Revision: 18269
http://sourceforge.net/p/jmol/code/18269
Author: hansonr
Date: 2013-05-31 15:20:56 +0000 (Fri, 31 May 2013)
Log Message:
-----------
super out for JS
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/awtjs2d/JSModelKitPopup.java
trunk/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/AtomPropertyMapper.java
trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyzReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/MsmsReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java
trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java
trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
trunk/Jmol/src/org/jmol/modelkit/ModelKitPopup.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/modelset/Measurement.java
trunk/Jmol/src/org/jmol/modelset/MeasurementPending.java
trunk/Jmol/src/org/jmol/modelset/Model.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/popup/GenericPopup.java
trunk/Jmol/src/org/jmol/quantum/NciCalculation.java
trunk/Jmol/src/org/jmol/quantum/QuantumCalculation.java
Modified: trunk/Jmol/src/org/jmol/awtjs2d/JSModelKitPopup.java
===================================================================
--- trunk/Jmol/src/org/jmol/awtjs2d/JSModelKitPopup.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/awtjs2d/JSModelKitPopup.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -67,7 +67,7 @@
viewer.evalStringQuiet("set picking assignAtom_C");
return;
}
- super.checkMenuClick(source, script);
+ checkMenuClickGP(source, script);
}
@Override
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -363,6 +363,10 @@
@Override
protected void setVolumeData() {
+ setVolumeDataADR();
+ }
+
+ protected void setVolumeDataADR() {
if (!setVolumeDataParams()) {
setVoxelRange(0, xyzMin.x, xyzMax.x, ptsPerAngstrom, maxGrid,
minPtsPerAng);
setVoxelRange(1, xyzMin.y, xyzMax.y, ptsPerAngstrom, maxGrid,
minPtsPerAng);
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/AtomPropertyMapper.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/AtomPropertyMapper.java
2013-05-31 14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/AtomPropertyMapper.java
2013-05-31 15:20:56 UTC (rev 18269)
@@ -112,7 +112,7 @@
@Override
protected void setVolumeData() {
if (params.thePlane != null)
- super.setVolumeData();// unnecessary -- point-specific property mapper
only
+ setVolumeDataADR();// unnecessary -- point-specific property mapper only
}
@Override
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -35,6 +35,10 @@
@Override
void init(SurfaceGenerator sg) {
+ initIFR(sg);
+ }
+
+ protected void initIFR(SurfaceGenerator sg) {
initADR(sg);
isXLowToHigh = true;
precalculateVoxelData = false;
@@ -73,7 +77,7 @@
@Override
protected void setVolumeData() {
if (data == null) {
- super.setVolumeData();
+ setVolumeDataADR();
return;
}
volumetricOrigin.setT((P3) params.functionInfo.get(1));
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyzReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyzReader.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyzReader.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -27,11 +27,6 @@
IsoFxyzReader(){}
- @Override
- void init(SurfaceGenerator sg) {
- super.init(sg);
- }
-
private float[][][] data;
@Override
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/MsmsReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/MsmsReader.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/MsmsReader.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -58,7 +58,7 @@
@Override
protected boolean readVertices() throws Exception {
skipHeader();
- return super.readVertices();
+ return readVerticesPM();
}
@Override
@@ -76,7 +76,7 @@
}
sg.addRequiredFile(fileName);
skipHeader();
- return super.readPolygons();
+ return readPolygonsPM();
}
private void skipHeader() throws Exception {
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -184,6 +184,10 @@
protected int[] vertexMap;
protected boolean readVertices() throws Exception {
+ return readVerticesPM();
+ }
+
+ protected boolean readVerticesPM() throws Exception {
pmeshError = type + " ERROR: vertex count must be positive";
if (!isBinary)
nVertices = getInt();
@@ -211,6 +215,10 @@
}
protected boolean readPolygons() throws Exception {
+ return readPolygonsPM();
+ }
+
+ protected boolean readPolygonsPM() throws Exception {
pmeshError = type + " ERROR: polygon count must be zero or positive";
