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[Jmol-commits] SF.net SVN: jmol:[17557] trunk/Jmol/src/org/jmol
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From: <ha...@us...> - 2012-09-12 11:46:04
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Revision: 17557
http://jmol.svn.sourceforge.net/jmol/?rev=17557&view=rev
Author: hansonr
Date: 2012-09-12 11:45:51 +0000 (Wed, 12 Sep 2012)
Log Message:
-----------
Refactoring for JavaScript
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/Group.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptFunction.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/script/ScriptVariable.java
trunk/Jmol/src/org/jmol/script/Token.java
trunk/Jmol/src/org/jmol/util/JmolFont.java
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Added Paths:
-----------
trunk/Jmol/src/org/jmol/script/ScriptVariableInt.java
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -332,20 +332,20 @@
private final static Token[][] tokenTypes = new Token[][] {
/*0*/ new Token[]{
Token.tokenExpressionBegin,
- new Token(Token.opEQ, Token.elemno),
+ Token.newToken(Token.opEQ, Token.elemno),
Token.intToken(0), //2
Token.tokenExpressionEnd},
/*1*/ new Token[]{
Token.tokenExpressionBegin,
- new Token(Token.opEQ, Token.elemno),
+ Token.newToken(Token.opEQ, Token.elemno),
Token.intToken(0), //2
Token.tokenAnd,
- new Token(Token.opEQ, Token.formalcharge),
+ Token.newToken(Token.opEQ, Token.formalcharge),
Token.intToken(0), //5
Token.tokenExpressionEnd},
/*2*/ new Token[]{
Token.tokenExpressionBegin,
- new Token(Token.opEQ, Token.elemno),
+ Token.newToken(Token.opEQ, Token.elemno),
Token.intToken(0) , // 2
Token.tokenAnd,
Token.tokenConnected,
@@ -359,7 +359,7 @@
Token.tokenExpressionEnd},
/*4*/ new Token[]{ //sp == connected(1,"triple") or connected(2, "double")
Token.tokenExpressionBegin,
- new Token(Token.opEQ, Token.elemno),
+ Token.newToken(Token.opEQ, Token.elemno),
Token.intToken(0) , // 2
Token.tokenAnd,
Token.tokenLeftParen,
@@ -380,7 +380,7 @@
Token.tokenExpressionEnd},
/*5*/ new Token[]{ // sp2 == connected(1, double)
Token.tokenExpressionBegin,
- new Token(Token.opEQ, Token.elemno),
+ Token.newToken(Token.opEQ, Token.elemno),
Token.intToken(0) , // 2
Token.tokenAnd,
new Token(Token.connected, "connected"),
@@ -392,7 +392,7 @@
Token.tokenExpressionEnd},
/*6*/ new Token[]{ //Nv vinylic == connected(3) && connected(connected("double"))
Token.tokenExpressionBegin,
- new Token(Token.opEQ, Token.elemno),
+ Token.newToken(Token.opEQ, Token.elemno),
Token.intToken(0) , // 2
Token.tokenAnd,
Token.tokenConnected,
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -58,7 +58,7 @@
public static final int RADIUS_MAX = 16;
- char alternateLocationID;
+ char alternateLocationID = '\0';
public byte atomID;
int atomSite;
Group group;
@@ -108,7 +108,7 @@
float x, float y, float z, float radius,
BitSet atomSymmetry, int atomSite,
short atomicAndIsotopeNumber, int formalCharge,
- boolean isHetero, char alternateLocationID) {
+ boolean isHetero) {
this.modelIndex = (short)modelIndex;
this.atomSymmetry = atomSymmetry;
this.atomSite = atomSite;
@@ -117,11 +117,18 @@
if (isHetero)
formalChargeAndFlags = IS_HETERO_FLAG;
setFormalCharge(formalCharge);
- this.alternateLocationID = alternateLocationID;
userDefinedVanDerWaalRadius = radius;
set(x, y, z);
}
+ public void setAltLoc(String altLoc) {
+ alternateLocationID = altLoc.charAt(0);
+ }
+
+ public void setAltLoc(char altLoc) {
+ alternateLocationID = altLoc;
+ }
+
public final void setShapeVisibilityFlags(int flag) {
shapeVisibilityFlags = flag;
}
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -1903,9 +1903,6 @@
// categorization is done simply by listing
// the number of 90, 120, and 180 angles.
