Revision: 5224
Author: hansonr
Date: 2006-06-14 14:10:07 -0700 (Wed, 14 Jun 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5224&view=rev
Log Message:
-----------
bob200603 measures -- better logic; code cleanup
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/viewer/Measures.java
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Measures.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Measures.java 2006-06-14
18:03:21 UTC (rev 5223)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Measures.java 2006-06-14
21:10:07 UTC (rev 5224)
@@ -50,14 +50,84 @@
font3d = g3d.getFont3D(JmolConstants.MEASURE_DEFAULT_FONTSIZE);
}
- void clear() {
+ void setSize(int size, BitSet bsSelected) {
+ mad = (short)size;
+ }
+
+ void setProperty(String propertyName, Object value,
+ BitSet bsSelected){
+ //System.out.println("Measures " + propertyName + " " + value);
+ if ("color".equals(propertyName)) {
+ colix = (value == null ? 0 : Graphics3D.getColix(value));
+ for (int i = 0; i < measurements.length; i++)
+ if (measurements[i] != null
+ && (colix == 0 || measurements[i].colix == 0))
+ measurements[i].colix = colix;
+ return;
+ }
+ if ("font".equals(propertyName))
+ { font3d = (Font3D)value; }
+ else if ("delete".equals(propertyName))
+ { delete(value); }
+ else if ("toggle".equals(propertyName))
+ { toggle((int[])value); }
+ else if ("deleteVector".equals(propertyName))
+ { define((Vector)value, true, false, false); }
+ else if ("defineVector".equals(propertyName))
+ { define((Vector)value, false, false, false); }
+ else if ("showVector".equals(propertyName))
+ { define((Vector)value, false, true, false); }
+ else if ("hideVector".equals(propertyName))
+ { define((Vector)value, false, false, true); }
+ else if ("setRange".equals(propertyName))
+ { setRange((float[])value); }
+ else if ("setConnected".equals(propertyName))
+ { setConnected(((Boolean)value).booleanValue()); }
+ else if ("pending".equals(propertyName))
+ { pending((int[])value); }
+ else if ("clear".equals(propertyName))
+ { clear(); }
+ else if ("hideAll".equals(propertyName))
+ { showHide(((Boolean)value).booleanValue()); }
+ else if ("show".equals(propertyName))
+ { showHide((int[])value, false); }
+ else if ("hide".equals(propertyName))
+ { showHide((int[])value, true); }
+ else if ("showMeasurementNumbers".equals(propertyName))
+ { showMeasurementNumbers = ((Boolean)value).booleanValue(); }
+ else if ("reformatDistances".equals(propertyName))
+ { reformatDistances(); }
+ }
+
+ Object getProperty(String property, int index) {
+ //System.out.println("Measures.getProperty(" +property + "," + index +")");
+ if ("count".equals(property))
+ { return new Integer(measurementCount); }
+ if ("countPlusIndices".equals(property)) {
+ return index < measurementCount
+ ? measurements[index].countPlusIndices : null;
+ }
+ if ("stringValue".equals(property)) {
+ return index < measurementCount
+ ? measurements[index].strMeasurement : null;
+ }
+ if ("info".equals(property)) {
+ return getAllInfo();
+ }
+ if ("infostring".equals(property)) {
+ return getAllInfoAsString();
+ }
+ return null;
+ }
+
+ private void clear() {
int countT = measurementCount;
measurementCount = 0;
for (int i = countT; --i >= 0; )
measurements[i] = null;
}
- int defined(int[] atomCountPlusIndices) {
+ private int defined(int[] atomCountPlusIndices) {
for (int i = measurementCount; --i >= 0; ) {
if (measurements[i].sameAs(atomCountPlusIndices))
return i;
@@ -65,33 +135,24 @@
return -1;
}
- void toggle(int[] atomCountPlusIndices) {
+ private void toggle(int[] atomCountPlusIndices) {
rangeMinMax[0] = Float.MAX_VALUE;
- if (defined(atomCountPlusIndices) >= 0)
- define(atomCountPlusIndices, true, false, false);
- else
- define(atomCountPlusIndices, false, false, false);
