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[Jmol-commits] SF.net SVN: jmol: [7434] trunk/Jmol/src/org/jmol
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From: <ha...@us...> - 2007-04-18 05:54:29
|
Revision: 7434
http://svn.sourceforge.net/jmol/?rev=7434&view=rev
Author: hansonr
Date: 2007-04-17 22:54:27 -0700 (Tue, 17 Apr 2007)
Log Message:
-----------
Java 1.1 Vector methods instated
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/adapter/smarter/CsfReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/GamessReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/GaussianReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/MopacDataReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/MopacGraphfReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/MopacReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/PsiReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/SpartanArchive.java
trunk/Jmol/src/org/jmol/adapter/smarter/WebMOReader.java
trunk/Jmol/src/org/jmol/util/CommandHistory.java
trunk/Jmol/src/org/jmol/util/CompoundDocument.java
trunk/Jmol/src/org/jmol/viewer/Compiler.java
trunk/Jmol/src/org/jmol/viewer/Dipoles.java
trunk/Jmol/src/org/jmol/viewer/Draw.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Frame.java
trunk/Jmol/src/org/jmol/viewer/Isosurface.java
trunk/Jmol/src/org/jmol/viewer/Measurement.java
trunk/Jmol/src/org/jmol/viewer/Measures.java
trunk/Jmol/src/org/jmol/viewer/Mmset.java
trunk/Jmol/src/org/jmol/viewer/ModelManager.java
trunk/Jmol/src/org/jmol/viewer/ScriptManager.java
trunk/Jmol/src/org/jmol/viewer/StatusManager.java
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -679,7 +679,7 @@
trajectory = new Point3f[atomCount];
for (int i = 0; i < atomCount; i++)
trajectory[i] = new Point3f(atoms[i]);
- trajectories.add(trajectory);
+ trajectories.addElement(trajectory);
nTrajectories++;
//System.out.println(" nTrajectories:" + nTrajectories + " coord 4: " + trajectory[4]);
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/CsfReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/CsfReader.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/CsfReader.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -558,7 +558,7 @@
System.out.print(" " + list[iMo][i]);
System.out.println();
*/
- orbitals.add(mo);
+ orbitals.addElement(mo);
}
setMOs("eV");
}
@@ -634,10 +634,10 @@
}
slater.put("gaussianPtr", new Integer(gaussianCount));
slater.put("nGaussians", new Integer(nZ));
- sdata.add(slater);
+ sdata.addElement(slater);
gaussianCount += nZ;
for (int i = 0; i < nZ; i++)
- gdata.add(new float[] {zetas[ipt][i], contractionCoefs[ipt][i]});
+ gdata.addElement(new float[] {zetas[ipt][i], contractionCoefs[ipt][i]});
}
}
float[][] garray = new float[gaussianCount][];
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/GamessReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/GamessReader.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/GamessReader.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -200,7 +200,7 @@
if (!tokens[0].equals(thisShell)) {
if (slater != null) {
slater.put("nGaussians", new Integer(nGaussians));
- sdata.add(slater);
+ sdata.addElement(slater);
}
thisShell = tokens[0];
shellCount++;
@@ -222,15 +222,15 @@
if (i >= 3)i += 2;
j++;
}
- gdata.add(s);
+ gdata.addElement(s);
} else {
- gdata.add(tokens);
+ gdata.addElement(tokens);
}
}
}
if (slater != null) {
slater.put("nGaussians", new Integer(nGaussians));
