.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -183,7 +183,7 @@
for (int i = scriptQueue.size(); --i >= 0;) {
String strScript = (String) (scriptQueue.get(i).get(0));
if (strScript.indexOf(command) == 0) {
- scriptQueue.remove(i);
+ scriptQueue.removeItemAt(i);
if (Logger.debugging)
Logger.debug(scriptQueue.size() + " scripts; removed: " + strScript);
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -143,7 +143,7 @@
for (int i = 0; i <= xPt; i++)
result.addLast(isSpecialAssignment ? xStack[i] :
SV.selectItemVar(xStack[i]));
if (lastAssignedString != null) {
- result.remove(0);
+ result.removeItemAt(0);
result.add(0, lastAssignedString);
lastAssignedString.intValue = xStack[0].intValue;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptParallelProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptParallelProcessor.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/org/jmol/script/ScriptParallelProcessor.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -77,7 +77,7 @@
sm.setParallel();
vShapeManagers.addLast(sm);
}
- runProcess(processes.remove(0), sm);
+ runProcess(processes.removeItemAt(0), sm);
}
synchronized (lock) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptQueueThread.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptQueueThread.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/org/jmol/script/ScriptQueueThread.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -102,7 +102,7 @@
+ "] scripts; running: " + script);
}
//System.out.println("removing: " + scriptItem + " " + script);
- queue.remove(0);
+ queue.removeItemAt(0);
//System.out.println("removed: " + scriptItem);
// if (isScriptFile) {
// script = "script " + PT.esc(script);
Modified: trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java 2016-08-10
01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java 2016-08-10
04:55:19 UTC (rev 21195)
@@ -368,7 +368,7 @@
if (token.tok == T.leftsquare && (lastToken.tok == T.per || lastToken.tok
== T.perper)) {
// new notation
int ipt = ltokenPostfix.size() - 1;
- ltokenPostfix.remove(ipt);
+ ltokenPostfix.removeItemAt(ipt);
ltokenPostfix.addLast(T.tokenRightParen);
int pcount = 0;
int tok;
@@ -592,7 +592,7 @@
if (isHash) {
isImplicitExpression = false;
returnToken();
- ltokenPostfix.remove(ltokenPostfix.size() - 1);
+ ltokenPostfix.removeItemAt(ltokenPostfix.size() - 1);
addNextToken();
int nBrace = 1;
while (nBrace != 0) {
Modified: trunk/Jmol/src/org/jmol/shape/Measures.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Measures.java 2016-08-10 01:21:37 UTC (rev
21194)
+++ trunk/Jmol/src/org/jmol/shape/Measures.java 2016-08-10 04:55:19 UTC (rev
21195)
@@ -559,7 +559,7 @@
if (i >= measurements.size() || i < 0)
return;
String msg = getMessage(measurements.get(i), true);
- measurements.remove(i);
+ measurements.removeItemAt(i);
measurementCount--;
vwr.setStatusMeasuring("measureDeleted", i, msg, 0);
}
@@ -578,7 +578,7 @@
break;
case T.delete:
String msg = getMessage(measurements.get(i), true);
- measurements.remove(i);
+ measurements.removeItemAt(i);
measurementCount--;
vwr.setStatusMeasuring("measureDeleted", i, msg, 0);
break;
Modified: trunk/Jmol/src/org/jmol/shape/Shape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Shape.java 2016-08-10 01:21:37 UTC (rev
21194)
+++ trunk/Jmol/src/org/jmol/shape/Shape.java 2016-08-10 04:55:19 UTC (rev
21195)
@@ -203,7 +203,7 @@
bsSelected = vwr.bsA();
Lst<Object[]> propertyList = (Lst<Object[]>) value;
while (propertyList.size() > 0) {
- Object[] data = propertyList.remove(0);
+ Object[] data = propertyList.removeItemAt(0);
setProperty(((String) data[0]).intern(), data[1], bsSelected);
}
return;
Modified: trunk/Jmol/src/org/jmol/shapesurface/Contact.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Contact.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/shapesurface/Contact.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -464,7 +464,7 @@
}
for (int i = bsBad.length(); --i >= 0;)
if (bsBad.get(i))
- list.remove(i);