n = ntypes[_90] * 100 + ntypes[_120] * 10 + ntypes[_180];
- if (Logger.debugging)
- Logger.debug("lcaoCartoon type is " + n);
-
if (z == null) {
// just return geometry
switch (n) {
Modified: trunk/Jmol/src/org/jmol/modelset/Group.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Group.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/modelset/Group.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -303,7 +303,20 @@
return getSeqcodeString(seqcode);
}
+ /**
+ * necessary for JavaScript due to problem with char
+ * @param sequenceNumber
+ * @param insertionCode
+ * @return seqcode << 8 + insertionCode
+ */
+ public static int getSeqcode(int sequenceNumber, String insertionCode) {
+ return getSeqcode2(sequenceNumber, insertionCode.charAt(0));
+ }
+
public static int getSeqcode(int sequenceNumber, char insertionCode) {
+ return getSeqcode2(sequenceNumber, insertionCode);
+ }
+ public static int getSeqcode2(int sequenceNumber, char insertionCode) {
if (sequenceNumber == Integer.MIN_VALUE)
return sequenceNumber;
if (! ((insertionCode >= 'A' && insertionCode <= 'Z') ||
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -4069,7 +4069,7 @@
int atomSerial, int atomSite, float x, float y, float z) {
return addAtom(modelIndex, group, atomicAndIsotopeNumber, atomName,
atomSerial, atomSite, x, y, z, Float.NaN, Float.NaN, Float.NaN,
- Float.NaN, 0, 0, 100, Float.NaN, null, false, '\0', (byte) 0, null);
+ Float.NaN, 0, 0, 100, Float.NaN, null, false, (byte) 0, null);
}
public Atom addAtom(int modelIndex, Group group,
@@ -4078,11 +4078,9 @@
float radius, float vectorX, float vectorY,
float vectorZ, int formalCharge, float partialCharge,
int occupancy, float bfactor, Quadric[] ellipsoid,
- boolean isHetero, char alternateLocationID,
- byte specialAtomID, BitSet atomSymmetry) {
+ boolean isHetero, byte specialAtomID, BitSet atomSymmetry) {
Atom atom = new Atom(modelIndex, atomCount, x, y, z, radius, atomSymmetry,
- atomSite, atomicAndIsotopeNumber, formalCharge, isHetero,
- alternateLocationID);
+ atomSite, atomicAndIsotopeNumber, formalCharge, isHetero);
models[modelIndex].atomCount++;
models[modelIndex].bsAtoms.set(atomCount);
if (atomicAndIsotopeNumber % 128 == 1)
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -835,7 +835,8 @@
Atom atom = modelSet.addAtom(currentModelIndex, nullGroup, atomicAndIsotopeNumber,
atomName, atomSerial, atomSite, x, y, z, radius, vectorX, vectorY,
vectorZ, formalCharge, partialCharge, occupancy, bfactor, ellipsoid,
- isHetero, alternateLocationID, specialAtomID, atomSymmetry);
+ isHetero, specialAtomID, atomSymmetry);
+ atom.setAltLoc(alternateLocationID);
htAtomMap.put(atomUid, atom);
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -226,7 +226,7 @@
for (int i = 0; i < nH; i++)
modelSet.addAtom(modelSet.atoms[iFirst].modelIndex, modelSet.atoms[iFirst].getGroup(), (short) 1, "H", 0,
0, Float.NaN, Float.NaN, Float.NaN, Float.NaN, Float.NaN, Float.NaN, Float.NaN, 0, 0, 1, 0,
- null, isHetero, '\0', (byte) 0, null).delete(null);
+ null, isHetero, (byte) 0, null).delete(null);
}
public void getBondInfo(JmolAdapter adapter, String group3, Object model) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -993,7 +993,7 @@
if (iident == Integer.MIN_VALUE || Math.abs(iident) < 1000)
addTokenToPrefix(new Token(Token.identifier, ident));
else
- addTokenToPrefix(new Token(Token.integer, iident));
+ addTokenToPrefix(Token.intToken(iident));
return CONTINUE;
}
switch (tokCommand) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -847,7 +847,7 @@
break;
case Token.spec_seqcode:
case Token.integer:
- rpn.addXNum(ScriptVariable.intVariable(theToken.intValue));
+ rpn.addXNum(new ScriptVariableInt(theToken.intValue));
break;
// these next are for the within() command
case Token.plane:
@@ -2069,8 +2069,7 @@
ScriptContext sc = getScriptContext();
if (isTry) {
- contextVariables.put("_breakval", ScriptVariable
- .intVariable(Integer.MAX_VALUE));
+ contextVariables.put("_breakval", new ScriptVariableInt(Integer.MAX_VALUE));
contextVariables.put("_errorval", ScriptVariable.getVariable(""));