- sdata.add(slater);
+ sdata.addElement(slater);
}
float[][] garray = new float[gaussianCount][];
for (int i = 0; i < gaussianCount; i++) {
@@ -278,7 +278,7 @@
for (int j = coefs.length; --j >= 0;)
coefs[j] = parseFloat((String) data[i].get(j));
mos[i].put("coefficients", coefs);
- orbitals.add(mos[i]);
+ orbitals.addElement(mos[i]);
}
nThisLine = 0;
continue;
@@ -302,7 +302,7 @@
}
int nSkip = tokens.length - nThisLine;
for (int i = 0; i < nThisLine; i++)
- data[i].add(tokens[i + nSkip]);
+ data[i].addElement(tokens[i + nSkip]);
}
Logger.debug(orbitals.size() + " molecular orbitals read in model " + modelNumber);
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/GaussianReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/GaussianReader.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/GaussianReader.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -335,10 +335,10 @@
int nGaussians = parseInt(tokens[5]);
slater.put("gaussianPtr", new Integer(gaussianCount)); // or parseInt(tokens[7]) - 1
slater.put("nGaussians", new Integer(nGaussians));
- sdata.add(slater);
+ sdata.addElement(slater);
gaussianCount += nGaussians;
for (int i = 0; i < nGaussians; i++)
- gdata.add(getTokens(readLine()));
+ gdata.addElement(getTokens(readLine()));
}
if (atomCount == -1)
atomCount = 0;
@@ -395,7 +395,7 @@
}
try {
for (int i = 0; i < nThisLine; i++)
- data[i].add(tokens[i + ptData]);
+ data[i].addElement(tokens[i + ptData]);
} catch (Exception e) {
Logger.error("Error reading Gaussian file Molecular Orbitals at line: "
+ line);
@@ -411,7 +411,7 @@
for (int j = coefs.length; --j >= 0;)
coefs[j] = parseFloat((String) data[i].get(j));
mos[i].put("coefficients", coefs);
- orbitals.add(mos[i]);
+ orbitals.addElement(mos[i]);
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/MopacDataReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/MopacDataReader.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/MopacDataReader.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -63,8 +63,8 @@
void addSlater(int i0, int i1, int i2, int i3, int i4,
float zeta, float coef) {
//System.out.println (i0 + " " + i1 + " " + i2 + " " + i3 + " " + i4 + " " + zeta + " " + coef);
- intinfo.add(new int[] {i0, i1, i2, i3, i4});
- floatinfo.add(new float[] {zeta, coef});
+ intinfo.addElement(new int[] {i0, i1, i2, i3, i4});
+ floatinfo.addElement(new float[] {zeta, coef});
}
void setSlaters() {
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/MopacGraphfReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/MopacGraphfReader.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/MopacGraphfReader.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -197,7 +197,7 @@
mo.put("energy", new Float(values[0]));
mo.put("occupancy", new Integer((int) values[1]));
mo.put("coefficients", list2[iMo]);
- orbitals.add(mo);
+ orbitals.addElement(mo);
}
setMOs("eV");
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/MopacReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/MopacReader.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/MopacReader.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -218,7 +218,7 @@
Hashtable info = new Hashtable();
info.put("freq", new Float(freq));
info.put("label", "");
- freqs.add(info);
+ freqs.addElement(info);
baseAtomIndex = atomSetCollection.atomCount;
atomSetCollection.cloneLastAtomSet();
Atom[] atoms = atomSetCollection.atoms;
