Revision: 18633
http://sourceforge.net/p/jmol/code/18633
Author: hansonr
Date: 2013-08-30 16:41:40 +0000 (Fri, 30 Aug 2013)
Log Message:
-----------
___JmolVersion="13.3.5_dev_2013.08.29"
new feature: show NMR taps into NMRDB directly
-- for now, application only
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/applet/Jmol.java
trunk/Jmol/src/org/jmol/appletjs/Jmol.java
trunk/Jmol/src/org/jmol/constant/EnumCallback.java
trunk/Jmol/src/org/jmol/viewer/JSpecView.java
trunk/Jmol/src/org/jmol/viewer/StatusManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jmol.java 2013-08-30 10:38:55 UTC (rev
18632)
+++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2013-08-30 16:41:40 UTC (rev
18633)
@@ -888,6 +888,7 @@
case MEASURE:
case MESSAGE:
case PICK:
+ case STRUCTUREMODIFIED:
case SYNC:
case SCRIPT:
return true;
@@ -1027,6 +1028,9 @@
output(strInfo);
showStatus(strInfo);
break;
+ case STRUCTUREMODIFIED:
+ notifyStructureModified(((Integer) data[1]).intValue(), ((Integer)
data[2]).intValue());
+ break;
case SYNC:
sendScript(strInfo, (String) data[2], true, doCallback);
return;
@@ -1057,6 +1061,11 @@
}
}
+ private void notifyStructureModified(int modelIndex, int mode) {
+ // TODO
+
+ }
+
private void output(String s) {
if (outputBuffer != null && s != null)
outputBuffer.append(s).append('\n');
Modified: trunk/Jmol/src/org/jmol/appletjs/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/appletjs/Jmol.java 2013-08-30 10:38:55 UTC (rev
18632)
+++ trunk/Jmol/src/org/jmol/appletjs/Jmol.java 2013-08-30 16:41:40 UTC (rev
18633)
@@ -506,6 +506,7 @@
case MEASURE:
case MESSAGE:
case PICK:
+ case STRUCTUREMODIFIED:
case SYNC:
case SCRIPT:
return true;
@@ -645,6 +646,9 @@
output(strInfo);
showStatus(strInfo);
break;
+ case STRUCTUREMODIFIED:
+ notifyStructureModified(((Integer) data[1]).intValue(), ((Integer)
data[2]).intValue());
+ break;
case SYNC:
sendScript(strInfo, (String) data[2], true, doCallback);
return;
@@ -671,6 +675,12 @@
}
}
+ private void notifyStructureModified(int modelIndex, int mode) {
+ // TODO
+
+ }
+
+
private void output(String s) {
if (outputBuffer != null && s != null)
outputBuffer.append(s).appendC('\n');
Modified: trunk/Jmol/src/org/jmol/constant/EnumCallback.java
===================================================================
--- trunk/Jmol/src/org/jmol/constant/EnumCallback.java 2013-08-30 10:38:55 UTC
(rev 18632)
+++ trunk/Jmol/src/org/jmol/constant/EnumCallback.java 2013-08-30 16:41:40 UTC
(rev 18633)
@@ -44,7 +44,7 @@
PICK,
RESIZE,
SCRIPT,
- SYNC;
+ SYNC, STRUCTUREMODIFIED;
public static EnumCallback getCallback(String name) {
Modified: trunk/Jmol/src/org/jmol/viewer/JSpecView.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JSpecView.java 2013-08-30 10:38:55 UTC
(rev 18632)
+++ trunk/Jmol/src/org/jmol/viewer/JSpecView.java 2013-08-30 16:41:40 UTC
(rev 18633)
@@ -19,13 +19,15 @@
}
public void atomPicked(int atomIndex) {
+ if (atomIndex < 0)
+ return;
String peak = getPeakAtomRecord(atomIndex);
if (peak != null)
sendJSpecView(peak + " src=\"JmolAtomSelect\"");
}
@SuppressWarnings("unchecked")
- public String getPeakAtomRecord(int atomIndex) {
+ private String getPeakAtomRecord(int atomIndex) {
Atom[] atoms = viewer.modelSet.atoms;
int iModel = atoms[atomIndex].modelIndex;
String type = null;
Modified: trunk/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2013-08-30 10:38:55 UTC
