Menu
▾
▴
[Jmol-commits] SF.net SVN: jmol:[16727] trunk/Jmol/src/org
|
From: <ha...@us...> - 2012-02-03 16:45:38
|
Revision: 16727
http://jmol.svn.sourceforge.net/jmol/?rev=16727&view=rev
Author: hansonr
Date: 2012-02-03 16:45:27 +0000 (Fri, 03 Feb 2012)
Log Message:
-----------
mol reader not assigning names; atom set chooser not handling vibrations properly
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/popup/SwingPopup.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AtomSetChooser.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java 2012-02-03 15:02:44 UTC (rev 16726)
+++ trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java 2012-02-03 16:45:27 UTC (rev 16727)
@@ -181,6 +181,7 @@
if (line == null)
return;
header += line + "\n";
+ Logger.info(header);
checkLineForScript();
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("fileHeader", header);
newAtomSet(thisDataSetName);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java 2012-02-03 15:02:44 UTC (rev 16726)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java 2012-02-03 16:45:27 UTC (rev 16727)
@@ -132,12 +132,11 @@
// process peak data
if (peakData.size() > 0) {
BitSet bsModels = new BitSet();
- bsModels.set(0);
int n = peakData.size();
for (int p = 0; p < n; p++) {
line = peakData.get(p);
String title = getAttribute(line, "title");
- String modelID = getAttribute(line, "model");
+ modelID = getAttribute(line, "model");
String key = "jdxAtomSelect_" + getAttribute(line, "type");
for (int i = atomSetCollection.getAtomSetCount(); --i >= 0;)
if (modelID.equals(atomSetCollection.getAtomSetAuxiliaryInfo(i,
@@ -145,20 +144,25 @@
bsModels.set(i);
if (modelID.indexOf('.') >= 0) {
atomSetCollection.setAtomSetAuxiliaryInfo("name", title, i);
- atomSetCollection.setAtomSetAuxiliaryInfo("jdxModelSelect", line, i);
+ atomSetCollection.setAtomSetAuxiliaryInfo("jdxModelSelect", line,
+ i);
} else if (getAttribute(line, "atoms").length() != 0) {
- List<String> peaks = (List<String>) atomSetCollection.getAtomSetAuxiliaryInfo(i, key);
+ List<String> peaks = (List<String>) atomSetCollection
+ .getAtomSetAuxiliaryInfo(i, key);
if (peaks == null)
- atomSetCollection.setAtomSetAuxiliaryInfo(key, peaks = new ArrayList<String>(), i);
+ atomSetCollection.setAtomSetAuxiliaryInfo(key,
+ peaks = new ArrayList<String>(), i);
peaks.add(line);
}
Logger.info(line);
break;
}
}
- for (int i = atomSetCollection.getAtomSetCount(); --i >= 0;)
- if (!bsModels.get(i))
+ for (int i = atomSetCollection.getAtomSetCount(); --i >= 0;) {
+ modelID = (String) atomSetCollection.getAtomSetAuxiliaryInfo(i, "modelID");
+ if (!bsModels.get(i) && modelID.indexOf(".") >= 0)
atomSetCollection.removeAtomSet(i);
+ }
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2012-02-03 15:02:44 UTC (rev 16726)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2012-02-03 16:45:27 UTC (rev 16727)
@@ -547,7 +547,7 @@
} else {
atomSetCollection.setCollectionName(name);
}
- Logger.debug(name);
+ atomSetCollection.setAtomSetAuxiliaryInfo("name", name, Math.max(0, atomSetCollection.getCurrentAtomSetIndex()));
}
protected int cloneLastAtomSet(int atomCount, Point3f[] pts) throws Exception {
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2012-02-03 15:02:44 UTC (rev 16726)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2012-02-03 16:45:27 UTC (rev 16727)
@@ -916,7 +916,7 @@
{"ZMatrix", "#ZMATRIX"};
