Revision: 20615
http://sourceforge.net/p/jmol/code/20615
Author: hansonr
Date: 2015-07-01 19:31:54 +0000 (Wed, 01 Jul 2015)
Log Message:
-----------
Modified Paths:
--------------
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialog.java
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogConfig.java
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogSearch.java
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogView.java
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
Modified: branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialog.java
===================================================================
--- branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialog.java
2015-07-01 15:48:43 UTC (rev 20614)
+++ branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialog.java
2015-07-01 19:31:54 UTC (rev 20615)
@@ -141,14 +141,12 @@
setVisible(true);
break;
case 'm':
- nboMode = NBOService.MODE_MODEL;
+ dialogMode = NBOService.MODE_MODEL;
modules.setSelectedIndex(0);
this.setMinimumSize(new Dimension(450, 550));
this.setSize(new Dimension(450, 550));
this.repaint();
this.revalidate();
- cmdFile = new File(nboService.serverPath);
- cmdFile = new File(cmdFile.getParent() + "/m_test.txt");
buildModel(this.getContentPane());
if (vwr.ms.ac != 0) {
loadModel();
@@ -157,7 +155,7 @@
}
break;
case 'r':
- nboMode = NBOService.MODE_RUN;
+ dialogMode = NBOService.MODE_RUN;
modules.setSelectedIndex(1);
this.setMinimumSize(new Dimension(300, 450));
this.setSize(new Dimension(300, 450));
@@ -172,10 +170,8 @@
}
break;
case 's':
- nboMode = NBOService.MODE_SEARCH;
+ dialogMode = NBOService.MODE_SEARCH;
modules.setSelectedIndex(3);
- cmdFile = new File(nboService.serverPath);
- cmdFile = new File(cmdFile.getParent() + "/s_test.txt");
this.setMinimumSize(new Dimension(1000, 500));
this.setSize(new Dimension(1000, 500));
this.repaint();
@@ -189,14 +185,12 @@
}
break;
case 'v':
- nboMode = NBOService.MODE_VIEW;
+ dialogMode = NBOService.MODE_VIEW;
modules.setSelectedIndex(2);
this.setMinimumSize(new Dimension(650, 400));
this.setSize(new Dimension(650, 400));
this.repaint();
this.revalidate();
- cmdFile = new File(nboService.serverPath);
- cmdFile = new File(cmdFile.getParent() + "/v_test.txt");
buildView(this.getContentPane());
String f = null;
if (vwr.ms.getInfo(vwr.am.cmi, "nboType") != null
@@ -227,7 +221,7 @@
int atomIndex = ((Integer) data[2]).intValue();
if (atomIndex >= 0) {
String st = vwr.ms.at[atomIndex].getInfo();
- switch (nboMode) {
+ switch (dialogMode) {
case NBOService.MODE_MODEL:
if (tf != null && tf2 != null && tf3 == null) {
if (tf.getText().equals("")
Modified:
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogConfig.java
===================================================================
--- branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogConfig.java
2015-07-01 15:48:43 UTC (rev 20614)
+++ branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogConfig.java
2015-07-01 19:31:54 UTC (rev 20615)
@@ -111,10 +111,8 @@
protected String jobStem;
- protected File cmdFile;
+ protected int dialogMode;
- protected int nboMode;
-
protected Font nboFont = new Font("Monospaced", Font.BOLD, 14);
/**
@@ -135,9 +133,9 @@
JPanel fp = buildFilePanel();
JPanel top = new JPanel();
top.setPreferredSize(new Dimension(400, 100));
- p.add(buildRightPanel(), BorderLayout.CENTER);
+ //p.add(buildRightPanel(), BorderLayout.CENTER);
p.add(fp, BorderLayout.NORTH);
- p.add(buildRightPanel(), BorderLayout.CENTER);