viewer.resetError();
parallelProcessor.addProcess("try", sc);
@@ -3397,7 +3396,7 @@
private boolean isBondSet;
private Object expressionResult;
- private BitSet atomExpression(int index) throws ScriptException {
+ private BitSet atomExpressionAt(int index) throws ScriptException {
if (!checkToken(index))
error(ERROR_badArgumentCount, index);
return atomExpression(statement, index, 0, true, false, true, true);
@@ -3628,16 +3627,16 @@
break;
case Token.spec_seqcode:
if (isInMath)
- rpn.addXNum(ScriptVariable.intVariable(instruction.intValue));
+ rpn.addXNum(new ScriptVariableInt(instruction.intValue));
else
rpn.addXBs(getAtomBits(Token.spec_seqcode, new Integer(
getSeqCode(instruction))));
break;
case Token.spec_seqcode_range:
if (isInMath) {
- rpn.addXNum(ScriptVariable.intVariable(instruction.intValue));
+ rpn.addXNum(new ScriptVariableInt(instruction.intValue));
rpn.addXObj(Token.tokenMinus);
- rpn.addXNum(ScriptVariable.intVariable(code[++pc].intValue));
+ rpn.addXNum(new ScriptVariableInt(code[++pc].intValue));
break;
}
int chainID = (pc + 3 < code.length && code[pc + 2].tok == Token.opAND
@@ -5952,7 +5951,7 @@
case Token.in:
nSkip -= 2;
if (tokAt(++i) == Token.expressionBegin || tokAt(i) == Token.bitset) {
- bsOrList = atomExpression(i);
+ bsOrList = atomExpressionAt(i);
if (isBondSet)
bsOrList = new BondSet((BitSet) bsOrList);
} else {
@@ -6256,7 +6255,7 @@
if (isSyntaxCheck)
return;
if (tv == null)
- tv = (v == null ? ScriptVariable.intVariable(0) : v);
+ tv = (v == null ? new ScriptVariableInt(0) : v);
t.value = tv.value;
t.intValue = tv.intValue;
t.tok = tv.tok;
@@ -6628,7 +6627,7 @@
case Token.trace:
Point3f[][] pathGuide;
List<Point3f[]> vp = new ArrayList<Point3f[]>();
- BitSet bs = atomExpression(++i);
+ BitSet bs = atomExpressionAt(++i);
i = iToken;
if (isSyntaxCheck)
return;
@@ -6832,8 +6831,8 @@
BitSet bsAtoms1 = null, bsAtoms2 = null;
List<BitSet[]> vAtomSets = null;
List<Object[]> vQuatSets = null;
- BitSet bsFrom = (tokAt(1) == Token.subset ? null : atomExpression(1));
- BitSet bsTo = (tokAt(++iToken) == Token.subset ? null : atomExpression(iToken));
+ BitSet bsFrom = (tokAt(1) == Token.subset ? null : atomExpressionAt(1));
+ BitSet bsTo = (tokAt(++iToken) == Token.subset ? null : atomExpressionAt(iToken));
if (bsFrom == null || bsTo == null)
error(ERROR_invalidArgument);
BitSet bsSubset = null;
@@ -6863,16 +6862,16 @@
case Token.comma:
break;
case Token.subset:
- bsSubset = atomExpression(++i);
+ bsSubset = atomExpressionAt(++i);
i = iToken;
break;
case Token.bitset:
case Token.expressionBegin:
if (vQuatSets != null)
error(ERROR_invalidArgument);
- bsAtoms1 = atomExpression(iToken);
+ bsAtoms1 = atomExpressionAt(iToken);
int tok = (isToSubsetOfFrom ? 0 : tokAt(iToken + 1));
- bsAtoms2 = (tok == Token.bitset || tok == Token.expressionBegin ? atomExpression(++iToken)
+ bsAtoms2 = (tok == Token.bitset || tok == Token.expressionBegin ? atomExpressionAt(++iToken)
: BitSetUtil.copy(bsAtoms1));
if (bsSubset != null) {
bsAtoms1.and(bsSubset);
@@ -7268,7 +7267,7 @@
error(ERROR_badArgumentCount);
if (haveType || isColorOrRadius)
error(ERROR_invalidParameterOrder);
- atomSets[nAtomSets++] = atomExpression(i);
+ atomSets[nAtomSets++] = atomExpressionAt(i);
isBonds = isBondSet;
if (nAtomSets == 2) {
int pt = iToken;
@@ -7428,7 +7427,7 @@
.nextSetBit(atom1 + 1)) {
bs.set(atom1);
result = viewer.makeConnections(distances[0], distances[1], bondOrder,
- operation, bs, atomExpression(expression2), bsBonds, isBonds,
+ operation, bs, atomExpressionAt(expression2), bsBonds, isBonds,
false, 0);
nNew += Math.abs(result[0]);
nModified += result[1];
@@ -7486,7 +7485,7 @@
int propertyID = PropertyManager.getPropertyNumber(name);
String param = optParameterAsString(2);
int tok = tokAt(2);
- BitSet bs = (tok == Token.expressionBegin || tok == Token.bitset ? atomExpression(2)
+ BitSet bs = (tok == Token.expressionBegin || tok == Token.bitset ? atomExpressionAt(2)
: null);
if (property.length() > 0 && propertyID < 0) {
// no such property
@@ -7822,7 +7821,7 @@