@@ -232,12 +232,12 @@
float dz = parseFloat(data[dataPt++][i + 1]);
atoms[baseAtomIndex + iatom].addVibrationVector(dx, dy, dz);
Vector vibatom = new Vector();
- vibatom.add(new Float(dx));
- vibatom.add(new Float(dy));
- vibatom.add(new Float(dz));
- vib.add(vibatom);
+ vibatom.addElement(new Float(dx));
+ vibatom.addElement(new Float(dy));
+ vibatom.addElement(new Float(dz));
+ vib.addElement(vibatom);
}
- vibrations.add(vib);
+ vibrations.addElement(vib);
}
}
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("VibFreqs", freqs);
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/PsiReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/PsiReader.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/PsiReader.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -199,7 +199,7 @@
}
if (ipt > 1) {
if (slater != null)
- sdata.add(slater);
+ sdata.addElement(slater);
slater = new Hashtable();
slater.put("atomCenter", new Integer(atomCenter));
shellCount++;
@@ -207,13 +207,13 @@
slater.put("gaussianPtr", new Integer(gaussianCount));
}
nGaussians++;
- gdata.add(new String[] { tokens[ipt], tokens[ipt + 1] });
+ gdata.addElement(new String[] { tokens[ipt], tokens[ipt + 1] });
slater.put("nGaussians", new Integer(nGaussians));
}
- sdata.add(slater);
+ sdata.addElement(slater);
gaussianCount += nGaussians;
if (slater != null)
- sdata.add(slater);
+ sdata.addElement(slater);
readLine();
}
float[][] garray = new float[gaussianCount][];
@@ -354,7 +354,7 @@
}
try {
for (int i = 0; i < nThisLine; i++)
- data[i].add(tokens[i + ptData]);
+ data[i].addElement(tokens[i + ptData]);
} catch (Exception e) {
Logger.error("Error reading Psi3 file molecular orbitals at line: "
+ line);
@@ -370,7 +370,7 @@
for (int j = coefs.length; --j >= 0;)
coefs[j] = parseFloat((String) data[i].get(j));
mos[i].put("coefficients", coefs);
- orbitals.add(mos[i]);
+ orbitals.addElement(mos[i]);
}
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/SpartanArchive.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/SpartanArchive.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/SpartanArchive.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -232,7 +232,7 @@
slater.put("basisType", basisType);
slater.put("nGaussians", new Integer(nGaussians));
slater.put("gaussianPtr", new Integer(gaussianPtr));
- sdata.add(slater);
+ sdata.addElement(slater);
}
for (int i = 0; i < gaussianCount; i++) {
float alpha = parseFloat(readLine());
@@ -293,7 +293,7 @@
mo.put("energy", new Float(energies[i]));
//mo.put("occupancy", new Integer(-1));
mo.put("coefficients", coefficients[i]);
- orbitals.add(mo);
+ orbitals.addElement(mo);
}
if (Logger.isActiveLevel(Logger.LEVEL_DEBUG)) {
Logger.debug(orbitals.size() + " molecular orbitals read");
@@ -350,19 +350,19 @@
&& !line.substring(0, 3).equals("END")) {
if (isString) {
value = getQuotedString("\"");
- vector.add(value);
+ vector.addElement(value);
} else {
String tokens2[] = getTokens();
for (int i = 0; i < tokens2.length; i++) {
if (isArray) {
- atomInfo.add(new Float(parseFloat(tokens2[i])));
+ atomInfo.addElement(new Float(parseFloat(tokens2[i])));
if ((i + 1) % nValues == 0) {
- vector.add(atomInfo);
+ vector.addElement(atomInfo);
atomInfo = new Vector();
}
} else {
value = new Float(parseFloat(tokens2[i]));
- vector.add(value);
+ vector.addElement(value);
}
}
}
@@ -403,7 +403,7 @@
if (line.length() > 15
&& !(label = line.substring(15, line.length())).equals("???"))