(rev 18632)
+++ trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2013-08-30 16:41:40 UTC
(rev 18633)
@@ -601,6 +601,12 @@
jmolCallbackListener.notifyCallback(EnumCallback.SYNC,
new Object[] { null, script, appletName, Integer.valueOf(port) });
}
+
+ void modifySend(int atomIndex, int modelIndex, int mode) {
+ if (notifyEnabled(EnumCallback.STRUCTUREMODIFIED))
+ jmolCallbackListener.notifyCallback(EnumCallback.STRUCTUREMODIFIED,
+ new Object[] { null, Integer.valueOf(mode),
Integer.valueOf(atomIndex), Integer.valueOf(modelIndex) });
+ }
int getSyncMode() {
return (!isSynced ? SYNC_OFF : drivingSync ? SYNC_DRIVER : SYNC_SLAVE);
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-30 10:38:55 UTC (rev
18632)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-30 16:41:40 UTC (rev
18633)
@@ -5790,6 +5790,8 @@
@Override
public boolean getBoolean(int tok) {
switch (tok) {
+ case T.pdb:
+ return modelSet.getModelSetAuxiliaryInfoBoolean("isPDB");
case T.allowgestures:
return global.allowGestures;
case T.allowmultitouch:
@@ -8894,16 +8896,20 @@
}
public int deleteAtoms(BS bs, boolean fullModels) {
+ int atomIndex = (bs == null ? -1 : bs.nextSetBit(0));
+ if (atomIndex < 0)
+ return 0;
clearModelDependentObjects();
if (!fullModels) {
+ statusManager.modifySend(atomIndex,
modelSet.atoms[atomIndex].modelIndex, 4);
modelSet.deleteAtoms(bs);
int n = selectionManager.deleteAtoms(bs);
setTainted(true);
+ statusManager.modifySend(atomIndex,
modelSet.atoms[atomIndex].modelIndex, -4);
return n;
}
- if (bs.cardinality() == 0)
- return 0;
// fileManager.addLoadScript("zap " + Escape.escape(bs));
+ statusManager.modifySend(-1, modelSet.atoms[atomIndex].modelIndex, 5);
setCurrentModelIndexClear(0, false);
animationManager.setAnimationOn(false);
BS bsD0 = BSUtil.copy(getDeletedAtoms());
@@ -8921,6 +8927,7 @@
refreshMeasures(true);
if (bsD0 != null)
bsDeleted.andNot(bsD0);
+ statusManager.modifySend(-1, modelSet.atoms[atomIndex].modelIndex, -5);
return BSUtil.cardinalityOf(bsDeleted);
}
@@ -9596,10 +9603,12 @@
return;
clearModelDependentObjects();
if (pt == null) {
+ statusManager.modifySend(atomIndex,
modelSet.atoms[atomIndex].modelIndex, 1);
int atomCount = modelSet.getAtomCount();
modelSet.assignAtom(atomIndex, type, true);
if (!Parser.isOneOf(type,";Mi;Pl;X;"))
modelSet.setAtomNamesAndNumbers(atomIndex, -atomCount, null);
+ statusManager.modifySend(atomIndex,
modelSet.atoms[atomIndex].modelIndex, -1);
refresh(3, "assignAtom");
return;
}
@@ -9608,6 +9617,8 @@
P3[] pts = new P3[] { pt };
JmolList<Atom> vConnections = new JmolList<Atom>();
vConnections.addLast(atom);
+ int modelIndex = atom.modelIndex;
+ statusManager.modifySend(atomIndex, modelIndex, 3);
try {
bs = addHydrogensInline(bs, vConnections, pts);
atomIndex = bs.nextSetBit(0);
@@ -9616,15 +9627,19 @@
//
}
modelSet.setAtomNamesAndNumbers(atomIndex, -1, null);
+ statusManager.modifySend(atomIndex, modelIndex,-3);
}
public void assignConnect(int index, int index2) {
clearModelDependentObjects();
float[][] connections = ArrayUtil.newFloat2(1);
connections[0] = new float[] { index, index2 };
+ int modelIndex = modelSet.atoms[index].modelIndex;
+ statusManager.modifySend(index, modelIndex, 2);
modelSet.connect(connections);
modelSet.assignAtom(index, ".", true);
modelSet.assignAtom(index2, ".", true);
+ statusManager.modifySend(index, modelIndex, -2);