if (!isBinary)
nPolygons = getInt();
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -71,6 +71,10 @@
@Override
protected void closeReader() {
+ closeReaderSFR();
+ }
+
+ protected void closeReaderSFR() {
if (br != null)
try {
br.close();
@@ -91,7 +95,7 @@
@Override
void discardTempData(boolean discardAll) {
closeReader();
- super.discardTempData(discardAll);
+ discardTempDataSR(discardAll);
}
protected String line;
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -467,6 +467,10 @@
}
void discardTempData(boolean discardAll) {
+ discardTempDataSR(discardAll);
+ }
+
+ protected void discardTempDataSR(boolean discardAll) {
if (!discardAll)
return;
voxelData = null;
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -88,7 +88,7 @@
if (readerClosed)
return;
readerClosed = true;
- super.closeReader();
+ closeReaderSFR();
if (nData == 0 || dataMax == -Float.MAX_VALUE)
return;
dataMean /= nData;
@@ -491,6 +491,10 @@
}
protected void skipData(int nPoints) throws Exception {
+ skipDataVFR(nPoints);
+ }
+
+ protected void skipDataVFR(int nPoints) throws Exception {
int iV = 0;
while (iV < nPoints)
iV += countData(readLine());
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java 2013-05-31 14:57:58 UTC
(rev 18268)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java 2013-05-31 15:20:56 UTC
(rev 18269)
@@ -113,7 +113,7 @@
@Override
protected void skipData(int nPoints) throws Exception {
- super.skipData(nPoints);
+ skipDataVFR(nPoints);
if (isBXSF)
Logger.info(readLine()); //"BAND: <n>" line
}
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java
2013-05-31 14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java
2013-05-31 15:20:56 UTC (rev 18269)
@@ -449,6 +449,10 @@
}
String getDebugLine(int iType, Calculation c) {
+ return getDebugLineC(iType, c);
+ }
+
+ protected String getDebugLineC(int iType, Calculation c) {
float energy = ff.toUserUnits(c.energy);
switch (iType) {
case CALC_DISTANCE:
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
2013-05-31 14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
2013-05-31 15:20:56 UTC (rev 18269)
@@ -577,7 +577,7 @@
new float[] { (float) (c.theta * RAD_TO_DEG), (float)
c.dData[0]/*v1*/, (float) c.dData[1]/*v2*/, (float) c.dData[2]/*v3*/,
energy } });
default:
- return super.getDebugLine(iType, c);
+ return getDebugLineC(iType, c);
}
}
Modified: trunk/Jmol/src/org/jmol/modelkit/ModelKitPopup.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelkit/ModelKitPopup.java 2013-05-31 14:57:58 UTC
(rev 18268)
+++ trunk/Jmol/src/org/jmol/modelkit/ModelKitPopup.java 2013-05-31 15:20:56 UTC
(rev 18269)
@@ -75,7 +75,7 @@
viewer.evalStringQuiet("set picking assignAtom_C");
return;
}
- super.checkMenuClick(source, script);
+ checkMenuClickGP(source, script);
}
@Override
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -69,6 +69,10 @@
private static final Float MINUSZERO = Float.valueOf(-0.0f);
protected void releaseModelSet() {
+ releaseModelSetAC();
+ }
+
+ protected void releaseModelSetAC() {
atoms = null;
viewer = null;
g3d = null;
@@ -86,7 +90,6 @@
partialCharges = null;
ionicRadii = null;
ellipsoids = null;
-
}
protected void mergeAtomArrays(AtomCollection mergeModelSet) {
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -42,9 +42,13 @@
@Override
protected void releaseModelSet() {
+ releaseModelSetBC();
+ }
+
+ protected void releaseModelSetBC() {
bonds = null;
freeBonds = null;
- super.releaseModelSet();
+ releaseModelSetAC();
}
//note: Molecules is set up to only be calculated WHEN NEEDED
Modified: trunk/Jmol/src/org/jmol/modelset/Measurement.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Measurement.java 2013-05-31 14:57:58 UTC
(rev 18268)
+++ trunk/Jmol/src/org/jmol/modelset/Measurement.java 2013-05-31 15:20:56 UTC
(rev 18269)
@@ -119,6 +119,10 @@
}
public void setCount(int count) {
+ setCountM(count);
+ }
+
+ protected void setCountM(int count) {
this.count = countPlusIndices[0] = count;
}
Modified: trunk/Jmol/src/org/jmol/modelset/MeasurementPending.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/MeasurementPending.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/modelset/MeasurementPending.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -71,7 +71,7 @@
@Override
public void setCount(int count) {
- super.setCount(count);
+ setCountM(count);
numSet = count;
}