info.put("label", label);
- freqs.add(info);
+ freqs.addElement(info);
atomSetCollection.setAtomSetName(label + " " + freq + " cm^-1");
atomSetCollection.setAtomSetProperty(SmarterJmolAdapter.PATH_KEY,
"Frequencies");
@@ -422,20 +422,20 @@
for (int i = 0; i < tokens2.length; i++) {
float f = parseFloat(tokens2[i]);
atomInfo[i % nValues] = f;
- vibatom.add(new Float(f));
+ vibatom.addElement(new Float(f));
if ((i + 1) % nValues == 0) {
//Logger.debug(ifreq + " atom " + iatom + "/" + atomCount
// + " vectors: " + atomInfo[0] + " " + atomInfo[1] + " "
// + atomInfo[2]);
atoms[iatom]
.addVibrationVector(atomInfo[0], atomInfo[1], atomInfo[2]);
- vib.add(vibatom);
+ vib.addElement(vibatom);
vibatom = new Vector();
++iatom;
}
}
if (iatom % atomCount == 0) {
- vibrations.add(vib);
+ vibrations.addElement(vib);
vib = new Vector();
if (++ifreq == frequencyCount)
break; ///loop exit
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/WebMOReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/WebMOReader.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/WebMOReader.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -222,10 +222,10 @@
float[] data = new float[nData];
for (int d = 0; d < nData; d++)
data[d] = parseFloat(strData[d]);
- gdata.add(data);
+ gdata.addElement(data);
gaussianPtr++;
}
- sdata.add(slater);
+ sdata.addElement(slater);
}
float[][] garray = new float[gaussianPtr][];
for (int i = 0; i < gaussianPtr; i++)
@@ -277,7 +277,7 @@
if (line.length() == 0)
continue;
String[] tokens = getTokens();
- data.add(tokens[1]);
+ data.addElement(tokens[1]);
}
float[] coefs = new float[data.size()];
for (int i = data.size(); --i >= 0;)
@@ -285,7 +285,7 @@
mo.put("energy", new Float(energy));
mo.put("occupancy", new Integer(occupancy));
mo.put("coefficients", coefs);
- orbitals.add(mo);
+ orbitals.addElement(mo);
setMOs("eV");
}
}
Modified: trunk/Jmol/src/org/jmol/util/CommandHistory.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/CommandHistory.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/util/CommandHistory.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -86,7 +86,7 @@
this.maxSize = maxSize;
commandList = new Vector();
nextCommand = 0;
- commandList.add("");
+ commandList.addElement("");
cursorPos = 0;
}
@@ -101,7 +101,7 @@
if (maxSize < 2)
maxSize = 2;
while (nextCommand > maxSize) {
- commandList.remove(0);
+ commandList.removeElementAt(0);
nextCommand--;
}
if (nextCommand > maxSize)
@@ -221,7 +221,7 @@
if (n < 0 || n >= nextCommand)
return "";
String str = (String) commandList.get(n);
- commandList.remove(n);
+ commandList.removeElementAt(n);
nextCommand--;
return str;
}
@@ -232,20 +232,20 @@
* @param command the String value of a command.
*/
private void addCommandLine(String command) {
- if(command == null || command.length() == 0)
+ if (command == null || command.length() == 0)
return;
if (command.endsWith(NOHISTORYLINE_FLAG))
return;
if (nextCommand >= maxSize) {
- commandList.remove(0);
+ commandList.removeElementAt(0);
nextCommand = maxSize - 1;
}
- commandList.add(nextCommand, command);
+ commandList.insertElementAt(command, nextCommand);
nextCommand++;
cursorPos = nextCommand;
- commandList.add(nextCommand, "");
+ commandList.insertElementAt("", nextCommand);
//for (int i = 0; i < nextCommand; i++)
- //System.out.println("HISTORY:" + i+" "+commandList.get(i));
+ //System.out.println("HISTORY:" + i+" "+commandList.get(i));
}
}
Modified: trunk/Jmol/src/org/jmol/util/CompoundDocument.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/CompoundDocument.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/util/CompoundDocument.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -349,7 +349,7 @@
thisEntry = new CmpDocDirectoryEntry();
thisEntry.readData();
if (thisEntry.lenStream > 0)
- directory.add(thisEntry);
+ directory.addElement(thisEntry);
if (thisEntry.entryType == 5)
rootEntry = thisEntry;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Compiler.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/Compiler.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -224,7 +224,7 @@
&& tokAttr(tokCommand, Token.setparam)) {
tokenCommand = Token.getTokenFromName("set");
tokCommand = Token.set;
- ltoken.add(0, tokenCommand);
+ ltoken.insertElementAt(tokenCommand, 0);
cchToken = 1;
continue;
}
@@ -394,8 +394,8 @@
// set x or x =
if (tok == Token.opEQ) {
token = (Token) ltoken.get(0);
- ltoken.remove(0);
- ltoken.add(Token.getTokenFromName("set"));
+ ltoken.removeElementAt(0);
+ ltoken.addElement(Token.getTokenFromName("set"));
tok = token.tok;
tokCommand = Token.set;
}
@@ -431,7 +431,7 @@
} else if (nTokens == 2 && tok == Token.opEQ) {
// we are looking at @x =.... just insert a SET command
// and ignore the =. It's the same as set @x ...