+ //toggling one that is hidden should be interpreted as DEFINE
+ int i = defined(atomCountPlusIndices);
+ if (i >= 0 && !measurements[i].isHidden) // delete it
+ define(atomCountPlusIndices, true, false);
+ else // define OR turn on if measureAllModels
+ define(atomCountPlusIndices, false, true);
}
- void define(int[] atomCountPlusIndices) {
- define(atomCountPlusIndices, false, false, false);
+ private void delete(Object value) {
+ if (value instanceof int[])
+ define((int[])value, true, false);
+ else if (value instanceof Integer)
+ define(measurements[((Integer)value).intValue()].countPlusIndices, true,
false);
}
-
- void define(int[] atomCountPlusIndices, boolean isDelete, boolean isShow,
boolean isHide) {
- 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, isDelete, isShow, isHide);
- return;
- }
- defineOnly(atomCountPlusIndices, isDelete);
- }
-
- void define(Vector monitorExpressions, boolean isDelete, boolean isShow,
boolean isHide) {
+
+ private void define(Vector monitorExpressions, boolean isDelete, boolean
isShow, boolean isHide) {
/*
* sets up measures based on an array of atom selection expressions -RMH
3/06
*
@@ -111,37 +172,84 @@
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, isDelete, isShow, isHide);
}
- void showHide(int[] atomCountPlusIndices, boolean isHide) {
+ private void define(int[] atomCountPlusIndices, boolean isDelete, boolean
isShow) {
+ if (viewer.getMeasureAllModelsFlag()) {
+ if (isShow) { // make sure all like this are deleted, not just hidden
+ define(atomCountPlusIndices, true, false); // self-reference
+ if (isDelete)
+ return;
+ }
+ 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, isDelete, false, false);
+ return;
+ }
+ define(atomCountPlusIndices, isDelete);
+ }
+
+ private void define(int[] atomCountPlusIndices, boolean isDelete) {
int i = defined(atomCountPlusIndices);
+ //System.out.println("define " + isDelete + " " + i + " [" +
atomCountPlusIndices[0] + " " + atomCountPlusIndices[1] + " " +
atomCountPlusIndices[2] + " " + atomCountPlusIndices[3] + " " +
atomCountPlusIndices[4] + "]");
+ if (i < 0 && isDelete)
+ return;
+ float value;
+ value = frame.getMeasurement(atomCountPlusIndices);
+ if (rangeMinMax[0] != Float.MAX_VALUE
+ && (value < rangeMinMax[0] || value > rangeMinMax[1]))
+ return;
+ if (i >= 0) {
+ if (isDelete) {
+ viewer.setStatusNewDefaultModeMeasurement("measureDeleted", i, "");
+ System.arraycopy(measurements, i + 1, measurements, i, measurementCount
+ - i - 1);
+ --measurementCount;
+ measurements[measurementCount] = null;
+ } else {
+ measurements[i].isHidden = false;
+ }
+ return;
+ }
+ Measurement measureNew = new Measurement(frame, atomCountPlusIndices,
+ value, colix);
+ if (measurementCount == measurements.length) {
+ measurements = (Measurement[]) Util.setLength(measurements,
+ measurementCount + measurementGrowthIncrement);
+ }
+ viewer.setStatusNewDefaultModeMeasurement("measureCompleted",
+ measurementCount, measureNew.toVector().toString());
+ measurements[measurementCount++] = measureNew;
+ }
+
+ private void showHide(int[] atomCountPlusIndices, boolean isHide) {
+ int i = defined(atomCountPlusIndices);
if (i < 0)
return;
measurements[i].isHidden = isHide;
}
- void showHide(boolean isHide) {
+ private void showHide(boolean isHide) {
for (int i = measurementCount; --i >= 0; )
measurements[i].isHidden = isHide;
}
- void nextMeasure(int thispt, int nPoints, Vector monitorExpressions,
+ private void nextMeasure(int thispt, int nPoints, Vector monitorExpressions,
int[] atomCountPlusIndices, int thisModel, boolean isDelete,
boolean isShow, boolean isHide) {
BitSet bs = (BitSet) monitorExpressions.get(thispt);
- //System.out.println("nextMeasure" + thispt + " acpi:" +
atomCountPlusIndices
- //+ " " + isDelete);
