private String jmolScript(String script)
{
+ return jmolScript(script, false);
+ }
+
+ private String jmolScript(String script, boolean useScriptWait)
+ {
Console.debug(">>Jmol>> " + script);
- String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
+ String s;
+ if (useScriptWait)
+ {
+ s = jmolViewer.scriptWait(script);
+ }
+ else
+ {
+ s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
+ }
Console.debug("<<Jmol<< " + s);
return s;
public void createImage(String file, String type, int quality)
{
- System.out.println("JMOL CREATE IMAGE");
+ jalview.bin.Console.outPrintln("JMOL CREATE IMAGE");
}
@Override
public String createImage(String fileName, String type,
Object textOrBytes, int quality)
{
- System.out.println("JMOL CREATE IMAGE");
+ jalview.bin.Console.outPrintln("JMOL CREATE IMAGE");
return null;
}
@Override
public String eval(String strEval)
{
- // System.out.println(strEval);
+ // jalview.bin.Console.outPrintln(strEval);
// "# 'eval' is implemented only for the applet.";
return null;
}
{
if (atoms != null)
{
+ boolean useScriptWait = atoms.size() > 1;
if (resetLastRes.length() > 0)
{
- jmolScript(resetLastRes.toString());
+ jmolScript(resetLastRes.toString(), useScriptWait);
resetLastRes.setLength(0);
}
for (AtomSpec atom : atoms)
{
highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
- atom.getChain(), atom.getPdbFile());
+ atom.getChain(), atom.getPdbFile(), useScriptWait);
}
+ // Highlight distances between atoms with a 'measure' command - not yet
+ // working
+ // if (atoms.size() >= 2)
+ // {
+ // StringBuilder sb = new StringBuilder();
+ // for (int a = 0; a < atoms.size(); a++)
+ // {
+ // AtomSpec speca = atoms.get(a);
+ // String a_model = getModelIdForFile(speca.getPdbFile());
+ // for (int b = a + 1; b < atoms.size(); b++)
+ // {
+ // AtomSpec specb = atoms.get(b);
+ // String b_model = getModelIdForFile(speca.getPdbFile());
+ // sb.append("measure ALL (" + speca.getAtomIndex() + " and */"
+ // + a_model + ") (" + specb.getAtomIndex() + " and */"
+ // + b_model + ");");
+ // }
+ // }
+ // jmolHistory(false, useScriptWait);
+ // jmolScript(sb.toString(), useScriptWait);
+ // jmolHistory(true, useScriptWait);
+ // }
+
}
+
}
// jmol/ssm only
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ String pdbfile, boolean useScriptWait)
{
String modelId = getModelIdForFile(pdbfile);
if (modelId.isEmpty())
return;
}
- jmolHistory(false);
+ jmolHistory(false, useScriptWait);
StringBuilder selection = new StringBuilder(32);
StringBuilder cmd = new StringBuilder(64);
resetLastRes.append(selection).append(";wireframe 0;").append(selection)
.append(" and not hetero; spacefill 0;");
- jmolScript(cmd.toString());
- jmolHistory(true);
+ jmolScript(cmd.toString(), useScriptWait);
+ jmolHistory(true, useScriptWait);
}
private boolean debug = true;
private void jmolHistory(boolean enable)
{
- jmolScript("History " + ((debug || enable) ? "on" : "off"));
+ jmolHistory(enable, false);
+ }
+
+ private void jmolHistory(boolean enable, boolean useScriptWait)
+ {
+ jmolScript("History " + ((debug || enable) ? "on" : "off"),
+ useScriptWait);
}
public void loadInline(String string)
lastMessage = strInfo;
if (data != null)
{
- System.err.println("Ignoring additional hover info: " + data
+ jalview.bin.Console.errPrintln("Ignoring additional hover info: " + data
+ " (other info: '" + strInfo + "' pos " + atomIndex + ")");
}
mouseOverStructure(atomIndex, strInfo);
*/
if (strData != null)
{
- System.err.println("Ignoring additional pick data string " + strData);
+ jalview.bin.Console.errPrintln("Ignoring additional pick data string " + strData);
}
int chainSeparator = strInfo.indexOf(":");
int p = 0;
(data == null) ? ((String) null) : (String) data[1]);
break;
case ERROR:
- // System.err.println("Ignoring error callback.");
+ // jalview.bin.Console.errPrintln("Ignoring error callback.");
break;
case SYNC:
case RESIZE:
case CLICK:
default:
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Unhandled callback " + type + " " + data[1].toString());
break;
}
} catch (Exception e)
{
- System.err.println("Squashed Jmol callback handler error:");
+ jalview.bin.Console.errPrintln("Squashed Jmol callback handler error:");
e.printStackTrace();
}
}
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
- System.err.println("Ignoring set-callback request to associate "
+ jalview.bin.Console.errPrintln("Ignoring set-callback request to associate "
+ callbackType + " with function " + callbackFunction);
}
String buttonsToShow)
{
- System.err.println("Allocating Jmol Viewer: " + commandOptions);
+ jalview.bin.Console.errPrintln("Allocating Jmol Viewer: " + commandOptions);
if (commandOptions == null)
{
console = createJmolConsole(consolePanel, buttonsToShow);
} catch (Throwable e)
{
- System.err.println("Could not create Jmol application console. "
+ jalview.bin.Console.errPrintln("Could not create Jmol application console. "
+ e.getMessage());
e.printStackTrace();
}