- ltoken.add(0, Token.getTokenFromName("set"));
+ ltoken.insertElementAt(Token.getTokenFromName("set"), 0);
continue;
} else {
// we are looking at the expression
Modified: trunk/Jmol/src/org/jmol/viewer/Dipoles.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Dipoles.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/Dipoles.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -463,14 +463,14 @@
atomInfo = new Hashtable();
viewer.getAtomIdentityInfo(dipole.atoms[0].atomIndex, atomInfo);
Vector atoms = new Vector();
- atoms.add(atomInfo);
+ atoms.addElement(atomInfo);
atomInfo = new Hashtable();
viewer.getAtomIdentityInfo(dipole.atoms[1].atomIndex, atomInfo);
- atoms.add(atomInfo);
+ atoms.addElement(atomInfo);
info.put("atoms", atoms);
info.put("magnitude", new Float(dipole.vector.length()));
}
- V.add(info);
+ V.addElement(info);
}
return V;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Draw.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Draw.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/Draw.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -895,14 +895,14 @@
mInfo.put("axis", mesh.axes[k]);
Vector v = new Vector();
for (int ipt = 0; ipt < nPoints; ipt++)
- v.add(mesh.vertices[mesh.polygonIndexes[k][ipt]]);
+ v.addElement(mesh.vertices[mesh.polygonIndexes[k][ipt]]);
mInfo.put("vertices", v);
if (mesh.drawTypes[k] == DrawMesh.DRAW_LINE) {
float d = mesh.vertices[mesh.polygonIndexes[k][0]]
.distance(mesh.vertices[mesh.polygonIndexes[k][1]]);
mInfo.put("length_Ang", new Float(d));
}
- m.add(mInfo);
+ m.addElement(mInfo);
}
info.put("models", m);
} else {
@@ -912,13 +912,13 @@
info.put("axis", mesh.axis);
Vector v = new Vector();
for (int j = 0; j < mesh.vertexCount; j++)
- v.add(mesh.vertices[j]);
+ v.addElement(mesh.vertices[j]);
info.put("vertices", v);
if (mesh.drawType == DrawMesh.DRAW_LINE)
info.put("length_Ang", new Float(mesh.vertices[0]
.distance(mesh.vertices[1])));
}
- V.add(info);
+ V.addElement(info);
}
return V;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -167,7 +167,7 @@
int atomCount = viewer.getAtomCount();
for (int i = 0; i < atomCount; i++)
if (bs.get(i))
- V.add(new Integer(i));
+ V.addElement(new Integer(i));
return V;
}
@@ -337,10 +337,10 @@
if (errorMessage != null)
return errorMessage;
Vector info = new Vector();
- info.add(compiler.getScript());
- info.add(compiler.getAatokenCompiled());
- info.add(compiler.getLineNumbers());
- info.add(compiler.getLineIndices());
+ info.addElement(compiler.getScript());
+ info.addElement(compiler.getAatokenCompiled());
+ info.addElement(compiler.getLineNumbers());
+ info.addElement(compiler.getLineIndices());
return info;
}
@@ -2705,7 +2705,7 @@
}
Vector v = new Vector();
while (isCenterParameter(i + 1)) {
- v.add(centerParameter(++i));
+ v.addElement(centerParameter(++i));
i = iToken;
}
if (v.size() > 0) {
@@ -3803,7 +3803,7 @@
if (isAll) {
if (++expressionCount > 4)
badArgumentCount();
- monitorExpressions.add(bs);
+ monitorExpressions.addElement(bs);
nAtoms = expressionCount;
} else {
if (++nAtoms > 4)
@@ -8349,11 +8349,11 @@
Vector v = new Vector();
if (getToken(++i).tok != Token.string)
invalidArgument();
- v.add(statement[i++].value);
- v.add(getPoint3f(i, false));
- v.add(getPoint4f(++iToken));
- v.add(getPoint4f(++iToken));
- v.add(getPoint4f(++iToken));
+ v.addElement(statement[i++].value);
+ v.addElement(getPoint3f(i, false));
+ v.addElement(getPoint4f(++iToken));
+ v.addElement(getPoint4f(++iToken));
+ v.addElement(getPoint4f(++iToken));
i = iToken;