boolean doClearBondSet = false;
float translucentLevel = Float.MAX_VALUE;
if (index < 0) {
- bs = atomExpression(-index);
+ bs = atomExpressionAt(-index);
index = iToken + 1;
if (isBondSet) {
doClearBondSet = true;
@@ -7852,7 +7851,7 @@
bs = (BondSet) theToken.value;
prefix = "vertex";
} else {
- bs = atomExpression(index);
+ bs = atomExpressionAt(index);
// don't allow isosurface partial translucency (yet)
prefix = "atom";
}
@@ -8133,15 +8132,15 @@
while (true) {
if (tokAt(1) == Token.selected) {
bsFrom = viewer.getSelectionSet(false);
- bsTo = atomExpression(2);
+ bsTo = atomExpressionAt(2);
property1 = property2 = "selected";
} else {
- bsFrom = atomExpression(1);
+ bsFrom = atomExpressionAt(1);
if (tokAt(++iToken) != Token.per
|| !Token.tokAttr(tokProp1 = tokAt(++iToken), Token.atomproperty))
break;
property1 = parameterAsString(iToken);
- bsTo = atomExpression(++iToken);
+ bsTo = atomExpressionAt(++iToken);
if (tokAt(++iToken) != Token.per
|| !Token.tokAttr(tokProp2 = tokAt(++iToken), Token.settable))
break;
@@ -8407,7 +8406,7 @@
//if (!isSite)
//viewer.addStateScript(thisCommand, false, true); removed for 12.1.16
} else {
- BitSet bs = atomExpression(2);
+ BitSet bs = atomExpressionAt(2);
definedAtomSets.put(setName, bs);
if (!isSyntaxCheck)
viewer.setUserVariable("@" + setName, ScriptVariable.getVariable(bs));
@@ -10030,7 +10029,7 @@
case Token.dollarsign:
if (tok == Token.bitset || tok == Token.expressionBegin) {
if (translation != null || q != null || nPoints == 2) {
- bsAtoms = atomExpression(i);
+ bsAtoms = atomExpressionAt(i);
ptsB = null;
isSelected = true;
break;
@@ -10131,8 +10130,8 @@
break;
case Token.branch:
haveRotation = true;
- int iAtom1 = atomExpression(++i).nextSetBit(0);
- int iAtom2 = atomExpression(++iToken).nextSetBit(0);
+ int iAtom1 = atomExpressionAt(++i).nextSetBit(0);
+ int iAtom2 = atomExpressionAt(++iToken).nextSetBit(0);
if (iAtom1 < 0 || iAtom2 < 0)
return;
bsAtoms = viewer.getBranchBitSet(iAtom2, iAtom1);
@@ -10190,7 +10189,7 @@
case Token.matrix3f:
haveRotation = true;
if (tok == Token.compare) {
- bsCompare = atomExpression(++i);
+ bsCompare = atomExpressionAt(++i);
ptsA = viewer.getAtomPointVector(bsCompare);
if (ptsA == null)
error(ERROR_invalidArgument, i);
@@ -10360,7 +10359,7 @@
return data;
}
if (i > 0)
- return viewer.getAtomPointVector(atomExpression(i));
+ return viewer.getAtomPointVector(atomExpressionAt(i));
return null;
}
@@ -10652,7 +10651,7 @@
bs = new BondSet(BitSetUtil.newBitSet(0, viewer.getModelSet()
.getBondCount()));
else
- bs = atomExpression(i);
+ bs = atomExpressionAt(i);
}
if (isSyntaxCheck)
return;
@@ -10717,7 +10716,7 @@
checkLength(3);
} else {
while (n < 4 && !isFloatParameter(i)) {
- aList[++n] = atomExpression(i).nextSetBit(0);
+ aList[++n] = atomExpressionAt(i).nextSetBit(0);
i = iToken + 1;
}
aList[0] = n;
@@ -10738,7 +10737,7 @@
case Token.fixed:
if (i != 1)
error(ERROR_invalidArgument);
- bsFixed = atomExpression(++i);
+ bsFixed = atomExpressionAt(++i);
if (bsFixed.nextSetBit(0) < 0)
bsFixed = null;
i = iToken;
@@ -10748,7 +10747,7 @@
return;
continue;
case Token.select:
- bsSelected = atomExpression(++i);
+ bsSelected = atomExpressionAt(++i);
i = iToken;
continue;
case Token.silent:
@@ -10816,7 +10815,7 @@
isGroup = (tok == Token.group);
if (isGroup)
tok = tokAt(++i);
- bs = atomExpression(i);
+ bs = atomExpressionAt(i);
}
if (isSyntaxCheck)
return;
@@ -10839,7 +10838,7 @@
viewer.setSelectionSubset(null);
if (statementLength != 1
&& (statementLength != 4 || !getToken(2).value.equals("off")))
- bs = atomExpression(1);
+ bs = atomExpressionAt(1);
if (!isSyntaxCheck)
viewer.setSelectionSubset(bs);
}
@@ -10862,9 +10861,9 @@
viewer.invertAtomCoord(pt, bs);
return;
case Token.stereo:
- iAtom = atomExpression(2).nextSetBit(0);
+ iAtom = atomExpressionAt(2).nextSetBit(0);
// and only these:
- bs = atomExpression(iToken + 1);
+ bs = atomExpressionAt(iToken + 1);
break;
case Token.point:
pt = centerParameter(2);
@@ -10902,7 +10901,7 @@
}
if (isPoint3f(i)) {
Point3f pt = getPoint3f(i, true);