- //System.out.println("bs "+ bs);
int iMax = bs.size();
for (int i = 0; i < iMax; i++) {
if (bs.get(i)) {
if (thispt > 0 && i == atomCountPlusIndices[thispt])
continue;
int modelIndex = frame.atoms[i].getModelIndex();
- //System.out.println("nextMeasure i "+i+" modelIndex:"+modelIndex + "
thismodel = "+thisModel);
if (thisModel >= 0) {
if (thispt == 0) {
thisModel = modelIndex;
@@ -154,14 +262,14 @@
if (isAllConnected && !isConnected(atomCountPlusIndices))
continue;
if (defined(atomCountPlusIndices) >= 0) {
- if (isHide || isShow)
+ if (isDelete)
+ define(atomCountPlusIndices, true);
+ else
showHide(atomCountPlusIndices, isHide);
- else if (isDelete)
- defineOnly(atomCountPlusIndices, true);
continue;
}
if (!isDelete && !isHide && !isShow)
- defineOnly(atomCountPlusIndices, false);
+ define(atomCountPlusIndices, false);
continue;
}
nextMeasure(thispt + 1, nPoints, monitorExpressions,
@@ -170,7 +278,7 @@
}
}
- boolean isConnected(int[] atomCountPlusIndices) {
+ private boolean isConnected(int[] atomCountPlusIndices) {
Atom[] atoms = frame.atoms;
for (int i = atomCountPlusIndices[0]; i > 1; --i)
if
(!atoms[atomCountPlusIndices[i]].isBonded(atoms[atomCountPlusIndices[i-1]]))
@@ -178,156 +286,28 @@
return true;
}
- void defineOnly(int[] atomCountPlusIndices, boolean isDelete) {
- float value = frame.getMeasurement(atomCountPlusIndices);
- //System.out.println("measures define value,maxmin "+value+"
"+rangeMinMax[0]+" "+rangeMinMax[1] + " " + isDelete);
-
- if (rangeMinMax[0] != Float.MAX_VALUE) {
- if (value < rangeMinMax[0] || value > rangeMinMax[1])
- return;
- }
-
- if (defined(atomCountPlusIndices) >= 0) {
- if(isDelete)
- delete(atomCountPlusIndices);
- return;
- }
- if (isDelete)
- return;
-
- //System.out.println("define " + rangeMinMax[0] + "-" + rangeMinMax[1] +
";" + value);
- Measurement measureNew = new Measurement(frame, atomCountPlusIndices,
value, colix);
- if (measurementCount == measurements.length) {
- measurements =(Measurement[])Util.setLength(measurements,
- measurementCount +
- measurementGrowthIncrement);
- }
- viewer.setStatusNewDefaultModeMeasurement("measureCompleted" ,
measurementCount, measureNew.toVector().toString());
- measurements[measurementCount++] = measureNew;
- }
-
- boolean delete(Object value) {
- if (value instanceof int[])
- return delete((int[])value);
- if (value instanceof Integer)
- return delete(((Integer)value).intValue());
- return false;
- }
-
- boolean delete(int[] atomCountPlusIndices) {
- for (int i = measurementCount; --i >= 0; ) {
- if (measurements[i].sameAs(atomCountPlusIndices))
- return delete(i);
- }
- return false;
- }
-
- boolean delete(int i) {
- if (i < measurementCount) {
- viewer.setStatusNewDefaultModeMeasurement("measureDeleted" , i, "");
- System.arraycopy(measurements, i+1,
- measurements, i,
- measurementCount - i - 1);
- --measurementCount;
- measurements[measurementCount] = null;
- return true;
- }
- return false;
- }
-
- void setRange(float[] rangeMinMax) {
+ private void setRange(float[] rangeMinMax) {
//System.out.println("setRange"+rangeMinMax[0]+rangeMinMax[1]);
this.rangeMinMax[0] = rangeMinMax[0];
this.rangeMinMax[1] = rangeMinMax[1];
}
- void setConnected(boolean isAllConnected) {
+ private void setConnected(boolean isAllConnected) {
this.isAllConnected = isAllConnected;
}
- void pending(int[] countPlusIndices) {
+ private void pending(int[] countPlusIndices) {
pendingMeasurement.setCountPlusIndices(countPlusIndices);
if (pendingMeasurement.count > 1)
viewer.setStatusNewDefaultModeMeasurement("measurePending" ,
pendingMeasurement.count, pendingMeasurement.strMeasurement);
}
- void setSize(int size, BitSet bsSelected) {
- mad = (short)size;
+ private void reformatDistances() {
+ for (int i = measurementCount; --i >= 0; )