private final static String[] jcampdxFileStartRecords =
- {"Jcampdx", "##TITLE=", "##JCAMP-DX"};
+ {"Jcampdx", "##TITLE="};
private final static String[][] fileStartsWithRecords =
{ cubeFileStartRecords, mol2Records, webmoFileStartRecords,
Modified: trunk/Jmol/src/org/jmol/popup/SwingPopup.java
===================================================================
--- trunk/Jmol/src/org/jmol/popup/SwingPopup.java 2012-02-03 15:02:44 UTC (rev 16726)
+++ trunk/Jmol/src/org/jmol/popup/SwingPopup.java 2012-02-03 16:45:27 UTC (rev 16727)
@@ -181,6 +181,10 @@
jm.addItemListener(cmil);
jm.setActionCommand(basename);
updateButton(jm, entry, basename);
+ if (id != null && id.startsWith("Focus")) {
+ jm.addMouseListener(mfl);
+ id = ((Component) menu).getName() + "." + id;
+ }
jm.setName(id == null ? ((Component) menu).getName() + "." : id);
addToMenu(menu, jm);
return jm;
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AtomSetChooser.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AtomSetChooser.java 2012-02-03 15:02:44 UTC (rev 16726)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AtomSetChooser.java 2012-02-03 16:45:27 UTC (rev 16727)
@@ -352,7 +352,7 @@
private JPanel createVCRController(String section) {
JPanel controlPanel = new JPanel();
controlPanel.setLayout(new BoxLayout(controlPanel, BoxLayout.X_AXIS));
- controlPanel.setBorder(new TitledBorder(GT._("Controller")));
+ controlPanel.setBorder(new TitledBorder((section.equals(COLLECTION) ? GT._("Frame") : GT._("Vibration"))));
Insets inset = new Insets(1,1,1,1);
// take out the save functionality until the XYZ file can properly be created
// String buttons[] = {REWIND,PREVIOUS,PLAY,PAUSE,NEXT,FF,SAVE};
@@ -369,12 +369,12 @@
};
} else if (section.equals(VECTOR)) {
tooltips = new String[] {
- GT._("Go to first vector in the collection"),
- GT._("Go to previous vector in the collection"),
- GT._("Play the whole collection of vectors"),
- GT._("Pause playing"),
- GT._("Go to next vector in the collection"),
- GT._("Jump to last vector in the collection")
+ GT._("Go to first atom set in the collection"),
+ GT._("Go to previous atom set in the collection"),
+ GT._("Vibration ON"),
+ GT._("Vibration OFF"),
+ GT._("Go to next atom set in the collection"),
+ GT._("Jump to last atom set in the collection")
};
}
for (int i=buttons.length, idx=0; --i>=0; idx++) {
@@ -491,9 +491,9 @@
} else if (PREVIOUS.equals(cmd)) {
findFrequency(currentIndex-1,-1);
} else if (PLAY.equals(cmd)) {
- viewer.evalStringQuiet("vibration on");
+ viewer.evalStringQuiet("vibration on; vectors " + radiusValue);
} else if (PAUSE.equals(cmd)) {
- viewer.evalStringQuiet("vibration off");
+ viewer.evalStringQuiet("vibration off; vectors off");
} else if (NEXT.equals(cmd)) {
findFrequency(currentIndex+1,1);
} else if (FF.equals(cmd)) {
@@ -573,6 +573,8 @@
showAtomSetIndex(index, true);
}
}
+
+ private int radiusValue = 1;
public void stateChanged(ChangeEvent e) {
Object src = e.getSource();
@@ -587,9 +589,10 @@
cmd = "animation fps " + value;
} else if (src == radiusSlider) {
if (value == 0)
- radiusSlider.setValue(1); // make sure I never set it to 0..
+ radiusSlider.setValue(value = 1); // make sure I never set it to 0..
else
cmd = "vector " + value;
+ radiusValue = value;
} else if (src == scaleSlider) {
cmd = "vector scale " + (value * SCALE_PRECISION);
} else if (src == amplitudeSlider) {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|