- bs = (!isSelected && iToken + 1 < statementLength ? atomExpression(++iToken)
+ bs = (!isSelected && iToken + 1 < statementLength ? atomExpressionAt(++iToken)
: null);
checkLast(iToken);
if (!isSyntaxCheck)
@@ -10927,7 +10926,7 @@
return;
iToken = i0 + (type == '\0' ? 2 : 3);
bs = (isSelected ? viewer.getSelectionSet(false)
- : iToken + 1 < statementLength ? atomExpression(++iToken) : null);
+ : iToken + 1 < statementLength ? atomExpressionAt(++iToken) : null);
checkLast(iToken);
if (!isSyntaxCheck)
viewer.translate(xyz, amount, type, bs);
@@ -10939,7 +10938,7 @@
refresh();
return;
}
- BitSet bs = atomExpression(1);
+ BitSet bs = atomExpressionAt(1);
if (isSyntaxCheck)
return;
int nDeleted = viewer.deleteAtoms(bs, true);
@@ -11024,7 +11023,7 @@
if (!viewer.isWindowCentered()) {
// do a smooth zoom only if not windowCentered
if (center != null) {
- BitSet bs = atomExpression(ptCenter);
+ BitSet bs = atomExpressionAt(ptCenter);
if (!isSyntaxCheck)
viewer.setCenterBitSet(bs, false);
}
@@ -11538,7 +11537,7 @@
switch (tokAt(2)) {
case Token.bitset:
case Token.expressionBegin:
- bs = atomExpression(2);
+ bs = atomExpressionAt(2);
checkLast(iToken);
break;
default:
@@ -11710,7 +11709,7 @@
case Token.expressionBegin:
if (propertyName == null)
propertyName = (iHaveAtoms || iHaveCoord ? "endSet" : "startSet");
- propertyValue = atomExpression(i);
+ propertyValue = atomExpressionAt(i);
i = iToken;
iHaveAtoms = true;
break;
@@ -11905,23 +11904,23 @@
if (asDSSP)
bs1 = viewer.getSelectionSet(false);
else
- bs1 = atomExpression(iToken);
+ bs1 = atomExpressionAt(iToken);
if (!asDSSP && !(asDSSP = (tokAt(++iToken) == Token.structure)))
- bs2 = atomExpression(iToken);
+ bs2 = atomExpressionAt(iToken);
if (!isSyntaxCheck) {
n = viewer.autoHbond(bs1, bs2, false);
break;
}
return;
case Token.hydrogen:
- bs = (statementLength == 2 ? null : atomExpression(2));
+ bs = (statementLength == 2 ? null : atomExpressionAt(2));
checkLast(iToken);
if (!isSyntaxCheck)
viewer.addHydrogens(bs, false, false);
return;
case Token.partialcharge:
iToken = 1;
- bs = (statementLength == 2 ? null : atomExpression(2));
+ bs = (statementLength == 2 ? null : atomExpressionAt(2));
checkLast(iToken);
if (!isSyntaxCheck)
viewer.calculatePartialCharges(bs);
@@ -11939,7 +11938,7 @@
}
return;
case Token.structure:
- bs = (statementLength < 4 ? null : atomExpression(2));
+ bs = (statementLength < 4 ? null : atomExpressionAt(2));
switch (tokAt(++iToken)) {
case Token.ramachandran:
break;
@@ -11956,8 +11955,8 @@
showString(viewer.calculateStructures(bs, asDSSP, true));
return;
case Token.struts:
- bs = (iToken + 1 < statementLength ? atomExpression(++iToken) : null);
- bs2 = (iToken + 1 < statementLength ? atomExpression(++iToken) : null);
+ bs = (iToken + 1 < statementLength ? atomExpressionAt(++iToken) : null);
+ bs2 = (iToken + 1 < statementLength ? atomExpressionAt(++iToken) : null);
checkLength(++iToken);
if (!isSyntaxCheck) {
n = viewer.calculateStruts(bs, bs2);
@@ -11993,7 +11992,7 @@
default:
isFrom = true;
}
- bs = (iToken + 1 < statementLength ? atomExpression(++iToken) : viewer
+ bs = (iToken + 1 < statementLength ? atomExpressionAt(++iToken) : viewer
.getSelectionSet(false));
checkLength(++iToken);
if (!isSyntaxCheck)
@@ -12164,13 +12163,13 @@
private void assign() throws ScriptException {
int atomsOrBonds = tokAt(1);
- int index = atomExpression(2).nextSetBit(0);
+ int index = atomExpressionAt(2).nextSetBit(0);
int index2 = -1;
String type = null;
if (index < 0)
error(ERROR_invalidArgument);
if (atomsOrBonds == Token.connect) {
- index2 = atomExpression(++iToken).nextSetBit(0);
+ index2 = atomExpressionAt(++iToken).nextSetBit(0);
} else {
type = parameterAsString(++iToken);
}
@@ -12210,7 +12209,7 @@
}
private void fixed() throws ScriptException {
- BitSet bs = (statementLength == 1 ? null : atomExpression(1));
+ BitSet bs = (statementLength == 1 ? null : atomExpressionAt(1));
if (isSyntaxCheck)
return;
viewer.setMotionFixedAtoms(bs);
@@ -12231,7 +12230,7 @@
switch (tokAt(1)) {
case Token.expressionBegin:
case Token.bitset:
- int i = atomExpression(1).nextSetBit(0);
+ int i = atomExpressionAt(1).nextSetBit(0);
checkLength(iToken + 1);
if (isSyntaxCheck || i < 0)
return;
@@ -12269,7 +12268,7 @@
return;
case Token.align:
BitSet bs = (statementLength == 2 || tokAt(2) == Token.none ? null
- : atomExpression(2));
+ : atomExpressionAt(2));
if (!isSyntaxCheck)
viewer.setFrameOffsets(bs);
return;
@@ -12630,7 +12629,7 @@
case Token.highlight:
shapeManager.loadShape(JmolConstants.SHAPE_HALOS);
setShapeProperty(JmolConstants.SHAPE_HALOS, "highlight",
- (tokAt(2) == Token.off ? null : atomExpression(2)));
+ (tokAt(2) == Token.off ? null : atomExpressionAt(2)));
return;
case Token.display:// deprecated
case Token.selectionhalos:
@@ -13266,7 +13265,7 @@
}
if (str.equals("toggle")) {
iToken = 1;
- BitSet bs = (statementLength == 2 ? null : atomExpression(2));
+ BitSet bs = (statementLength == 2 ? null : atomExpressionAt(2));
checkLast(iToken);
if (!isSyntaxCheck)
viewer.togglePickingLabel(bs);
@@ -13291,7 +13290,7 @@
}
return false;
}
- BitSet bs = (iToken + 1 < statementLength ? atomExpression(++iToken) : null);
+ BitSet bs = (iToken + 1 < statementLength ? atomExpressionAt(++iToken) : null);
checkLast(iToken);
if (isSyntaxCheck)
return true;
@@ -13578,7 +13577,7 @@
ScriptVariable t = (settingData ? null : getContextVariableAsVariable(key));
boolean isUserVariable = (t != null);
if (pt > 0 && tokAt(pt - 1) == Token.expressionBegin) {
- bs = atomExpression(pt - 1);
+ bs = atomExpressionAt(pt - 1);
pt = iToken + 1;
isExpression = true;
}
@@ -15159,9 +15158,9 @@
iConnect = 0;
connections = new int[] { -1, -1, -1, -1 };
}
- connections[iConnect++] = atomExpression(++i).nextSetBit(0);
+ connections[iConnect++] = atomExpressionAt(++i).nextSetBit(0);
i = iToken;
- connections[iConnect++] = (theTok == Token.bonds ? atomExpression(++i)
+ connections[iConnect++] = (theTok == Token.bonds ? atomExpressionAt(++i)
.nextSetBit(0) : -1);
i = iToken;
havePoints = true;
@@ -15276,7 +15275,7 @@
// draw ID xxx symop [n or "x,-y,-z"] [optional {center}]
// so we also check here for the atom set to get the right model
bsAtoms = (tokAt(i) == Token.bitset
- || tokAt(i) == Token.expressionBegin ? atomExpression(i) : null);
+ || tokAt(i) == Token.expressionBegin ? atomExpressionAt(i) : null);
i = iToken + 1;
}
checkLast(iToken);
@@ -15346,7 +15345,7 @@
case Token.bitset:
case Token.expressionBegin:
propertyName = "atomSet";
- propertyValue = atomExpression(i);
+ propertyValue = atomExpressionAt(i);
if (isFrame)
center = centerParameter(i);
i = iToken;
@@ -15659,7 +15658,7 @@
needsGenerating = true;
propertyName = setPropertyName;
setPropertyName = "to";
- propertyValue = atomExpression(i);
+ propertyValue = atomExpressionAt(i);
i = iToken;
break;
case Token.to:
@@ -15668,7 +15667,7 @@
if (tokAt(i + 1) == Token.bitset
|| tokAt(i + 1) == Token.expressionBegin && !needsGenerating) {
propertyName = "toBitSet";
- propertyValue = atomExpression(++i);
+ propertyValue = atomExpressionAt(++i);
i = iToken;
needsGenerating = true;
break;
@@ -15916,7 +15915,7 @@
case Token.expressionBegin:
if (isWild || bsB != null)
error(ERROR_invalidArgument);
- bs = BitSetUtil.copy(atomExpression(i));
+ bs = BitSetUtil.copy(atomExpressionAt(i));
i = iToken;
if (bsA == null)
bsA = bs;
@@ -16120,7 +16119,7 @@
case Token.bitset:
case Token.expressionBegin:
propertyName = "select";
- propertyValue = atomExpression(i);
+ propertyValue = atomExpressionAt(i);
i = iToken;
break;
case Token.color:
@@ -16153,7 +16152,7 @@
if (tokAt(i + 1) == Token.bitset
|| tokAt(i + 1) == Token.expressionBegin) {
propertyName = "select";
- propertyValue = atomExpression(i + 1);
+ propertyValue = atomExpressionAt(i + 1);
i = iToken;
} else {
propertyName = "selectType";
@@ -16256,7 +16255,7 @@
switch (tok) {
case Token.bitset:
case Token.expressionBegin:
- data = atomExpression(i + 1);
+ data = atomExpressionAt(i + 1);
tok = Token.decimal;
iToken++;
break;
@@ -16849,12 +16848,12 @@
case Token.intersection:
// isosurface intersection {A} {B} VDW....
// isosurface intersection {A} {B} function "a-b" VDW....
