Revision: 5198
Author: hansonr
Date: 2006-06-03 02:41:15 -0700 (Sat, 03 Jun 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5198&view=rev
Log Message:
-----------
bob200603 set measureAllModels
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java
branches/bob200603/Jmol/src/org/jmol/viewer/Measures.java
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java 2006-06-03
09:39:58 UTC (rev 5197)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java 2006-06-03
09:41:15 UTC (rev 5198)
@@ -708,7 +708,8 @@
}
int getAtomIndexFromAtomNumber(int atomNumber) {
- for (int i = atomCount; --i >= 0;) {
+ //definitely want FIRST (model) not last here
+ for (int i = 0; i < atomCount; i++) {
if (atoms[i].getAtomNumber() == atomNumber)
return i;
}
@@ -1797,7 +1798,7 @@
}
int firstAtomOf(BitSet bs) {
- for (int i = atomCount; --i >= 0;)
+ for (int i = 0; i < atomCount; i++)
if (bs.get(i)) {
return i;
}
@@ -1939,6 +1940,8 @@
return getSpecSeqcode(specInfo);
if (setType.equals("SpecChain"))
return getSpecChain((char) specInfo);
+ if (setType.equals("atomno"))
+ return getSpecAtomNumber(specInfo);
return null;
}
@@ -1952,6 +1955,15 @@
return bsRes;
}
+ BitSet getSpecAtomNumber(int atomno) {
+ BitSet bsRes = new BitSet();
+ for (int i = atomCount; --i >= 0;) {
+ if (atoms[i].getAtomNumber() == atomno)
+ bsRes.set(i);
+ }
+ return bsRes;
+ }
+
BitSet getSpecResid(int resid) {
BitSet bsRes = new BitSet();
for (int i = atomCount; --i >= 0;) {
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Measures.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Measures.java 2006-06-03
09:39:58 UTC (rev 5197)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Measures.java 2006-06-03
09:41:15 UTC (rev 5198)
@@ -64,9 +64,23 @@
}
void define(int[] atomCountPlusIndices) {
-
+ if (viewer.getMeasureAllModelsFlag()) {
+ Vector measureList = new Vector();
+ int nPoints = atomCountPlusIndices[0];
+ for (int i = 1; i <= nPoints; i++) {
+ Atom atom = frame.atoms[atomCountPlusIndices[i]];
+ measureList.add(viewer.getAtomBits("atomno", atom.getAtomNumber()));
+ }
+ define(measureList);
+ return;
+ }
+ defineOnly(atomCountPlusIndices);
+ }
+
+ void defineOnly(int[] atomCountPlusIndices) {
if (isDefined(atomCountPlusIndices))
return;
+
float value = frame.getMeasurement(atomCountPlusIndices);
//System.out.println("measures define value,maxmin "+value+"
"+rangeMinMax[0]+" "+rangeMinMax[1]);
@@ -82,9 +96,9 @@
measurementGrowthIncrement);
}
viewer.setStatusNewDefaultModeMeasurement("measureCompleted" ,
measurementCount, measureNew.toVector().toString());
- measurements[measurementCount++] = measureNew;
+ measurements[measurementCount++] = measureNew;
}
-
+
boolean delete(Object value) {
if (value instanceof int[])
return delete((int[])value);
@@ -139,7 +153,6 @@
*simple!
*
*/
-
int nPoints = monitorExpressions.size();
if (nPoints < 2)
return;
@@ -149,6 +162,7 @@
isOneToOne = false;
int[] atomCountPlusIndices = new int[5];
atomCountPlusIndices[0] = nPoints;
+ //System.out.println("measure define "+ nPoints + " " + isOneToOne);
nextMeasure(0, nPoints, monitorExpressions, atomCountPlusIndices,
isOneToOne ? -1 : 0);
}
@@ -162,7 +176,7 @@
if (thispt > 0 && i == atomCountPlusIndices[thispt])
continue;
int modelIndex = frame.atoms[i].getModelIndex();
- //System.out.println("nextMeasure i"+i+" modelIndex:"+modelIndex);
+ //System.out.println("nextMeasure i "+i+" modelIndex:"+modelIndex + "
thismodel = "+thisModel);
if (thisModel >= 0) {
if (thispt == 0) {
thisModel = modelIndex;
@@ -173,7 +187,7 @@
atomCountPlusIndices[thispt + 1] = i;
if (thispt == nPoints - 1) {
if (!isDefined(atomCountPlusIndices))
- define(atomCountPlusIndices);
+ defineOnly(atomCountPlusIndices);
} else {
nextMeasure(thispt + 1, nPoints, monitorExpressions,
atomCountPlusIndices, thisModel);
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