propertyName = "functionXY";
propertyValue = v;
Modified: trunk/Jmol/src/org/jmol/viewer/Frame.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Frame.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/Frame.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -1530,7 +1530,7 @@
void rebond() {
// from eval "connect" or from app preferences panel
- stateScripts.add("connect;");
+ stateScripts.addElement("connect;");
deleteAllBonds();
autoBond(null, null, null);
}
@@ -1784,7 +1784,7 @@
script = "frame " + (iFrame < 0 ? "" + iFrame : getModelName(-iFrame))
+ ";\n" + script;
}
- stateScripts.add(script);
+ stateScripts.addElement(script);
}
int makeConnections(float minDistance, float maxDistance, short order,
@@ -1800,7 +1800,7 @@
stateScript += JmolConstants.getBondOrderNameFromOrder(order) + " "
+ JmolConstants.connectOperationName(connectOperation);
stateScript += ";";
- stateScripts.add(stateScript);
+ stateScripts.addElement(stateScript);
}
if (connectOperation == JmolConstants.CONNECT_DELETE_BONDS)
return deleteConnections(minDistance, maxDistance, order, bsA, bsB,
@@ -2808,7 +2808,7 @@
bsTemp = (BitSet) bsAtoms.clone();
bsTemp.and(molecules[i].atomList);
if (bsTemp.length() > 0)
- V.add(molecules[i].getInfo());
+ V.addElement(molecules[i].getInfo());
}
return V;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Isosurface.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/Isosurface.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -6200,7 +6200,7 @@
info.put("modelIndex", new Integer(mesh.modelIndex));
if (mesh.title != null)
info.put("title", mesh.title);
- V.add(info);
+ V.addElement(info);
}
return V;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Measurement.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Measurement.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/Measurement.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -289,8 +289,8 @@
Vector toVector() {
Vector V = new Vector();
- for (int i = 0; i < count + 1; i++ ) V.add(new Integer(countPlusIndices[i]));
- V.add(strMeasurement);
+ for (int i = 0; i < count + 1; i++ ) V.addElement(new Integer(countPlusIndices[i]));
+ V.addElement(strMeasurement);
return V;
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/Measures.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Measures.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/Measures.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -243,7 +243,7 @@
int nPoints = atomCountPlusIndices[0];
for (int i = 1; i <= nPoints; i++) {
Atom atom = frame.atoms[atomCountPlusIndices[i]];
- measureList.add(viewer.getAtomBits("atomno", atom.getAtomNumber()));
+ measureList.addElement(viewer.getAtomBits("atomno", atom.getAtomNumber()));
}
define(measureList, isDelete, false, false);
return;
@@ -384,7 +384,7 @@
private Vector getAllInfo() {
Vector info = new Vector();
for (int i = 0; i< measurementCount; i++) {
- info.add(getInfo(i));
+ info.addElement(getInfo(i));
}
return info;
}
@@ -413,7 +413,7 @@
atomInfo.put("_ipt", new Integer(atom.atomIndex));
atomInfo.put("atomno", new Integer(atom.getAtomNumber()));
atomInfo.put("info", atom.getInfo());
- atomsInfo.add(atomInfo);
+ atomsInfo.addElement(atomInfo);
}
info.put("atoms", atomsInfo);
return info;
Modified: trunk/Jmol/src/org/jmol/viewer/Mmset.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Mmset.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/Mmset.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -508,7 +508,7 @@
Vector getStructureInfo() {
Vector info = new Vector();