- bsSelect = atomExpression(++i);
+ bsSelect = atomExpressionAt(++i);
if (isSyntaxCheck) {
bs = new BitSet();
} else if (tokAt(iToken + 1) == Token.expressionBegin
|| tokAt(iToken + 1) == Token.bitset) {
- bs = atomExpression(++iToken);
+ bs = atomExpressionAt(++iToken);
bs.and(viewer.getAtomsWithin(5.0f, bsSelect, false, null));
} else {
// default is "within(5.0, selected) and not within(molecule,selected)"
@@ -17059,7 +17058,7 @@
// we PREPEND the selection to the command if no surface object
// has been seen yet, and APPEND it if it has.
propertyName = "select";
- BitSet bs1 = atomExpression(++i);
+ BitSet bs1 = atomExpressionAt(++i);
propertyValue = bs1;
i = iToken;
boolean isOnly = (tokAt(i + 1) == Token.only);
@@ -17245,7 +17244,7 @@
break;
} catch (ScriptException e) {
}
- bs = atomExpression(i);
+ bs = atomExpressionAt(i);
sbCommand.append(" ellipsoid ").append(Escape.escape(bs));
int iAtom = bs.nextSetBit(0);
Atom[] atoms = viewer.getModelSet().atoms;
@@ -17276,7 +17275,7 @@
case Token.expressionBegin:
// automatically selects just the model of the first atom in the set.
propertyName = "lcaoCartoon";
- bs = atomExpression(i);
+ bs = atomExpressionAt(i);
i = iToken;
if (isSyntaxCheck)
continue;
@@ -17729,7 +17728,7 @@
break;
case Token.ignore:
propertyName = "ignore";
- propertyValue = bsIgnore = atomExpression(++i);
+ propertyValue = bsIgnore = atomExpressionAt(++i);
sbCommand.append(" ignore ").append(Escape.escape(propertyValue));
i = iToken;
break;
@@ -18060,7 +18059,7 @@
switch (tokAt(++i)) {
case Token.bitset:
case Token.expressionBegin:
- propertyValue = new int[] { atomExpression(i).nextSetBit(0) };
+ propertyValue = new int[] { atomExpressionAt(i).nextSetBit(0) };
break;
default:
propertyValue = new int[] { (int) floatParameterSet(i, 1, 1)[0] };
Modified: trunk/Jmol/src/org/jmol/script/ScriptFunction.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptFunction.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/script/ScriptFunction.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -82,7 +82,7 @@
contextVariables.put(name, (var == null ?
(new ScriptVariable(Token.string, "")).setName(name) : var));
}
- contextVariables.put("_retval", ScriptVariable.intVariable(tok == Token.trycmd ? Integer.MAX_VALUE : 0));
+ contextVariables.put("_retval", new ScriptVariableInt(tok == Token.trycmd ? Integer.MAX_VALUE : 0));
}
public void unsetVariables(Map<String, ScriptVariable> contextVariables, List<ScriptVariable> params) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -213,7 +213,7 @@
case Token.integer:
if (x.intValue < 0) {
addOp(Token.tokenMinus);
- x = ScriptVariable.intVariable(-x.intValue);
+ x = new ScriptVariableInt(-x.intValue);
}
break;
case Token.decimal:
@@ -235,7 +235,7 @@
private boolean addXInt(int x) {
// no check for unary minus
- putX(ScriptVariable.intVariable(x));
+ putX(new ScriptVariableInt(x));
return wasX = true;
}
@@ -949,7 +949,7 @@
y.add(count);
counts.add(ScriptVariable.getVariable(y));
}
- count = ScriptVariable.intVariable(1);
+ count = new ScriptVariableInt(1);
last = a;
}
if (match == null)
Modified: trunk/Jmol/src/org/jmol/script/ScriptVariable.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptVariable.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/script/ScriptVariable.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -80,10 +80,6 @@
super(tok, value);
}
- public ScriptVariable(int tok, int intValue) {
- super(tok, intValue);
- }
-
public ScriptVariable(BitSet bs, int index) {
value = bs;
this.index = index;
@@ -150,10 +146,6 @@
}
}
- public static ScriptVariable intVariable(int intValue) {
- return new ScriptVariable(integer, intValue);
- }
-
static public boolean isVariableType(Object x) {
return (x instanceof ScriptVariable
|| x instanceof BitSet
@@ -199,7 +191,7 @@
if (x instanceof Boolean)
return getBoolean(((Boolean) x).booleanValue());
if (x instanceof Integer)
- return new ScriptVariable(integer, ((Integer) x).intValue());
+ return new ScriptVariableInt(((Integer) x).intValue());
if (x instanceof Float)
return new ScriptVariable(decimal, x);
if (x instanceof String) {
@@ -564,15 +556,14 @@
case bitset:
return Escape.escapeBs(bsSelectToken(x), !(x.value instanceof BondSet));
case varray:
+ List<ScriptVariable> sv = ((ScriptVariable) x).getList();
+ i = x.intValue;
+ if (i <= 0)
+ i = sv.size() - i;
+ if (i != Integer.MAX_VALUE)
+ return (i < 1 || i > sv.size() ? "" : sValue(sv.get(i - 1)));
+ //$FALL-THROUGH$
case hash:
- if (x.tok == Token.varray) {
- List<ScriptVariable> sv = ((ScriptVariable) x).getList();
- i = x.intValue;
- if (i <= 0)
- i = sv.size() - i;
- if (i != Integer.MAX_VALUE)
- return (i < 1 || i > sv.size() ? "" : sValue(sv.get(i - 1)));
- }
sb = new StringBuffer();
map = new Hashtable<Object, Boolean>();
sValueArray(sb, (ScriptVariable) x, map, 0, false);
@@ -790,7 +781,7 @@
}
int len = 0;
boolean isInputSelected = (tokenIn instanceof ScriptVariable && ((ScriptVariable) tokenIn).index != Integer.MAX_VALUE);
- ScriptVariable tokenOut = new ScriptVariable(tokenIn.tok, Integer.MAX_VALUE);
+ ScriptVariable tokenOut = new ScriptVariableInt(Integer.MAX_VALUE);
switch (tokenIn.tok) {
case bitset:
Added: trunk/Jmol/src/org/jmol/script/ScriptVariableInt.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptVariableInt.java (rev 0)
+++ trunk/Jmol/src/org/jmol/script/ScriptVariableInt.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -0,0 +1,33 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2009-06-05 07:42:12 -0500 (Fri, 05 Jun 2009) $
+ * $Revision: 10958 $
+ *
+ * Copyright (C) 2003-2005 The Jmol Development Team
+ *
+ * Contact: jmo...@li...