+ //p.add(buildRightPanel(), BorderLayout.CENTER);
centerDialog(this);
}
@@ -209,7 +207,15 @@
nboInput.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
- rawCmd(null);
+ String cmd = nboInput.getText();
+ if (cmd.startsWith("!")) {
+ cmd = cmd.substring(1);
+ // a synchonous Jmol command
+ String msg = nboService.runScriptNow(cmd);
+ Logger.info(msg);
+ return;
+ }
+ nboService.rawCmdNew(cmd, null, false);
}
});
JPanel showPanel = new JPanel(new BorderLayout());
@@ -225,17 +231,7 @@
}
protected void rawCmd(String cmd) {
- if (cmd == null) {
- cmd = nboInput.getText();
- if (cmd.startsWith("!")) {
- cmd = cmd.substring(1);
- // a synchonous Jmol command
- String msg = nboService.runScriptNow(cmd);
- Logger.info(msg);
- return;
- }
- }
- nboService.rawCmd(cmd);
+ nboService.rawCmdNew(cmd, null, false);
}
protected void connectPressed() {
Modified:
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogSearch.java
===================================================================
--- branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogSearch.java
2015-07-01 15:48:43 UTC (rev 20614)
+++ branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogSearch.java
2015-07-01 19:31:54 UTC (rev 20615)
@@ -746,7 +746,6 @@
goRunClicked(DEFAULT_PARAMS, inputFile);
while (!f.exists() || f.length() / 1024 == 0) {
}
- cmdFile = new File(cmdFile.getParent() + "/s_test.txt");
}
//workingPath =
f.toString().substring(0,inputFile.toString().lastIndexOf("."))+".nbo";
//inputFile = new File(workingPath);
@@ -758,7 +757,6 @@
+ ".47"));
while (!f2.exists() || f2.length() / 1024 == 0) {
}
- cmdFile = new File(cmdFile.getParent() + "/s_test.txt");
}
nboService.runScriptNow("load "
+ inputFile.toString().substring(0,
@@ -796,7 +794,7 @@
appendToFile("GLOBAL C_JOBSTEM " + jobStem + sep, sb);
appendToFile("GLOBAL I_BAS_1 " + keywordNumber + sep, sb);
appendToFile("CMD " + get, sb);
- nboMode = NBOService.MODE_SEARCH;
+ dialogMode = NBOService.MODE_SEARCH;
nboService.rawCmdNew("s", sb, true);
String[] st = new String[reqInfo.length() / 20];
for (int i = 0; (i + 1) * 20 <= reqInfo.length(); i++)
@@ -813,7 +811,7 @@
appendToFile("GLOBAL C_JOBSTEM " + jobStem + sep, sb);
appendToFile("GLOBAL I_BAS_1 " + keywordNumber + sep, sb);
appendToFile("CMD r", sb);
- nboMode = NBOService.MODE_SEARCH_7;
+ dialogMode = NBOService.MODE_SEARCH_7;
nboService.rawCmdNew("s", sb, true);
int r = Integer.parseInt(reqInfo.substring(reqInfo.indexOf("-") + 1,
reqInfo.indexOf(")")));
@@ -826,7 +824,7 @@
}
protected void goSearchClicked() {
- nboMode = NBOService.MODE_SEARCH;
+ dialogMode = NBOService.MODE_SEARCH;
if (!keyProp.equals(""))
if (w != null)
w.interrupt();
@@ -889,7 +887,7 @@
w.start();
} else if ((keywordNumber == 1 && op == 12)
|| (keywordNumber == 6 && (op == 9 || op == 10))) {
- nboMode = NBOService.MODE_SEARCH_6;
+ dialogMode = NBOService.MODE_SEARCH_6;
nboService.inRequest = false;
reqInfo = "";
new NBOSearchWorker1(sb).start();
Modified: branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogView.java
===================================================================
--- branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogView.java
2015-07-01 15:48:43 UTC (rev 20614)
+++ branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogView.java
2015-07-01 19:31:54 UTC (rev 20615)
@@ -26,6 +26,7 @@
import java.awt.BorderLayout;
import java.awt.Container;
import java.awt.Dimension;
+import java.awt.EventQueue;
import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