Modified: trunk/Jmol/src/org/jmol/modelset/Model.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Model.java 2013-05-31 14:57:58 UTC (rev
18268)
+++ trunk/Jmol/src/org/jmol/modelset/Model.java 2013-05-31 15:20:56 UTC (rev
18269)
@@ -271,6 +271,10 @@
}
public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted) {
+ fixIndicesM(modelIndex, nAtomsDeleted, bsDeleted);
+ }
+
+ protected void fixIndicesM(int modelIndex, int nAtomsDeleted, BS bsDeleted) {
if (dataSourceFrame > modelIndex)
dataSourceFrame--;
if (trajectoryBaseIndex > modelIndex)
@@ -283,6 +287,10 @@
}
public void freeze() {
+ freezeM();
+ }
+
+ protected void freezeM() {
chains = (Chain[]) ArrayUtil.arrayCopyObject(chains, chainCount);
groupCount = -1;
getGroupCount();
@@ -462,6 +470,10 @@
}
public void getChimeInfo(SB sb, int nHetero) {
+ getChimeInfoM(sb, nHetero);
+ }
+
+ protected void getChimeInfoM(SB sb, int nHetero) {
sb.append("\nNumber of Atoms ..... " + (modelSet.atomCount - nHetero));
if (nHetero > 0)
sb.append(" (" + nHetero + ")");
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -119,7 +119,7 @@
bsSymmetry = null;
bsAll = null;
unitCells = null;
- super.releaseModelSet();
+ releaseModelSetBC();
}
protected BS bsSymmetry;
@@ -1814,6 +1814,10 @@
* @return number of struts added
*/
public int calculateStruts(BS bs1, BS bs2) {
+ return calculateStrutsMC(bs1, bs2);
+ }
+
+ protected int calculateStrutsMC(BS bs1, BS bs2) {
// select only ONE model
makeConnections2(0, Float.MAX_VALUE, JmolEdge.BOND_STRUT, T.delete, bs1,
bs2, null, false, false, 0);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2013-05-31 14:57:58 UTC
(rev 18268)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2013-05-31 15:20:56 UTC
(rev 18269)
@@ -714,7 +714,7 @@
@Override
public int calculateStruts(BS bs1, BS bs2) {
viewer.setModelVisibility();
- return super.calculateStruts(bs1, bs2);
+ return calculateStrutsMC(bs1, bs2);
}
/**
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2013-05-31 14:57:58 UTC
(rev 18268)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2013-05-31 15:20:56 UTC
(rev 18269)
@@ -85,7 +85,7 @@
@Override
public void freeze() {
- super.freeze();
+ freezeM();
bioPolymers = (BioPolymer[])ArrayUtil.arrayCopyObject(bioPolymers,
bioPolymerCount);
}
@@ -185,7 +185,7 @@
@Override
public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted) {
- super.fixIndices(modelIndex, nAtomsDeleted, bsDeleted);
+ fixIndicesM(modelIndex, nAtomsDeleted, bsDeleted);
for (int i = 0; i < bioPolymerCount; i++)
bioPolymers[i].recalculateLeadMidpointsAndWingVectors();
}
@@ -481,7 +481,7 @@
for (int i = atomCount; --i >= 0;)
if (atoms[i].isHetero())
nHetero++;
- super.getChimeInfo(sb, nHetero);
+ getChimeInfoM(sb, nHetero);
int nH = 0;
int nS = 0;
int nT = 0;
Modified: trunk/Jmol/src/org/jmol/popup/GenericPopup.java
===================================================================
--- trunk/Jmol/src/org/jmol/popup/GenericPopup.java 2013-05-31 14:57:58 UTC
(rev 18268)
+++ trunk/Jmol/src/org/jmol/popup/GenericPopup.java 2013-05-31 15:20:56 UTC
(rev 18269)
@@ -583,6 +583,10 @@
}
public void checkMenuClick(Object source, String script) {
+ checkMenuClickGP(source, script);
+ }
+
+ protected void checkMenuClickGP(Object source, String script) {
restorePopupMenu();
if (script == null || script.length() == 0)
return;
Modified: trunk/Jmol/src/org/jmol/quantum/NciCalculation.java
===================================================================
--- trunk/Jmol/src/org/jmol/quantum/NciCalculation.java 2013-05-31 14:57:58 UTC
(rev 18268)
+++ trunk/Jmol/src/org/jmol/quantum/NciCalculation.java 2013-05-31 15:20:56 UTC
(rev 18269)
@@ -282,7 +282,7 @@
if (eigen == null)
initializeEigen();
isReducedDensity = false;
- super.initializeOnePoint();
+ initializeOnePointQC();
}
private void initializeEigen() {
Modified: trunk/Jmol/src/org/jmol/quantum/QuantumCalculation.java
===================================================================
--- trunk/Jmol/src/org/jmol/quantum/QuantumCalculation.java 2013-05-31
14:57:58 UTC (rev 18268)
+++ trunk/Jmol/src/org/jmol/quantum/QuantumCalculation.java 2013-05-31
15:20:56 UTC (rev 18269)
@@ -169,6 +169,10 @@
}
protected void initializeOnePoint() {
+ initializeOnePointQC();
+ }
+
+ protected void initializeOnePointQC() {
points = new P3[1];
points[0] = new P3();
if (voxelData == null || voxelData == voxelDataTemp) {
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