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package org.jmol.script;
+
+public class ScriptVariableInt extends ScriptVariable {
+ public ScriptVariableInt(int intValue) {
+ super(Token.integer);
+ this.intValue = intValue;
+ }
+
+}
Modified: trunk/Jmol/src/org/jmol/script/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/Token.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/script/Token.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -60,18 +60,21 @@
this.tok = tok;
}
- public Token(int tok, int intValue) {
- this.tok = tok;
- this.intValue = intValue;
- }
-
public Token(int tok, Object value) {
this.tok = tok;
this.value = value;
}
+ public final static Token newToken(int tok, int intValue) {
+ Token token = new Token(tok);
+ token.intValue = intValue;
+ return token;
+ }
+
public final static Token intToken(int intValue) {
- return new Token(integer, intValue);
+ Token token = new Token(integer);
+ token.intValue = intValue;
+ return token;
}
public final static int nada = 0;
@@ -101,11 +104,11 @@
};
public static boolean tokAttr(int a, int b) {
- return (a & b) == b;
+ return (a & b) == (b & b);
}
public static boolean tokAttrOr(int a, int b1, int b2) {
- return (a & b1) == b1 || (a & b2) == b2;
+ return (a & b1) == (b1 & b1) || (a & b2) == (b2 & b2);
}
@@ -1305,7 +1308,7 @@
final static Token tokenCoordinateBegin = new Token(leftbrace, "{");
final static Token tokenRightBrace = new Token(rightbrace, "}");
final static Token tokenCoordinateEnd = tokenRightBrace;
- final static Token tokenColon = new Token(colon, ':');
+ final static Token tokenColon = new Token(colon, ":");
final static Token tokenSetCmd = new Token(set, "set");
final static Token tokenSet = new Token(set, '=', "");
final static Token tokenSetArray = new Token(set, '[', "");
Modified: trunk/Jmol/src/org/jmol/util/JmolFont.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/JmolFont.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/util/JmolFont.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -47,7 +47,7 @@
public final int idFontStyle;
public final float fontSize;
public final Object font;
- public final Object fontMetrics;
+ private final Object fontMetrics;
private ApiPlatform apiPlatform;
private JmolFont(ApiPlatform apiPlatform, byte fid,
int idFontFace, int idFontStyle, float fontSize,
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -35,6 +35,7 @@
import org.jmol.script.ScriptEvaluator;
import org.jmol.script.ScriptVariable;
+import org.jmol.script.ScriptVariableInt;
import org.jmol.script.Token;
import org.jmol.util.Escape;
import org.jmol.util.Logger;
@@ -200,7 +201,7 @@
int n;
for (int i = 1; i < names.length; i++) {
if ((n = Parser.parseInt(names[i])) != Integer.MIN_VALUE)
- args[i] = new ScriptVariable(Token.integer, n);
+ args[i] = new ScriptVariableInt(n);
else
args[i] = new ScriptVariable(Token.string, names[i]);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2012-09-12 00:29:26 UTC (rev 17556)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2012-09-12 11:45:51 UTC (rev 17557)
@@ -30,6 +30,7 @@
import org.jmol.script.ScriptEvaluator;
import org.jmol.script.ScriptFunction;
import org.jmol.script.ScriptVariable;
+import org.jmol.script.ScriptVariableInt;
import org.jmol.script.Token;
import org.jmol.shape.Shape;
import org.jmol.i18n.GT;
@@ -447,7 +448,7 @@
o = info.get("repaintManager");
if (o == null)
o = (Interface.getOptionInterface("render.RepaintManager"));
- if (o != null)
+ if (o != null && !o.equals(""))
(repaintManager = (JmolRepaintInterface) o).set(this, shapeManager);
initialize(true);
fileManager = new FileManager(this);
@@ -6477,7 +6478,7 @@
default:
// stateversion is not tokenized
if (!global.htNonbooleanParameterValues.containsKey(key)) {
- global.setUserVariable(key, ScriptVariable.intVariable(value));
+ global.setUserVariable(key, new ScriptVariableInt(value));
return;
}
}
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