@@ -918,20 +919,35 @@
@Override
public void valueChanged(ListSelectionEvent e) {
int i = list.getSelectedIndex();
- showOrbJmol(list, i);
+ System.out.println("-----------------------" + iLast + " " + i);
+ if (i == iLast)
+ return;
+ showOrbJmol(list, iLast = i);
}
});
- list.setSelectedIndex(0);
go.setEnabled(true);
p.getViewport().add(list);
p.setMinimumSize(new Dimension(100, 400));
selectPanel.add(p);
selectPanel.repaint();
selectPanel.revalidate();
+ int i = iLast;
+ iLast = -1;
+ if (i > 0 && i < list.getComponentCount())
+ i = 0;
+ final int i0 = i;
+ EventQueue.invokeLater(new Runnable() {
+ @Override
+ public void run() {
+ list.setSelectedIndex(i0);
+ }
+ });
}
+ protected int iLast = -1;
+
private NBOPanel display() {
NBOPanel s = new NBOPanel(this, PANEL_RIGHT);
s.setBorder(new TitledBorder("Display"));
@@ -988,7 +1004,7 @@
sLab.setText("+");
vLab.setText("1, 2");
pLab.setText("1, 2, 3");
- getList("LABEL", "<v_test.txt>");
+ getViewList("LABEL");
}
protected void nboViewAddLine(String line) {
@@ -1028,10 +1044,10 @@
inputFile.getName().lastIndexOf("."));
workPathLabel.setText(jobStem);
workingPath = inputFile.getAbsolutePath();
- basisSel();
tfFolder.setText(inputFile.getParent());
tfName.setText(jobStem);
tfExt.setText(".nbo");
+ basisSel();
}
protected void goViewClicked() {
@@ -1137,7 +1153,7 @@
}
}
- protected void getList(String get, String cmd) {
+ protected void getViewList(String get) {
rawCmd("");
SB sb = new SB();
reqInfo = "";
@@ -1152,7 +1168,6 @@
}
class NBOViewWorker2 extends Thread {
- private String[] st;
private SB sb;
public NBOViewWorker2(SB sb) {
@@ -1164,18 +1179,27 @@
//File f = new File(inputFile.getParent() + "\\" + jobStem + ".bmp");
Thread.currentThread().setName(
"NBOViewThread" + System.currentTimeMillis());
- nboMode = NBOService.MODE_VIEW_4;
+ dialogMode = NBOService.MODE_VIEW_4;
nboService.rawCmdNew("v", sb, true);
- st = new String[reqInfo.length() / 20];
- for (int i = 0; (i + 1) * 20 <= reqInfo.length(); i++)
- st[i] = reqInfo.substring(i * 20, (i + 1) * 20);
done();
}
protected void done() {
+ System.out.println("processing list " + reqInfo);
+ try {
+ String[] st = new String[reqInfo.length() / 20];
+ for (int i = 0; (i + 1) * 20 <= reqInfo.length(); i++)
+ st[i] = reqInfo.substring(i * 20, (i + 1) * 20);
select(st);
- nboMode = NBOService.MODE_VIEW;
+ } catch (Exception e) {
+ System.out.println(e);
+ }
+ dialogMode = NBOService.MODE_VIEW;
}
}
+ @Override
+ protected void reset() {
+ iLast = -1;
+ }
}
Modified: branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
===================================================================
--- branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
2015-07-01 15:48:43 UTC (rev 20614)
+++ branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
2015-07-01 19:31:54 UTC (rev 20615)
@@ -62,7 +62,8 @@
static final int MODE_SEARCH_6 = 6;
static final int MODE_SEARCH_7 = 7;
- private int nboMode = MODE_RAW;
+ private static final int MODE_ERR = -1;
+ private int serverMode = MODE_RAW;
private transient Viewer vwr;
@@ -76,7 +77,6 @@
private PrintWriter stdinWriter;
private SB sbRet;
- private String nboAction;
private boolean inData;
protected boolean inRequest, isWorking;
@@ -144,17 +144,20 @@
closeProcess();
startProcess(nboSync);
}
- nboMode = ((Integer) info.get("mode")).intValue();
+ serverMode = ((Integer) info.get("mode")).intValue();
if (stdinWriter == null) {
closeProcess();
sbRet
.append("ERROR: Could not connect to NBOServe -- Use Tools...NBO...