for (int i = 0; i < structureCount; i++)
- info.add(structures[i].toHashtable());
+ info.addElement(structures[i].toHashtable());
return info;
}
Modified: trunk/Jmol/src/org/jmol/viewer/ModelManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ModelManager.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/ModelManager.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -899,7 +899,7 @@
props = viewer.getModelProperties(i);
if (props != null)
model.put("modelProperties", props);
- models.add(model);
+ models.addElement(model);
}
info.put("models",models);
return info;
@@ -913,7 +913,7 @@
int modelCount = viewer.getModelCount();
for (int i = 0; i < modelCount; ++i) {
Hashtable modelinfo = getModelAuxiliaryInfo(i);
- models.add(modelinfo);
+ models.addElement(modelinfo);
}
info.put("models",models);
return info;
@@ -924,7 +924,7 @@
int atomCount = viewer.getAtomCount();
for (int i = 0; i < atomCount; i++)
if (bs.get(i))
- V.add(getAtomInfoLong(i));
+ V.addElement(getAtomInfoLong(i));
return V;
}
@@ -1000,7 +1000,7 @@
for (int i = 0; i < bondCount; i++)
if (bs.get(frame.getBondAt(i).getAtom1().atomIndex)
&& bs.get(frame.getBondAt(i).getAtom2().atomIndex))
- V.add(getBondInfo(i));
+ V.addElement(getBondInfo(i));
return V;
}
@@ -1068,7 +1068,7 @@
if (info.size() > 0) {
modelInfo.put("modelIndex",new Integer(i));
modelInfo.put("chains",info);
- modelVector.add(modelInfo);
+ modelVector.addElement(modelInfo);
}
}
finalInfo.put("models",modelVector);
@@ -1089,14 +1089,14 @@
Vector3f[] vectors = polymer.wingVectors;
for (int j = 0; j < polymer.monomerCount; j++)
if (bs.get(polymer.monomers[j].getLeadAtomIndex())) {
- vList.add(new Point3f[] { points[j], new Point3f(vectors[j]) });
+ vList.addElement(new Point3f[] { points[j], new Point3f(vectors[j]) });
last = j;
} else if (last != Integer.MAX_VALUE - 1) {
- vList.add(new Point3f[] { points[j], new Point3f(vectors[j]) });
+ vList.addElement(new Point3f[] { points[j], new Point3f(vectors[j]) });
last = Integer.MAX_VALUE - 1;
}
if (last + 1 < polymer.monomerCount)
- vList.add(new Point3f[] { points[last + 1],
+ vList.addElement(new Point3f[] { points[last + 1],
new Point3f(vectors[last + 1]) });
}
}
@@ -1124,11 +1124,11 @@
infoGroup.put("atomInfo1", getAtomInfo(group.firstAtomIndex));
infoGroup.put("atomInfo2", getAtomInfo(group.lastAtomIndex));
infoGroup.put("visibilityFlags", new Integer(group.shapeVisibilityFlags));
- infoChain.add(infoGroup);
+ infoChain.addElement(infoGroup);
}
if (! infoChain.isEmpty()) {
arrayName.put("residues",infoChain);
- infoChains.add(arrayName);
+ infoChains.addElement(arrayName);
}
}
return infoChains;
@@ -1145,12 +1145,12 @@
for (int ip = 0; ip < polymerCount; ip++) {
Hashtable polyInfo = getPolymerInfo(i, ip, bs);
if (! polyInfo.isEmpty())
- info.add(polyInfo);
+ info.addElement(polyInfo);
}
if (info.size() > 0) {
modelInfo.put("modelIndex",new Integer(i));
modelInfo.put("polymers",info);
- modelVector.add(modelInfo);
+ modelVector.addElement(modelInfo);
}
}
finalInfo.put("models",modelVector);
@@ -1189,7 +1189,7 @@
if (bs.get(polymer.monomers[i].getLeadAtomIndex())) {
Hashtable monomerInfo = polymer.monomers[i].getMyInfo();
monomerInfo.put("monomerIndex", new Integer(i));
- info.add(monomerInfo);
+ info.addElement(monomerInfo);
sequence += polymer.monomers[i].getGroup1();
}
}
@@ -1232,6 +1232,8 @@
for (int i = 1; i < JmolConstants.SHAPE_MAX; i++)
if (frame.shapes[i] != null)
frame.shapes[i].setVisibilityFlags(bs);
+ //s(bs);
+ //
// BALLS sets the JmolConstants.ATOM_IN_MODEL flag.