+ measurements[i].reformatDistanceIfSelected();
}
-
- void setProperty(String propertyName, Object value,
- BitSet bsSelected){
-
- //System.out.println("Measures " + propertyName + " " + value);
- if ("color".equals(propertyName)) {
- //System.out.println("Measures.color set to:" + value);
- colix = (value == null ? 0 : Graphics3D.getColix(value));
- for (int i = 0; i < measurements.length; i++)
- if (measurements[i] != null
- && (colix == 0 || measurements[i].colix == 0))
- measurements[i].colix = colix;
- return;
- }
- if ("font".equals(propertyName))
- { font3d = (Font3D)value; return; }
- else if ("define".equals(propertyName))
- { define((int[])value); }
- else if ("delete".equals(propertyName))
- { delete(value); }
- else if ("toggle".equals(propertyName))
- { toggle((int[])value); }
- else if ("deleteVector".equals(propertyName))
- { define((Vector)value, true, false, false); }
- else if ("defineVector".equals(propertyName))
- { define((Vector)value, false, false, false); }
- else if ("showVector".equals(propertyName))
- { define((Vector)value, false, true, false); }
- else if ("hideVector".equals(propertyName))
- { define((Vector)value, false, false, true); }
- else if ("setRange".equals(propertyName))
- { setRange((float[])value); }
- else if ("setConnected".equals(propertyName))
- { setConnected(((Boolean)value).booleanValue()); }
- else if ("pending".equals(propertyName))
- { pending((int[])value); }
- else if ("clear".equals(propertyName))
- { clear(); }
- else if ("hideAll".equals(propertyName))
- { showHide(((Boolean)value).booleanValue()); }
- else if ("show".equals(propertyName))
- { showHide((int[])value, false); }
- else if ("hide".equals(propertyName))
- { showHide((int[])value, true); }
- else if ("showMeasurementNumbers".equals(propertyName))
- { showMeasurementNumbers = ((Boolean)value).booleanValue(); }
- else if ("reformatDistances".equals(propertyName))
- { reformatDistances(); }
- else
- return;
- }
-
- Object getProperty(String property, int index) {
- //System.out.println("Measures.getProperty(" +property + "," + index +")");
- if ("count".equals(property))
- { return new Integer(measurementCount); }
- if ("countPlusIndices".equals(property)) {
- return index < measurementCount
- ? measurements[index].countPlusIndices : null;
- }
- if ("stringValue".equals(property)) {
- return index < measurementCount
- ? measurements[index].strMeasurement : null;
- }
- if ("info".equals(property)) {
- return getAllInfo();
- }
- if ("infostring".equals(property)) {
- return getAllInfoAsString();
- }
- return null;
- }
-
- Vector getAllInfo() {
+
+ private Vector getAllInfo() {
Vector info = new Vector();
for (int i = 0; i< measurementCount; i++) {
info.add(getInfo(i));
@@ -335,7 +315,7 @@
return info;
}
- String getAllInfoAsString() {
+ private String getAllInfoAsString() {
String info = "Measurement Information";
for (int i = 0; i< measurementCount; i++) {
info += "\n" + getInfoAsString(i);
@@ -343,7 +323,7 @@
return info;
}
- Hashtable getInfo(int index) {
+ private Hashtable getInfo(int index) {
int count = measurements[index].count;
Hashtable info = new Hashtable();
info.put("index", new Integer(index));
@@ -365,7 +345,7 @@
return info;
}
- String getInfoAsString(int index) {
+ private String getInfoAsString(int index) {
int count = measurements[index].count;
String info = (count == 2 ? "distance" : count == 3 ? "angle" : "dihedral")
+ " \t" + measurements[index].value + " \t"
@@ -377,11 +357,6 @@
return info;
}
- void reformatDistances() {
- for (int i = measurementCount; --i >= 0; )
- measurements[i].reformatDistanceIfSelected();
- }
-
void setVisibilityInfo() {
out:
for (int i = measurementCount; --i >= 0; ) {
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