to set up NBOServe");
- nboMode = 0;
+ serverMode = MODE_ERR;
}
- nboAction = (String) info.get("action");
+ String nboAction = (String) info.get("action");
+ if (nboAction == null)
+ System.out.println("HOH");
String s;
- switch (nboMode) {
+ switch (serverMode) {
case MODE_MODEL:
+ // from Jmol script, not dialog
s = (String) info.get("value");
if (nboAction.equals("load")) {
s = "sh " + s;
@@ -173,7 +176,7 @@
break;
}
if (s != null) {
- sendToNBO(nboMode, s);
+ sendToNBO(serverMode, s);
if (nboSync) {
try {
nboServer.waitFor();
@@ -195,47 +198,55 @@
* @param s
*/
private void sendToNBO(int mode, String s) {
- s = (mode == MODE_RAW ? s : mode + "\n" + s + "\nexit"
- + (nboSync ? "\nexit" : ""));
+ s = (mode == MODE_RAW ? s : mode + "\r\n" + s + "\r\n"
+ + (nboSync ? "x\r\n" : ""));
sendCmd(s);
}
private void sendCmd(String s) {
- //vwr.log("sending:\n>>>\n" + s + "\n<<<");
- stdinWriter.println(s);
- stdinWriter.flush();
+ try {
+ stdinWriter.println(s);
+ stdinWriter.flush();
+ Thread.sleep(10);
+ } catch (InterruptedException e) {
+ // TODO
+ }
}
protected void nboReport(String line) {
- if (Logger.debugging)
- Logger.debug(inData + " " + nboSync + " " + sbRet.length() + " " +
"receiving: " + line);
- if (line.startsWith("DATA ")) {
- if (line.startsWith("DATA \"model")) {
- sbRet.setLength(0);
- nboModel = PT.getQuotedStringAt(line, 0);
- line += " NBO " + nboModel;
- }
- inData = (line.indexOf("exit") < 0);
- if (inData)
- sbRet.append(line + "\n");
- return;
- }
- if (!inData && line.indexOf("NBO") < 0 && nboDialog.nboMode == MODE_MODEL)
- nboDialog.appendModelOutPanel(line);
- if (inData) {
- sbRet.append(line + "\n");
- if (line.indexOf("END") >= 0) {
- inData = false;
- String m = "\"" + nboModel + "\"";
- nboModel = "\0";
- if (!nboSync && line.indexOf(m) >= 0) {
- String s = sbRet.toString();
+ if (Logger.debugging)
+ Logger.debug(inData + " " + nboSync + " " + sbRet.length() + " "
+ + "receiving: " + line);
+ if (line.startsWith("DATA \" \"")) {
+ isWorking = false;
+ } else if (line.startsWith("DATA ")) {
+ if (line.startsWith("DATA \"model")) {
sbRet.setLength(0);
- runScriptQueued(s);
+ nboModel = PT.getQuotedStringAt(line, 0);
+ line += " NBO " + nboModel;
}
+ inData = (line.indexOf("exit") < 0);
+ if (inData)
+ sbRet.append(line + "\n");
return;
}
- }
+ if (!inData && line.indexOf("NBO") < 0
+ && nboDialog.dialogMode == MODE_MODEL)
+ nboDialog.appendModelOutPanel(line);
+ if (inData && sbRet != null) {
+ sbRet.append(line + "\n");
+ if (line.indexOf("END") >= 0) {
+ inData = false;
+ String m = "\"" + nboModel + "\"";
+ nboModel = "\0";
+ if (!nboSync && line.indexOf(m) >= 0) {
+ String s = sbRet.toString();
+ sbRet.setLength(0);
+ runScriptQueued(s);
+ }
+ return;
+ }
+ }
if (nboDialog != null)
nboDialog.nboReport(line);
}
@@ -261,16 +272,18 @@
Thread.sleep(10);
while ((line = nboReader.readLine()) != null) {
Logger.info(line);
- switch (nboDialog.nboMode) {
+ switch (nboDialog.dialogMode) {
case MODE_RUN:
if (line.contains("Job"))
isWorking = false;
break;
case MODE_VIEW_4:
- if (nboDialog != null) {
+ if (nboDialog == null) {
+ isWorking = inRequest = false;
+ } else {
if (line.indexOf("1.") > 0)
inRequest = true;
- if (line.startsWith("DATA")) {
+ if (line.startsWith("DATA") || line.startsWith("END")) {