frame.shapes[JmolConstants.SHAPE_BALLS]
.setVisibilityFlags(bs);
@@ -1369,7 +1371,7 @@
}
void setAtomCoord(int atomIndex, float x, float y, float z) {
- frame.setAtomCoord(atomIndex,x,y,z);
+ frame.setAtomCoord(atomIndex,x,y,z);
}
void setAtomCoordRelative(int atomIndex, float x, float y, float z) {
Modified: trunk/Jmol/src/org/jmol/viewer/ScriptManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ScriptManager.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/ScriptManager.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -56,17 +56,17 @@
String statusList, boolean isScriptFile,
boolean isQuiet) {
Vector scriptItem = new Vector();
- scriptItem.add(strScript);
- scriptItem.add(statusList);
- scriptItem.add(returnType);
- scriptItem.add(isScriptFile ? Boolean.TRUE : Boolean.FALSE);
- scriptItem.add(isQuiet ? Boolean.TRUE : Boolean.FALSE);
+ scriptItem.addElement(strScript);
+ scriptItem.addElement(statusList);
+ scriptItem.addElement(returnType);
+ scriptItem.addElement(isScriptFile ? Boolean.TRUE : Boolean.FALSE);
+ scriptItem.addElement(isQuiet ? Boolean.TRUE : Boolean.FALSE);
if (!useQueue) {
clearQueue();
viewer.haltScriptExecution();
}
- scriptQueue.add(scriptItem);
+ scriptQueue.addElement(scriptItem);
if (Logger.isActiveLevel(Logger.LEVEL_DEBUG)) {
Logger.debug(scriptQueue.size() + " scripts; added: " + strScript);
}
@@ -109,7 +109,7 @@
if (Logger.isActiveLevel(Logger.LEVEL_DEBUG)) {
Logger.debug(scriptQueue.size() + " scripts; running: " + script);
}
- scriptQueue.remove(0);
+ scriptQueue.removeElementAt(0);
Object returnInfo = runScript(returnType, script, statusList, isScriptFile,
isQuiet);
if (scriptQueue.size() == 0) // might have been cleared with an exit
Modified: trunk/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2007-04-18 05:47:17 UTC (rev 7433)
+++ trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2007-04-18 05:54:27 UTC (rev 7434)
@@ -319,10 +319,10 @@
statusPtr++;
Vector statusRecordSet;
Vector msgRecord = new Vector();
- msgRecord.add(new Integer(statusPtr));
- msgRecord.add(statusName);
- msgRecord.add(new Integer(intInfo));
- msgRecord.add(statusInfo);
+ msgRecord.addElement(new Integer(statusPtr));
+ msgRecord.addElement(statusName);
+ msgRecord.addElement(new Integer(intInfo));
+ msgRecord.addElement(statusInfo);
if (isReplace && messageQueue.containsKey(statusName)) {
messageQueue.remove(statusName);
}
@@ -332,9 +332,9 @@
statusRecordSet = new Vector();
}
if (statusRecordSet.size() == MAXIMUM_QUEUE_LENGTH)
- statusRecordSet.remove(0);
+ statusRecordSet.removeElementAt(0);
- statusRecordSet.add(msgRecord);
+ statusRecordSet.addElement(msgRecord);
messageQueue.put(statusName, statusRecordSet);
}
@@ -354,7 +354,7 @@
int n = 0;
while (e.hasMoreElements()) {
String statusName = (String)e.nextElement();
- msgList.add(messageQueue.remove(statusName));
+ msgList.addElement(messageQueue.remove(statusName));
n++;
}
return msgList;
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