+ list.removeItemAt(i);
if (Logger.debugging)
for (int i = 0; i < list.size(); i++)
Logger.debug(list.get(i).toString());
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -567,10 +567,10 @@
checkBridges(lstAromatic, bsBad, lstSP2, bsBad2, bs);
for (int i = lstAromatic.size(); --i >= 0;)
if (bsBad.get(i))
- lstAromatic.remove(i);
+ lstAromatic.removeItemAt(i);
for (int i = lstSP2.size(); --i >= 0;)
if (bsBad2.get(i))
- lstSP2.remove(i);
+ lstSP2.removeItemAt(i);
}
private static void checkBridges(Lst<?> lst, BS bsBad, Lst<?> lst2,
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -703,7 +703,7 @@
bondNext = bond0t;
String branch = s2.toString();
// catch is that if there are
- v.remove(i--);
+ v.removeItemAt(i--);
if (bondNext == null)
vBranches.addLast(branch);
else
Modified: trunk/Jmol/src/org/jmol/util/CommandHistory.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/CommandHistory.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/util/CommandHistory.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -94,7 +94,7 @@
if (maxSize < 2)
maxSize = 2;
while (nextCommand > maxSize) {
- commandList.remove(0);
+ commandList.removeItemAt(0);
nextCommand--;
}
if (nextCommand > maxSize)
@@ -228,7 +228,7 @@
public String removeCommand(int n) {
if (n < 0 || n >= nextCommand)
return "";
- String str = commandList.remove(n);
+ String str = commandList.removeItemAt(n);
nextCommand--;
return str;
}
@@ -244,7 +244,7 @@
if (command.endsWith(NOHISTORYLINE_FLAG))
return;
if (nextCommand >= maxSize) {
- commandList.remove(0);
+ commandList.removeItemAt(0);
nextCommand = maxSize - 1;
}
commandList.add(nextCommand, command);
Modified: trunk/Jmol/src/org/jmol/viewer/OutputManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -276,9 +276,9 @@
return true;
}
objImage = null;
- v.remove(0);
- v.remove(0); // also "_IMAGE_"
- params.put("pngImgData", v.remove(0));
+ v.removeItemAt(0);
+ v.removeItemAt(0); // also "_IMAGE_"
+ params.put("pngImgData", v.removeItemAt(0));
OC oz = getOutputChannel(null, null);
errRet[0] = writeZipFile(oz, v, "OK JMOL", null);
params.put("type", "PNGJ");
@@ -286,7 +286,7 @@
params.put("pngAppPrefix", "Jmol Type");
params.put("pngAppData", oz.toByteArray());
} else if (v.size() == 1) {
- byte[] b = (byte[]) v.remove(0);
+ byte[] b = (byte[]) v.removeItemAt(0);
out.write(b, 0, b.length);
return true;
} else {
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -1700,7 +1700,7 @@
if (list1.size() == 0 || undoWorking)
return;
undoWorking = true;
- list2.add(0, list1.remove(0));
+ list2.add(0, list1.removeItemAt(0));
s = vwr.actionStatesRedo.get(0);
if (type == T.undomove && list2.size() == 1) {
// must save current state, coord, etc.
@@ -1753,7 +1753,7 @@
vwr.actionStatesRedo.add(1, sb.toString());
}
if (vwr.actionStates.size() == MAX_ACTION_UNDO) {
- vwr.actionStates.remove(MAX_ACTION_UNDO - 1);
+ vwr.actionStates.removeItemAt(MAX_ACTION_UNDO - 1);
}
}
undoWorking = !clearRedo;
Modified: trunk/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2016-08-10 01:21:37 UTC
(rev 21194)
+++ trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2016-08-10 04:55:19 UTC
(rev 21195)
@@ -198,7 +198,7 @@
if (statusRecordSet == null)
messageQueue.put(statusName, statusRecordSet = new Lst<Lst<Object>>());
else if (statusRecordSet.size() == MAXIMUM_QUEUE_LENGTH)
- statusRecordSet.remove(0);
+ statusRecordSet.removeItemAt(0);
statusRecordSet.addLast(msgRecord);
}
Modified: trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOJobQueueManager.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOJobQueueManager.java
2016-08-10 01:21:37 UTC (rev 21194)
+++ trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOJobQueueManager.java
2016-08-10 04:55:19 UTC (rev 21195)
@@ -115,7 +115,7 @@
if (!running || interrupted())
break;
busy = true;
- thisJob = list.remove(0);
+ thisJob = list.removeItemAt(0);
thisJob.service.jobCanceled = false;
thisJob.run();
busy = false;
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