refresh(3, "assignConnect");
}
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
2013-08-30 10:38:55 UTC (rev 18632)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
2013-08-30 16:41:40 UTC (rev 18633)
@@ -973,7 +973,7 @@
guimap.setSelected("measurementsCheck",
viewer.getBoolean(T.showmeasurements));
guimap.setSelected("axesCheck", viewer.getShowAxes());
guimap.setSelected("boundboxCheck", viewer.getShowBbcage());
- guimap.setEnabled("openJSpecViewScript", display.isRotateMode());
+ guimap.setEnabled("openJSpecViewScript", !viewer.getBoolean(T.pdb));
}
private static class ActionChangedListener implements PropertyChangeListener
{
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
2013-08-30 10:38:55 UTC (rev 18632)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
2013-08-30 16:41:40 UTC (rev 18633)
@@ -91,6 +91,7 @@
case ANIMFRAME:
case ECHO:
case LOADSTRUCT:
+ case STRUCTUREMODIFIED:
case MEASURE:
case MESSAGE:
case PICK:
@@ -168,6 +169,13 @@
case PICK:
notifyAtomPicked(strInfo);
break;
+ case STRUCTUREMODIFIED:
+ // 0 DONE; 1 in process
+ int mode = ((Integer) data[1]).intValue();
+ int atomIndex = ((Integer) data[2]).intValue();
+ int modelIndexx = ((Integer) data[3]).intValue();
+ notifyStructureModified(atomIndex, modelIndexx, mode);
+ break;
case SYNC:
if (strInfo != null && strInfo.toLowerCase().startsWith("jspecview")) {
setJSpecView(strInfo.substring(9).trim(), false, false);
@@ -191,6 +199,21 @@
appConsole.notifyCallback(type, data);
}
+ private void notifyStructureModified(int atomIndex, int modelIndex, int
mode) {
+ modificationMode = mode;
+ if (mode < 0) {
+ switch (mode) {
+ case -1: // assign atom
+ case -2: // assign bond
+ case -3: //
+ case -4: // delete atoms
+ case -5: // delete models
+ checkJSpecView(false);
+ return;
+ }
+ }
+ }
+
public void setCallbackFunction(String callbackType, String
callbackFunction) {
if (callbackType.equals("modelkit")) {
if (callbackFunction.equals("ON"))
@@ -254,19 +277,25 @@
}
if (!display.haveDisplay)
return;
-
+System.out.println("StatusListener notifyFileLoaded: " + fileName);
// this code presumes only ptLoad = -1 (error), 0 (zap), or 3 (completed)
String title = "Jmol";
if (modelName != null && fileName != null)
- title = fileName + " - " + modelName;
+ title = (fileName.contains("&") ? "" : fileName + " - ") + modelName;
else if (fileName != null)
title = fileName;
else if (modelName != null)
title = modelName;
- jmol.notifyFileOpen(fullPathName == null ? null : fullPathName + (isAsync
== Boolean.TRUE ? " (*)" : ""), title);
- if (jSpecViewFrame != null) {
+ jmol.notifyFileOpen(fullPathName == null ? null : fullPathName + (isAsync
== Boolean.TRUE ? " (*)" : ""), title);
+ checkJSpecView(fullPathName == null);
+ }
+
+ private int modificationMode;
+
+ private void checkJSpecView(boolean closeAll) {
+ if (jSpecViewFrame != null && modificationMode <= 0) {
jSpecViewForceNew = jSpecViewFrame.isVisible();
- if (fullPathName == null) {
+ if (closeAll) {
jSpecViewFrame.syncScript("close ALL");
} else {
setJSpecView("", true, true);
@@ -366,8 +395,8 @@
}
public void setJSpecView(String peaks, boolean doLoadCheck, boolean
isFileLoad) {
- if (!display.isRotateMode())
- return;
+ //if (!display.isRotateMode())
+ //return;
if (peaks.startsWith(":"))
peaks = peaks.substring(1);
if (jSpecViewFrame == null) {
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