if (inRequest)
isWorking = false;
inRequest = false;
@@ -278,6 +291,8 @@
if (inRequest)
nboDialog.nboViewAddLine(line);
}
+ if (!isWorking)
+ nboDialog.dialogMode = MODE_RAW;
break;
case MODE_SEARCH:
if (nboDialog != null)
@@ -363,59 +378,85 @@
return (nboServer != null);
}
- synchronized void runScriptQueued(String script) {
+ void runScriptQueued(String script) {
Logger.info("NBO->JMOL ASYNC: " + script);
vwr.script(script);
}
+
+ private Object lock = "";
synchronized String runScriptNow(String script) {
- Logger.info("NBO->JMOL SYNC: " + script);
- return vwr.runScript(script);
+ synchronized (lock) {
+ Logger.info("NBO->JMOL SYNC: " + script);
+ return vwr.runScript(script);
+ }
}
synchronized public SV evaluateJmol(String expr) {
+ synchronized (lock) {
return vwr.evaluateExpressionAsVariable(expr);
+ }
}
synchronized public String evaluateJmolString(String expr) {
+ synchronized (lock) {
return evaluateJmol(expr).asString();
+ }
}
synchronized public String getJmolFilename() {
+ synchronized (lock) {
return evaluateJmolString("getProperty('filename')");
+ }
}
- protected void rawCmdNew(String mode, SB data, boolean doWait) {
- String fname = mode + "_test.txt";
- File cmdFile = new File(new File(serverPath).getParent() + "/" + fname);
- try {
- Logger.info("issuing " + fname + "\n" + data);
- writeToFile(data.toString(), cmdFile);
- isWorking = doWait;
- rawCmd("<" + fname + ">");
- if (doWait) {
- while (isWorking) {
- Thread.sleep(10);
- restartIfNecessary();
+ private Object nbo = "";
+
+
+ protected void rawCmdNew(String cmd, SB data, boolean doWait) {
+ synchronized (nbo) {
+ String fname = null;
+ File cmdFile = null;
+ try {
+ if (data == null) {
+ Logger.info("issuing\n" + cmd);
+ } else {
+ fname = cmd + "_test" + System.currentTimeMillis() + ".txt";
+ cmdFile = new File(new File(serverPath).getParent() + "/" + fname);
+ Logger.info("issuing " + fname + "\n" + data);
+ writeToFile(data.toString(), cmdFile);
+ cmd = "<" + fname + ">";
+ isWorking = doWait;
}
+ Map<String, Object> info = new Hashtable<String, Object>();
+ info.put("mode", Integer.valueOf(NBOService.MODE_RAW));
+ info.put("sync", Boolean.FALSE);
+ info.put("action", "cmd");
+ info.put("value", cmd);
+ if (!processRequest(info)) {
+ nboReport(null);
+ nboReport("not implemented");
+ isWorking = false;
+ }
+ if (doWait) {
+ while (isWorking) {
+ Thread.sleep(10);
+ restartIfNecessary();
+ }
+ }
+ if (cmdFile != null) {
+ cmdFile = new File(new File(serverPath).getParent() + "/" + fname +
"DONE");
+ writeToFile("", cmdFile);
+ }
+
+ } catch (IOException e) {
+ System.out.println("Could not write to " + fname);
+ isWorking = false;
+ } catch (InterruptedException e) {
+ isWorking = false;
}
- } catch (IOException e) {
- System.out.println("Could not write to " + fname);
- } catch (InterruptedException e) {
}
-
- }
- void rawCmd(String cmd) {
- Map<String, Object> info = new Hashtable<String, Object>();
- info.put("mode", Integer.valueOf(NBOService.MODE_RAW));
- info.put("sync", Boolean.FALSE);
- info.put("action", "cmd");
- info.put("value", cmd);
- if (!processRequest(info)) {
- nboReport(null);
- nboReport("not implemented");
- }
}
void writeToFile(String s, File file) throws IOException {
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